{ "num_pairs": 1, "pairs": [ { "index": 1, "nt1": "///B/6", "nt2": "///B/7", "bp": "T+A", "name": "Platform", "Saenger": "--", "LW": "cSH", "DSSR": "cm+M", "intra_chain": true, "chi1": -114.267, "conf1": "anti", "pucker1": "~C2'-endo", "lambda1": 126.747, "chi2": -99.530, "conf2": "anti", "pucker2": "pucker-CHK", "lambda2": 42.387, "C1C1_dist": 6.238, "N1N9_dist": 6.062, "C6C8_dist": 6.396, "CNNC_torsion": 15.222, "hbonds_num": 1, "hbonds_desc": "O2(carbonyl)-N6(amino)[2.61]", "interBase_angle": 28.071, "planarity": 0.579, "simple_Shear": 0.161, "simple_Stretch": 4.298, "simple_Buckle": -15.848, "simple_Propeller": -23.169, "bp_simpleParams": [ 0.161, 4.298, -1.285, -15.848, -23.169, -14.760 ], "bp_params": [ 4.296, -0.220, -1.285, -23.005, 16.086, -14.614 ], "frame": { "rmsd": null, "origin": [ -1.382, 1.810, -22.437 ], "x_axis": [ 0.934, 0.326, -0.148 ], "y_axis": [ 0.294, -0.934, -0.202 ], "z_axis": [ -0.205, 0.145, -0.968 ], "quaternion": [ -0.089, 0.979, 0.158, -0.090 ] } } ], "num_stacks": 6, "stacks": [ { "index": 1, "num_nts": 2, "nts_short": "FA", "nts_long": "///A/47,///B/7" }, { "index": 2, "num_nts": 2, "nts_short": "RG", "nts_long": "///A/57,///B/10" }, { "index": 3, "num_nts": 2, "nts_short": "WG", "nts_long": "///A/72,///B/3" }, { "index": 4, "num_nts": 2, "nts_short": "HC", "nts_long": "///A/109,///B/2" }, { "index": 5, "num_nts": 3, "nts_short": "HTG", "nts_long": "///A/100,///B/5,///B/4" }, { "index": 6, "num_nts": 5, "nts_short": "YTWGC", "nts_long": "///A/28,///B/11,///A/27,///B/9,///B/8" } ], "nonStack": { "num_nts": 2, "nts_short": "AT", "nts_long": "///B/1,///B/6" }, "num_ssSegments": 1, "ssSegments": [ { "index": 1, "num_nts": 11, "nts_short": "ACGGTTACGGT", "nts_long": "///B/1,///B/2,///B/3,///B/4,///B/5,///B/6,///B/7,///B/8,///B/9,///B/10,///B/11" } ], "dbn": { "all_chains": { "num_nts": 11, "num_chars": 11, "bseq": "ACGGTTACGGT", "sstr": "...........", "form": "...A......-" }, "chain_B": { "num_nts": 11, "num_chars": 11, "bseq": "ACGGTTACGGT", "sstr": "...........", "form": "...A......-" } }, "chains": { "chain_B": { "num_nts": 11, "bseq": "ACGGTTACGGT", "sstr": "...........", "form": "...A......-", "helical_rise": 2.453, "helical_rise_std": 1.938, "helical_axis": [ -0.398, -0.894, 0.207 ], "point1": [ 4.405, 8.016, -17.370 ], "point2": [ -5.332, -13.871, -12.309 ], "num_chars": 31, "suite": "A!!C!!G!!G!!T!!T!!A!!C!!G!!G0aT" } }, "num_nts": 11, "nts": [ { "index": 1, "index_chain": 1, "chain_name": "B", "nt_resnum": 1, "nt_name": "DA", "nt_code": "A", "nt_id": "///B/1", "linked_nts": [ null, "///B/2" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop", "alpha": null, "beta": null, "gamma": 102.313, "delta": 66.746, "epsilon": -100.823, "zeta": -81.998, "epsilon_zeta": -18.824, "bb_type": "--", "chi": -168.414, "glyco_bond": "anti", "C5prime_xyz": [ -2.084, 8.851, 0.922 ], "P_xyz": [ null, null, null ], "form": ".", "ssZp": 4.381, "Dp": 4.836, "splay_angle": 63.840, "splay_distance": 10.142, "splay_ratio": 0.531, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": -2.880, "v1": -29.340, "v2": 48.189, "v3": -51.295, "v4": 34.162, "amplitude": 51.861, "phase_angle": 21.692, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "inc", "cluster": "__", "suiteness": 0.000, "filter_rmsd": 0.039, "frame": { "rmsd": 0.008, "origin": [ 12.051, 12.619, -4.357 ], "x_axis": [ -0.644, 0.503, -0.577 ], "y_axis": [ -0.160, -0.825, -0.541 ], "z_axis": [ -0.748, -0.256, 0.612 ], "quaternion": [ 0.189, -0.378, -0.227, 0.878 ] } }, { "index": 2, "index_chain": 2, "chain_name": "B", "nt_resnum": 2, "nt_name": "DC", "nt_code": "C", "nt_id": "///B/2", "linked_nts": [ "///B/1", "///B/3" ], "nt_type": "DNA", "dbn": ".", "summary": "~C2'-endo,non-pair-contact,ss-non-loop", "alpha": 67.205, "beta": 64.763, "gamma": -121.330, "delta": 111.878, "epsilon": 135.755, "zeta": -156.875, "epsilon_zeta": -67.370, "bb_type": "--", "chi": -13.913, "glyco_bond": "--", "C5prime_xyz": [ -5.650, 5.009, -1.614 ], "P_xyz": [ -7.793, 6.319, -0.644 ], "form": ".", "ssZp": 0.175, "Dp": 2.315, "splay_angle": 33.506, "splay_distance": 5.330, "splay_ratio": 0.300, "d22": null, "d64": null, "eta": 47.845, "theta": 36.083, "eta_prime": 62.432, "theta_prime": 61.405, "eta_base": 76.104, "theta_base": 57.539, "v0": -41.346, "v1": 38.748, "v2": -21.984, "v3": -1.126, "v4": 26.503, "amplitude": 41.333, "phase_angle": 122.132, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.062, "frame": { "rmsd": 0.004, "origin": [ 1.997, 11.353, -3.934 ], "x_axis": [ -0.358, 0.777, -0.517 ], "y_axis": [ 0.582, -0.247, -0.775 ], "z_axis": [ -0.730, -0.579, -0.364 ], "quaternion": [ -0.087, 0.560, 0.608, -0.557 ] } }, { "index": 3, "index_chain": 3, "chain_name": "B", "nt_resnum": 3, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/3", "linked_nts": [ "///B/2", "///B/4" ], "nt_type": "DNA", "dbn": ".", "summary": "~C2'-endo,BI,non-pair-contact,ss-non-loop", "alpha": -39.949, "beta": 119.055, "gamma": 69.656, "delta": 148.800, "epsilon": -139.940, "zeta": -99.361, "epsilon_zeta": -40.579, "bb_type": "BI", "chi": -89.459, "glyco_bond": "--", "C5prime_xyz": [ -2.650, 7.932, -2.284 ], "P_xyz": [ -0.325, 7.352, -3.366 ], "form": ".", "ssZp": 1.810, "Dp": 1.863, "splay_angle": 72.867, "splay_distance": 11.503, "splay_ratio": 0.594, "d22": null, "d64": null, "eta": 150.462, "theta": -40.987, "eta_prime": -176.815, "theta_prime": -101.058, "eta_base": 175.726, "theta_base": -77.053, "v0": -23.424, "v1": 41.040, "v2": -41.941, "v3": 29.732, "v4": -4.240, "amplitude": 43.096, "phase_angle": 166.709, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.007, "frame": { "rmsd": 0.007, "origin": [ 1.820, 6.058, -4.523 ], "x_axis": [ -0.402, 0.815, -0.417 ], "y_axis": [ 0.526, -0.167, -0.834 ], "z_axis": [ -0.749, -0.555, -0.362 ], "quaternion": [ -0.132, 0.531, 0.632, -0.549 ] } }, { "index": 4, "index_chain": 4, "chain_name": "B", "nt_resnum": 4, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/4", "linked_nts": [ "///B/3", "///B/5" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C3'-endo,BI,non-pair-contact,ss-non-loop", "alpha": -158.679, "beta": -108.965, "gamma": 60.011, "delta": 88.266, "epsilon": -177.591, "zeta": -64.698, "epsilon_zeta": -112.893, "bb_type": "BI", "chi": -140.496, "glyco_bond": "anti", "C5prime_xyz": [ -2.174, 8.808, -0.604 ], "P_xyz": [ 0.116, 9.400, 0.549 ], "form": "A", "ssZp": 3.920, "Dp": 4.250, "splay_angle": 21.756, "splay_distance": 3.474, "splay_ratio": 0.189, "d22": null, "d64": null, "eta": 106.167, "theta": -165.077, "eta_prime": 146.996, "theta_prime": -168.603, "eta_base": -177.759, "theta_base": -149.806, "v0": -2.900, "v1": -21.041, "v2": 34.971, "v3": -37.725, "v4": 25.656, "amplitude": 37.935, "phase_angle": 22.798, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "23p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.010, "frame": { "rmsd": 0.010, "origin": [ 1.596, 4.309, -15.890 ], "x_axis": [ 0.313, 0.846, 0.432 ], "y_axis": [ 0.515, -0.533, 0.671 ], "z_axis": [ 0.798, 0.012, -0.603 ], "quaternion": [ 0.210, 0.782, 0.435, 0.393 ] } }, { "index": 5, "index_chain": 5, "chain_name": "B", "nt_resnum": 5, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/5", "linked_nts": [ "///B/4", "///B/6" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,non-pair-contact,ss-non-loop", "alpha": -110.362, "beta": 111.445, "gamma": 151.038, "delta": 147.924, "epsilon": -140.944, "zeta": -138.466, "epsilon_zeta": -2.478, "bb_type": "--", "chi": -155.169, "glyco_bond": "anti", "C5prime_xyz": [ -1.089, 7.998, 1.199 ], "P_xyz": [ 0.942, 9.163, 0.006 ], "form": ".", "ssZp": 2.197, "Dp": 2.255, "splay_angle": 26.036, "splay_distance": 4.453, "splay_ratio": 0.230, "d22": 6.383, "d64": 6.091, "eta": -134.874, "theta": 155.756, "eta_prime": -139.217, "theta_prime": 169.111, "eta_base": -120.756, "theta_base": 166.697, "v0": 14.326, "v1": 6.384, "v2": -23.127, "v3": 31.585, "v4": -29.560, "amplitude": 32.230, "phase_angle": 224.146, "puckering": "C4'-endo", "sugar_class": "--", "bin": "32t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.114, "frame": { "rmsd": 0.014, "origin": [ 3.268, 4.323, -18.935 ], "x_axis": [ 0.565, 0.591, 0.576 ], "y_axis": [ 0.417, -0.807, 0.419 ], "z_axis": [ 0.712, 0.003, -0.702 ], "quaternion": [ 0.119, 0.877, 0.287, 0.367 ] } }, { "index": 6, "index_chain": 6, "chain_name": "B", "nt_resnum": 6, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/6", "linked_nts": [ "///B/5", "///B/7" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C2'-endo,non-stack,non-canonical,ss-non-loop", "alpha": -43.319, "beta": 143.557, "gamma": 48.286, "delta": 134.517, "epsilon": -157.253, "zeta": -171.674, "epsilon_zeta": 14.421, "bb_type": "--", "chi": -114.267, "glyco_bond": "anti", "C5prime_xyz": [ -2.338, 8.466, -1.693 ], "P_xyz": [ 0.215, 9.080, -1.678 ], "form": ".", "ssZp": 2.003, "Dp": 2.022, "splay_angle": 27.435, "splay_distance": 4.489, "splay_ratio": 0.246, "d22": null, "d64": null, "eta": 171.072, "theta": 170.869, "eta_prime": -162.341, "theta_prime": 160.091, "eta_base": -164.180, "theta_base": 153.363, "v0": -26.717, "v1": 34.366, "v2": -28.891, "v3": 14.433, "v4": 7.567, "amplitude": 33.838, "phase_angle": 148.628, "puckering": "C2'-endo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.102, "frame": { "rmsd": 0.006, "origin": [ 0.722, 2.519, -22.112 ], "x_axis": [ 0.901, 0.434, -0.009 ], "y_axis": [ 0.433, -0.901, -0.005 ], "z_axis": [ -0.010, 0.001, -1.000 ], "quaternion": [ -0.001, 0.975, 0.222, -0.005 ] } }, { "index": 7, "index_chain": 7, "chain_name": "B", "nt_resnum": 7, "nt_name": "DA", "nt_code": "A", "nt_id": "///B/7", "linked_nts": [ "///B/6", "///B/8" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,non-canonical,ss-non-loop", "alpha": -44.069, "beta": 166.451, "gamma": 21.962, "delta": 96.212, "epsilon": 78.212, "zeta": -131.569, "epsilon_zeta": -150.220, "bb_type": "--", "chi": -99.530, "glyco_bond": "anti", "C5prime_xyz": [ -1.592, 7.653, -2.407 ], "P_xyz": [ 0.943, 8.205, -2.092 ], "form": ".", "ssZp": 0.562, "Dp": 1.851, "splay_angle": 59.660, "splay_distance": 9.701, "splay_ratio": 0.498, "d22": null, "d64": null, "eta": -168.320, "theta": 81.571, "eta_prime": -167.446, "theta_prime": 52.217, "eta_base": -179.863, "theta_base": 41.305, "v0": 1.111, "v1": -11.268, "v2": 16.618, "v3": -16.660, "v4": 9.759, "amplitude": 17.233, "phase_angle": 15.350, "puckering": "C3'-endo", "sugar_class": "pucker-CHK", "bin": "23p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.034, "frame": { "rmsd": 0.007, "origin": [ -3.487, 1.101, -22.762 ], "x_axis": [ 0.915, 0.240, -0.326 ], "y_axis": [ 0.119, -0.929, -0.350 ], "z_axis": [ -0.387, 0.281, -0.878 ], "quaternion": [ -0.164, 0.965, 0.093, -0.185 ] } }, { "index": 8, "index_chain": 8, "chain_name": "B", "nt_resnum": 8, "nt_name": "DC", "nt_code": "C", "nt_id": "///B/8", "linked_nts": [ "///B/7", "///B/9" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate", "alpha": 69.134, "beta": -122.375, "gamma": -128.457, "delta": 160.433, "epsilon": -159.739, "zeta": -75.003, "epsilon_zeta": -84.736, "bb_type": "BI", "chi": -101.645, "glyco_bond": "anti", "C5prime_xyz": [ -1.593, 8.010, -1.784 ], "P_xyz": [ -0.735, 8.371, -4.267 ], "form": ".", "ssZp": 1.235, "Dp": 1.340, "splay_angle": 24.909, "splay_distance": 4.274, "splay_ratio": 0.216, "d22": null, "d64": null, "eta": 179.979, "theta": -162.024, "eta_prime": -179.074, "theta_prime": -148.863, "eta_base": 171.662, "theta_base": -94.775, "v0": -8.608, "v1": 32.475, "v2": -42.518, "v3": 38.322, "v4": -19.166, "amplitude": 42.851, "phase_angle": 187.146, "puckering": "C3'-exo", "sugar_class": "~C2'-endo", "bin": "trig", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.066, "frame": { "rmsd": 0.009, "origin": [ 0.008, -6.905, -18.544 ], "x_axis": [ -0.350, 0.877, 0.330 ], "y_axis": [ -0.926, -0.271, -0.264 ], "z_axis": [ -0.142, -0.398, 0.906 ], "quaternion": [ 0.567, 0.059, -0.208, 0.795 ] } }, { "index": 9, "index_chain": 9, "chain_name": "B", "nt_resnum": 9, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/9", "linked_nts": [ "///B/8", "///B/10" ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate", "alpha": -81.951, "beta": 168.562, "gamma": 48.414, "delta": 123.634, "epsilon": -156.697, "zeta": -72.597, "epsilon_zeta": -84.100, "bb_type": "BI", "chi": -87.265, "glyco_bond": "anti", "C5prime_xyz": [ -3.608, 7.654, -2.520 ], "P_xyz": [ -1.823, 8.997, -3.898 ], "form": ".", "ssZp": 2.074, "Dp": 2.381, "splay_angle": 66.247, "splay_distance": 9.700, "splay_ratio": 0.567, "d22": null, "d64": null, "eta": 144.247, "theta": -85.879, "eta_prime": -173.985, "theta_prime": -99.837, "eta_base": -121.353, "theta_base": -30.655, "v0": -36.798, "v1": 39.820, "v2": -27.322, "v3": 6.915, "v4": 18.658, "amplitude": 39.633, "phase_angle": 133.581, "puckering": "C1'-exo", "sugar_class": "~C2'-endo", "bin": "22p", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.011, "frame": { "rmsd": 0.011, "origin": [ -3.111, -6.769, -15.625 ], "x_axis": [ -0.780, 0.600, -0.174 ], "y_axis": [ -0.550, -0.792, -0.266 ], "z_axis": [ -0.298, -0.112, 0.948 ], "quaternion": [ 0.307, -0.126, -0.101, 0.938 ] } }, { "index": 10, "index_chain": 10, "chain_name": "B", "nt_resnum": 10, "nt_name": "DG", "nt_code": "G", "nt_id": "///B/10", "linked_nts": [ "///B/9", "///B/11" ], "nt_type": "DNA", "dbn": ".", "summary": "turn,syn,~C2'-endo,non-pair-contact,ss-non-loop", "alpha": 128.554, "beta": -179.665, "gamma": -170.352, "delta": 157.655, "epsilon": -100.916, "zeta": 102.285, "epsilon_zeta": 156.799, "bb_type": "--", "chi": 72.495, "glyco_bond": "syn", "C5prime_xyz": [ -5.058, 4.157, 1.395 ], "P_xyz": [ -5.507, 2.645, 3.465 ], "form": ".", "ssZp": -0.439, "Dp": 0.502, "splay_angle": 79.934, "splay_distance": 12.537, "splay_ratio": 0.643, "d22": null, "d64": null, "eta": -167.916, "theta": 53.562, "eta_prime": -142.880, "theta_prime": 64.761, "eta_base": -87.637, "theta_base": 87.665, "v0": -10.602, "v1": 33.431, "v2": -42.040, "v3": 37.122, "v4": -16.957, "amplitude": 42.167, "phase_angle": 184.440, "puckering": "C3'-exo", "sugar_class": "~C2'-endo", "bin": "22t", "cluster": "!!", "suiteness": 0.000, "filter_rmsd": 0.018, "frame": { "rmsd": 0.018, "origin": [ -8.450, -13.469, -20.174 ], "x_axis": [ -0.133, 0.899, -0.418 ], "y_axis": [ -0.170, 0.395, 0.903 ], "z_axis": [ 0.976, 0.191, 0.100 ], "quaternion": [ 0.584, 0.305, 0.597, 0.458 ] } }, { "index": 11, "index_chain": 11, "chain_name": "B", "nt_resnum": 11, "nt_name": "DT", "nt_code": "T", "nt_id": "///B/11", "linked_nts": [ "///B/10", null ], "nt_type": "DNA", "dbn": ".", "summary": "anti,~C3'-endo,ss-non-loop", "alpha": -102.416, "beta": 170.269, "gamma": 46.982, "delta": 86.349, "epsilon": null, "zeta": null, "epsilon_zeta": null, "bb_type": "--", "chi": -153.789, "glyco_bond": "anti", "C5prime_xyz": [ -1.490, 8.773, 0.147 ], "P_xyz": [ 1.116, 9.226, 0.216 ], "form": "-", "ssZp": null, "Dp": null, "splay_angle": null, "splay_distance": null, "splay_ratio": null, "d22": null, "d64": null, "eta": null, "theta": null, "eta_prime": null, "theta_prime": null, "eta_base": null, "theta_base": null, "v0": 1.223, "v1": -24.302, "v2": 36.789, "v3": -36.940, "v4": 22.596, "amplitude": 38.412, "phase_angle": 16.720, "puckering": "C3'-endo", "sugar_class": "~C3'-endo", "bin": "23p", "cluster": "0a", "suiteness": 0.028, "filter_rmsd": 0.106, "frame": { "rmsd": 0.006, "origin": [ -4.959, -7.541, -9.694 ], "x_axis": [ -0.884, 0.377, -0.277 ], "y_axis": [ -0.378, -0.924, -0.051 ], "z_axis": [ -0.275, 0.059, 0.960 ], "quaternion": [ 0.195, -0.142, 0.002, 0.971 ] } } ], "num_hbonds": 156, "hbonds": [ { "index": 1, "atom1_serNum": 1, "atom2_serNum": 8, "donAcc_type": "standard", "distance": 2.886, "atom1_id": "///A/3/N", "atom2_id": "///A/3/OD2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 2, "atom1_serNum": 26, "atom2_serNum": 124, "donAcc_type": "standard", "distance": 2.802, "atom1_id": "///A/6/N", "atom2_id": "///A/18/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 3, "atom1_serNum": 32, "atom2_serNum": 61, "donAcc_type": "standard", "distance": 2.791, "atom1_id": "///A/7/N", "atom2_id": "///A/10/OE1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 4, "atom1_serNum": 35, "atom2_serNum": 54, "donAcc_type": "standard", "distance": 2.805, "atom1_id": "///A/7/O", "atom2_id": "///A/10/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 5, "atom1_serNum": 40, "atom2_serNum": 311, "donAcc_type": "standard", "distance": 2.736, "atom1_id": "///A/8/N", "atom2_id": "///A/39/OD2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 6, "atom1_serNum": 43, "atom2_serNum": 347, "donAcc_type": "standard", "distance": 2.959, "atom1_id": "///A/8/O", "atom2_id": "///A/43/ND2", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7, "atom1_serNum": 48, "atom2_serNum": 329, "donAcc_type": "acceptable", "distance": 2.989, "atom1_id": "///A/9/N", "atom2_id": "///A/41/OG1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 8, "atom1_serNum": 66, "atom2_serNum": 347, "donAcc_type": "standard", "distance": 3.011, "atom1_id": "///A/11/O", "atom2_id": "///A/43/ND2", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 9, "atom1_serNum": 71, "atom2_serNum": 102, "donAcc_type": "standard", "distance": 2.930, "atom1_id": "///A/12/N", "atom2_id": "///A/15/OE1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 10, "atom1_serNum": 74, "atom2_serNum": 804, "donAcc_type": "acceptable", "distance": 2.653, "atom1_id": "///A/12/O", "atom2_id": "///A/96/OG1", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 11, "atom1_serNum": 85, "atom2_serNum": 802, "donAcc_type": "standard", "distance": 2.837, "atom1_id": "///A/14/N", "atom2_id": "///A/96/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 12, "atom1_serNum": 95, "atom2_serNum": 804, "donAcc_type": "acceptable", "distance": 3.042, "atom1_id": "///A/15/N", "atom2_id": "///A/96/OG1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 13, "atom1_serNum": 98, "atom2_serNum": 799, "donAcc_type": "standard", "distance": 2.904, "atom1_id": "///A/15/O", "atom2_id": "///A/96/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 14, "atom1_serNum": 115, "atom2_serNum": 784, "donAcc_type": "standard", "distance": 2.950, "atom1_id": "///A/17/N", "atom2_id": "///A/94/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 15, "atom1_serNum": 118, "atom2_serNum": 781, "donAcc_type": "standard", "distance": 2.903, "atom1_id": "///A/17/O", "atom2_id": "///A/94/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 16, "atom1_serNum": 126, "atom2_serNum": 773, "donAcc_type": "acceptable", "distance": 2.909, "atom1_id": "///A/18/OG", "atom2_id": "///A/93/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 17, "atom1_serNum": 127, "atom2_serNum": 759, "donAcc_type": "standard", "distance": 2.924, "atom1_id": "///A/19/N", "atom2_id": "///A/91/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 18, "atom1_serNum": 130, "atom2_serNum": 756, "donAcc_type": "standard", "distance": 2.909, "atom1_id": "///A/19/O", "atom2_id": "///A/91/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 19, "atom1_serNum": 150, "atom2_serNum": 745, "donAcc_type": "standard", "distance": 3.016, "atom1_id": "///A/21/N", "atom2_id": "///A/89/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 20, "atom1_serNum": 153, "atom2_serNum": 742, "donAcc_type": "standard", "distance": 2.906, "atom1_id": "///A/21/O", "atom2_id": "///A/89/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 21, "atom1_serNum": 155, "atom2_serNum": 300, "donAcc_type": "standard", "distance": 2.794, "atom1_id": "///A/22/N", "atom2_id": "///A/38/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 22, "atom1_serNum": 158, "atom2_serNum": 297, "donAcc_type": "standard", "distance": 2.954, "atom1_id": "///A/22/O", "atom2_id": "///A/38/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 23, "atom1_serNum": 162, "atom2_serNum": 323, "donAcc_type": "acceptable", "distance": 3.660, "atom1_id": "///A/22/OE1", "atom2_id": "///A/40/OH", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 24, "atom1_serNum": 162, "atom2_serNum": 1139, "donAcc_type": "standard", "distance": 3.852, "atom1_id": "///A/22/OE1", "atom2_id": "///A/137/NZ", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 25, "atom1_serNum": 163, "atom2_serNum": 721, "donAcc_type": "standard", "distance": 3.069, "atom1_id": "///A/22/NE2", "atom2_id": "///A/86/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 26, "atom1_serNum": 164, "atom2_serNum": 725, "donAcc_type": "standard", "distance": 2.894, "atom1_id": "///A/23/N", "atom2_id": "///A/87/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 27, "atom1_serNum": 167, "atom2_serNum": 718, "donAcc_type": "standard", "distance": 2.654, "atom1_id": "///A/23/O", "atom2_id": "///A/86/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 28, "atom1_serNum": 171, "atom2_serNum": 281, "donAcc_type": "standard", "distance": 2.786, "atom1_id": "///A/24/N", "atom2_id": "///A/36/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 29, "atom1_serNum": 179, "atom2_serNum": 281, "donAcc_type": "standard", "distance": 3.286, "atom1_id": "///A/25/N", "atom2_id": "///A/36/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 30, "atom1_serNum": 182, "atom2_serNum": 278, "donAcc_type": "standard", "distance": 2.803, "atom1_id": "///A/25/O", "atom2_id": "///A/36/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 31, "atom1_serNum": 187, "atom2_serNum": 1353, "donAcc_type": "standard", "distance": 2.763, "atom1_id": "///A/25/NZ", "atom2_id": "///B/9/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 32, "atom1_serNum": 187, "atom2_serNum": 1375, "donAcc_type": "standard", "distance": 3.138, "atom1_id": "///A/25/NZ", "atom2_id": "///B/10/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 33, "atom1_serNum": 188, "atom2_serNum": 717, "donAcc_type": "standard", "distance": 3.125, "atom1_id": "///A/26/N", "atom2_id": "///A/85/OE2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 34, "atom1_serNum": 195, "atom2_serNum": 266, "donAcc_type": "standard", "distance": 2.881, "atom1_id": "///A/27/N", "atom2_id": "///A/34/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 35, "atom1_serNum": 198, "atom2_serNum": 263, "donAcc_type": "standard", "distance": 2.926, "atom1_id": "///A/27/O", "atom2_id": "///A/34/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 36, "atom1_serNum": 209, "atom2_serNum": 1400, "donAcc_type": "standard", "distance": 2.811, "atom1_id": "///A/28/N", "atom2_id": "///B/11/O4", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 37, "atom1_serNum": 212, "atom2_serNum": 1398, "donAcc_type": "standard", "distance": 2.808, "atom1_id": "///A/28/O", "atom2_id": "///B/11/N3", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 38, "atom1_serNum": 221, "atom2_serNum": 247, "donAcc_type": "standard", "distance": 2.985, "atom1_id": "///A/29/N", "atom2_id": "///A/32/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 39, "atom1_serNum": 224, "atom2_serNum": 670, "donAcc_type": "standard", "distance": 3.099, "atom1_id": "///A/29/O", "atom2_id": "///A/80/NH1", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 40, "atom1_serNum": 224, "atom2_serNum": 671, "donAcc_type": "standard", "distance": 3.166, "atom1_id": "///A/29/O", "atom2_id": "///A/80/NH2", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 41, "atom1_serNum": 226, "atom2_serNum": 235, "donAcc_type": "acceptable", "distance": 3.020, "atom1_id": "///A/29/OG", "atom2_id": "///A/31/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 42, "atom1_serNum": 226, "atom2_serNum": 244, "donAcc_type": "acceptable", "distance": 3.064, "atom1_id": "///A/29/OG", "atom2_id": "///A/32/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 43, "atom1_serNum": 252, "atom2_serNum": 578, "donAcc_type": "standard", "distance": 3.060, "atom1_id": "///A/33/N", "atom2_id": "///A/71/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 44, "atom1_serNum": 255, "atom2_serNum": 575, "donAcc_type": "standard", "distance": 2.718, "atom1_id": "///A/33/O", "atom2_id": "///A/71/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 45, "atom1_serNum": 270, "atom2_serNum": 564, "donAcc_type": "standard", "distance": 2.941, "atom1_id": "///A/35/N", "atom2_id": "///A/69/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 46, "atom1_serNum": 273, "atom2_serNum": 561, "donAcc_type": "standard", "distance": 2.660, "atom1_id": "///A/35/O", "atom2_id": "///A/69/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 47, "atom1_serNum": 289, "atom2_serNum": 559, "donAcc_type": "acceptable", "distance": 3.489, "atom1_id": "///A/36/OH", "atom2_id": "///A/68/NH1", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 48, "atom1_serNum": 289, "atom2_serNum": 1337, "donAcc_type": "acceptable", "distance": 3.826, "atom1_id": "///A/36/OH", "atom2_id": "///B/8/N4", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 49, "atom1_serNum": 290, "atom2_serNum": 545, "donAcc_type": "standard", "distance": 3.061, "atom1_id": "///A/37/N", "atom2_id": "///A/67/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 50, "atom1_serNum": 293, "atom2_serNum": 542, "donAcc_type": "standard", "distance": 2.917, "atom1_id": "///A/37/O", "atom2_id": "///A/67/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 51, "atom1_serNum": 302, "atom2_serNum": 312, "donAcc_type": "acceptable", "distance": 2.826, "atom1_id": "///A/38/OG1", "atom2_id": "///A/40/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 52, "atom1_serNum": 302, "atom2_serNum": 528, "donAcc_type": "acceptable", "distance": 2.678, "atom1_id": "///A/38/OG1", "atom2_id": "///A/65/O", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 53, "atom1_serNum": 307, "atom2_serNum": 1127, "donAcc_type": "standard", "distance": 2.959, "atom1_id": "///A/39/O", "atom2_id": "///A/136/NE", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 54, "atom1_serNum": 307, "atom2_serNum": 1130, "donAcc_type": "standard", "distance": 2.905, "atom1_id": "///A/39/O", "atom2_id": "///A/136/NH2", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 55, "atom1_serNum": 310, "atom2_serNum": 324, "donAcc_type": "standard", "distance": 3.048, "atom1_id": "///A/39/OD1", "atom2_id": "///A/41/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 56, "atom1_serNum": 310, "atom2_serNum": 329, "donAcc_type": "acceptable", "distance": 2.554, "atom1_id": "///A/39/OD1", "atom2_id": "///A/41/OG1", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 57, "atom1_serNum": 339, "atom2_serNum": 356, "donAcc_type": "questionable", "distance": 2.373, "atom1_id": "///A/42/OE2", "atom2_id": "///A/44/OE2", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 58, "atom1_serNum": 340, "atom2_serNum": 517, "donAcc_type": "standard", "distance": 3.132, "atom1_id": "///A/43/N", "atom2_id": "///A/64/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 59, "atom1_serNum": 343, "atom2_serNum": 365, "donAcc_type": "standard", "distance": 2.897, "atom1_id": "///A/43/O", "atom2_id": "///A/46/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 60, "atom1_serNum": 346, "atom2_serNum": 357, "donAcc_type": "standard", "distance": 2.907, "atom1_id": "///A/43/OD1", "atom2_id": "///A/45/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 61, "atom1_serNum": 360, "atom2_serNum": 865, "donAcc_type": "standard", "distance": 2.852, "atom1_id": "///A/45/O", "atom2_id": "///A/104/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 62, "atom1_serNum": 368, "atom2_serNum": 523, "donAcc_type": "standard", "distance": 2.875, "atom1_id": "///A/46/O", "atom2_id": "///A/64/NH1", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 63, "atom1_serNum": 379, "atom2_serNum": 394, "donAcc_type": "standard", "distance": 3.087, "atom1_id": "///A/47/O", "atom2_id": "///A/49/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 64, "atom1_serNum": 379, "atom2_serNum": 513, "donAcc_type": "questionable", "distance": 3.101, "atom1_id": "///A/47/O", "atom2_id": "///A/63/O", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 65, "atom1_serNum": 394, "atom2_serNum": 513, "donAcc_type": "standard", "distance": 3.128, "atom1_id": "///A/49/N", "atom2_id": "///A/63/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 66, "atom1_serNum": 397, "atom2_serNum": 510, "donAcc_type": "standard", "distance": 2.930, "atom1_id": "///A/49/O", "atom2_id": "///A/63/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 67, "atom1_serNum": 407, "atom2_serNum": 415, "donAcc_type": "acceptable", "distance": 2.911, "atom1_id": "///A/50/OG", "atom2_id": "///A/52/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 68, "atom1_serNum": 432, "atom2_serNum": 1322, "donAcc_type": "acceptable", "distance": 2.666, "atom1_id": "///A/53/OG1", "atom2_id": "///B/8/OP1", "atom_pair": "O:O", "residue_pair": "aa:nt" }, { "index": 69, "atom1_serNum": 445, "atom2_serNum": 1342, "donAcc_type": "acceptable", "distance": 2.820, "atom1_id": "///A/55/OG", "atom2_id": "///B/9/OP2", "atom_pair": "O:O", "residue_pair": "aa:nt" }, { "index": 70, "atom1_serNum": 449, "atom2_serNum": 486, "donAcc_type": "standard", "distance": 2.870, "atom1_id": "///A/56/O", "atom2_id": "///A/59/NH1", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 71, "atom1_serNum": 451, "atom2_serNum": 463, "donAcc_type": "acceptable", "distance": 2.949, "atom1_id": "///A/56/OG", "atom2_id": "///A/58/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 72, "atom1_serNum": 466, "atom2_serNum": 486, "donAcc_type": "standard", "distance": 3.075, "atom1_id": "///A/58/O", "atom2_id": "///A/59/NH1", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 73, "atom1_serNum": 471, "atom2_serNum": 488, "donAcc_type": "questionable", "distance": 3.180, "atom1_id": "///A/58/NE1", "atom2_id": "///A/60/N", "atom_pair": "N:N", "residue_pair": "aa:aa" }, { "index": 74, "atom1_serNum": 471, "atom2_serNum": 495, "donAcc_type": "standard", "distance": 2.976, "atom1_id": "///A/58/NE1", "atom2_id": "///A/61/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 75, "atom1_serNum": 513, "atom2_serNum": 525, "donAcc_type": "standard", "distance": 3.044, "atom1_id": "///A/63/O", "atom2_id": "///A/65/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 76, "atom1_serNum": 553, "atom2_serNum": 882, "donAcc_type": "standard", "distance": 2.990, "atom1_id": "///A/68/O", "atom2_id": "///A/106/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 77, "atom1_serNum": 557, "atom2_serNum": 881, "donAcc_type": "standard", "distance": 2.779, "atom1_id": "///A/68/NE", "atom2_id": "///A/105/OE2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 78, "atom1_serNum": 559, "atom2_serNum": 1293, "donAcc_type": "standard", "distance": 3.299, "atom1_id": "///A/68/NH1", "atom2_id": "///B/6/O2", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 79, "atom1_serNum": 560, "atom2_serNum": 830, "donAcc_type": "standard", "distance": 3.259, "atom1_id": "///A/68/NH2", "atom2_id": "///A/99/OD2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 80, "atom1_serNum": 560, "atom2_serNum": 881, "donAcc_type": "standard", "distance": 3.169, "atom1_id": "///A/68/NH2", "atom2_id": "///A/105/OE2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 81, "atom1_serNum": 560, "atom2_serNum": 1293, "donAcc_type": "standard", "distance": 2.919, "atom1_id": "///A/68/NH2", "atom2_id": "///B/6/O2", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 82, "atom1_serNum": 567, "atom2_serNum": 885, "donAcc_type": "standard", "distance": 2.896, "atom1_id": "///A/70/N", "atom2_id": "///A/106/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 83, "atom1_serNum": 570, "atom2_serNum": 896, "donAcc_type": "standard", "distance": 2.946, "atom1_id": "///A/70/O", "atom2_id": "///A/108/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 84, "atom1_serNum": 583, "atom2_serNum": 899, "donAcc_type": "standard", "distance": 2.935, "atom1_id": "///A/72/N", "atom2_id": "///A/108/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 85, "atom1_serNum": 586, "atom2_serNum": 614, "donAcc_type": "standard", "distance": 3.166, "atom1_id": "///A/72/O", "atom2_id": "///A/75/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 86, "atom1_serNum": 600, "atom2_serNum": 624, "donAcc_type": "standard", "distance": 2.959, "atom1_id": "///A/73/O", "atom2_id": "///A/76/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 87, "atom1_serNum": 600, "atom2_serNum": 632, "donAcc_type": "standard", "distance": 2.916, "atom1_id": "///A/73/O", "atom2_id": "///A/77/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 88, "atom1_serNum": 603, "atom2_serNum": 1235, "donAcc_type": "standard", "distance": 2.730, "atom1_id": "///A/73/OD1", "atom2_id": "///B/3/N2", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 89, "atom1_serNum": 604, "atom2_serNum": 914, "donAcc_type": "standard", "distance": 2.970, "atom1_id": "///A/73/OD2", "atom2_id": "///A/110/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 90, "atom1_serNum": 604, "atom2_serNum": 1233, "donAcc_type": "standard", "distance": 2.749, "atom1_id": "///A/73/OD2", "atom2_id": "///B/3/N1", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 91, "atom1_serNum": 605, "atom2_serNum": 612, "donAcc_type": "standard", "distance": 2.909, "atom1_id": "///A/74/N", "atom2_id": "///A/74/OE1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 92, "atom1_serNum": 608, "atom2_serNum": 643, "donAcc_type": "standard", "distance": 2.870, "atom1_id": "///A/74/O", "atom2_id": "///A/78/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 93, "atom1_serNum": 613, "atom2_serNum": 918, "donAcc_type": "standard", "distance": 2.944, "atom1_id": "///A/74/OE2", "atom2_id": "///A/111/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 94, "atom1_serNum": 617, "atom2_serNum": 655, "donAcc_type": "standard", "distance": 3.119, "atom1_id": "///A/75/O", "atom2_id": "///A/79/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 95, "atom1_serNum": 623, "atom2_serNum": 907, "donAcc_type": "standard", "distance": 2.783, "atom1_id": "///A/75/NE2", "atom2_id": "///A/109/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 96, "atom1_serNum": 627, "atom2_serNum": 661, "donAcc_type": "standard", "distance": 2.827, "atom1_id": "///A/76/O", "atom2_id": "///A/80/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 97, "atom1_serNum": 630, "atom2_serNum": 670, "donAcc_type": "standard", "distance": 2.870, "atom1_id": "///A/76/OD1", "atom2_id": "///A/80/NH1", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 98, "atom1_serNum": 654, "atom2_serNum": 1006, "donAcc_type": "acceptable", "distance": 2.574, "atom1_id": "///A/78/OH", "atom2_id": "///A/121/OE1", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 99, "atom1_serNum": 658, "atom2_serNum": 680, "donAcc_type": "standard", "distance": 2.927, "atom1_id": "///A/79/O", "atom2_id": "///A/82/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 100, "atom1_serNum": 658, "atom2_serNum": 692, "donAcc_type": "standard", "distance": 2.960, "atom1_id": "///A/79/O", "atom2_id": "///A/83/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 101, "atom1_serNum": 683, "atom2_serNum": 1016, "donAcc_type": "standard", "distance": 2.814, "atom1_id": "///A/82/O", "atom2_id": "///A/122/NZ", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 102, "atom1_serNum": 700, "atom2_serNum": 729, "donAcc_type": "standard", "distance": 2.618, "atom1_id": "///A/84/N", "atom2_id": "///A/87/OD2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 103, "atom1_serNum": 703, "atom2_serNum": 722, "donAcc_type": "standard", "distance": 2.983, "atom1_id": "///A/84/O", "atom2_id": "///A/87/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 104, "atom1_serNum": 733, "atom2_serNum": 1017, "donAcc_type": "standard", "distance": 2.823, "atom1_id": "///A/88/O", "atom2_id": "///A/123/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 105, "atom1_serNum": 749, "atom2_serNum": 1002, "donAcc_type": "standard", "distance": 2.904, "atom1_id": "///A/90/N", "atom2_id": "///A/121/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 106, "atom1_serNum": 752, "atom2_serNum": 999, "donAcc_type": "standard", "distance": 3.180, "atom1_id": "///A/90/O", "atom2_id": "///A/121/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 107, "atom1_serNum": 764, "atom2_serNum": 988, "donAcc_type": "standard", "distance": 2.852, "atom1_id": "///A/92/N", "atom2_id": "///A/119/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 108, "atom1_serNum": 767, "atom2_serNum": 985, "donAcc_type": "standard", "distance": 3.169, "atom1_id": "///A/92/O", "atom2_id": "///A/119/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 109, "atom1_serNum": 780, "atom2_serNum": 960, "donAcc_type": "standard", "distance": 3.964, "atom1_id": "///A/93/ND2", "atom2_id": "///A/116/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 110, "atom1_serNum": 780, "atom2_serNum": 972, "donAcc_type": "standard", "distance": 3.106, "atom1_id": "///A/93/ND2", "atom2_id": "///A/117/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 111, "atom1_serNum": 788, "atom2_serNum": 891, "donAcc_type": "standard", "distance": 3.393, "atom1_id": "///A/95/N", "atom2_id": "///A/107/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 112, "atom1_serNum": 791, "atom2_serNum": 888, "donAcc_type": "standard", "distance": 2.841, "atom1_id": "///A/95/O", "atom2_id": "///A/107/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 113, "atom1_serNum": 806, "atom2_serNum": 876, "donAcc_type": "standard", "distance": 2.857, "atom1_id": "///A/97/N", "atom2_id": "///A/105/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 114, "atom1_serNum": 809, "atom2_serNum": 873, "donAcc_type": "standard", "distance": 2.988, "atom1_id": "///A/97/O", "atom2_id": "///A/105/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 115, "atom1_serNum": 814, "atom2_serNum": 880, "donAcc_type": "standard", "distance": 3.812, "atom1_id": "///A/97/NZ", "atom2_id": "///A/105/OE1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 116, "atom1_serNum": 814, "atom2_serNum": 1254, "donAcc_type": "standard", "distance": 2.855, "atom1_id": "///A/97/NZ", "atom2_id": "///B/4/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 117, "atom1_serNum": 814, "atom2_serNum": 1276, "donAcc_type": "standard", "distance": 3.865, "atom1_id": "///A/97/NZ", "atom2_id": "///B/5/O4", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 118, "atom1_serNum": 823, "atom2_serNum": 856, "donAcc_type": "standard", "distance": 2.839, "atom1_id": "///A/99/N", "atom2_id": "///A/103/O", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 119, "atom1_serNum": 826, "atom2_serNum": 849, "donAcc_type": "standard", "distance": 3.171, "atom1_id": "///A/99/O", "atom2_id": "///A/102/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 120, "atom1_serNum": 829, "atom2_serNum": 841, "donAcc_type": "standard", "distance": 2.839, "atom1_id": "///A/99/OD1", "atom2_id": "///A/101/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 121, "atom1_serNum": 829, "atom2_serNum": 849, "donAcc_type": "standard", "distance": 3.011, "atom1_id": "///A/99/OD1", "atom2_id": "///A/102/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 122, "atom1_serNum": 829, "atom2_serNum": 853, "donAcc_type": "standard", "distance": 2.897, "atom1_id": "///A/99/OD1", "atom2_id": "///A/103/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 123, "atom1_serNum": 830, "atom2_serNum": 1294, "donAcc_type": "standard", "distance": 2.731, "atom1_id": "///A/99/OD2", "atom2_id": "///B/6/N3", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 124, "atom1_serNum": 830, "atom2_serNum": 1316, "donAcc_type": "standard", "distance": 3.085, "atom1_id": "///A/99/OD2", "atom2_id": "///B/7/N6", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 125, "atom1_serNum": 831, "atom2_serNum": 1296, "donAcc_type": "standard", "distance": 2.895, "atom1_id": "///A/100/N", "atom2_id": "///B/6/O4", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 126, "atom1_serNum": 880, "atom2_serNum": 1255, "donAcc_type": "standard", "distance": 2.761, "atom1_id": "///A/105/OE1", "atom2_id": "///B/4/N1", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 127, "atom1_serNum": 880, "atom2_serNum": 1257, "donAcc_type": "standard", "distance": 3.162, "atom1_id": "///A/105/OE1", "atom2_id": "///B/4/N2", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 128, "atom1_serNum": 881, "atom2_serNum": 1257, "donAcc_type": "standard", "distance": 2.916, "atom1_id": "///A/105/OE2", "atom2_id": "///B/4/N2", "atom_pair": "O:N", "residue_pair": "aa:nt" }, { "index": 129, "atom1_serNum": 910, "atom2_serNum": 1229, "donAcc_type": "acceptable", "distance": 3.148, "atom1_id": "///A/109/ND1", "atom2_id": "///B/3/N7", "atom_pair": "N:N", "residue_pair": "aa:nt" }, { "index": 130, "atom1_serNum": 910, "atom2_serNum": 1232, "donAcc_type": "acceptable", "distance": 2.783, "atom1_id": "///A/109/ND1", "atom2_id": "///B/3/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 131, "atom1_serNum": 914, "atom2_serNum": 1232, "donAcc_type": "standard", "distance": 3.291, "atom1_id": "///A/110/N", "atom2_id": "///B/3/O6", "atom_pair": "N:O", "residue_pair": "aa:nt" }, { "index": 132, "atom1_serNum": 921, "atom2_serNum": 937, "donAcc_type": "standard", "distance": 3.048, "atom1_id": "///A/111/O", "atom2_id": "///A/114/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 133, "atom1_serNum": 924, "atom2_serNum": 946, "donAcc_type": "standard", "distance": 2.960, "atom1_id": "///A/111/OD1", "atom2_id": "///A/115/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 134, "atom1_serNum": 925, "atom2_serNum": 957, "donAcc_type": "standard", "distance": 2.961, "atom1_id": "///A/111/OD2", "atom2_id": "///A/116/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 135, "atom1_serNum": 1027, "atom2_serNum": 1038, "donAcc_type": "standard", "distance": 2.602, "atom1_id": "///A/124/O", "atom2_id": "///A/126/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 136, "atom1_serNum": 1027, "atom2_serNum": 1047, "donAcc_type": "standard", "distance": 2.787, "atom1_id": "///A/124/O", "atom2_id": "///A/127/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 137, "atom1_serNum": 1031, "atom2_serNum": 1038, "donAcc_type": "standard", "distance": 3.100, "atom1_id": "///A/124/OD2", "atom2_id": "///A/126/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 138, "atom1_serNum": 1035, "atom2_serNum": 1113, "donAcc_type": "standard", "distance": 2.361, "atom1_id": "///A/125/O", "atom2_id": "///A/134/NZ", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 139, "atom1_serNum": 1050, "atom2_serNum": 1072, "donAcc_type": "standard", "distance": 3.032, "atom1_id": "///A/127/O", "atom2_id": "///A/130/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 140, "atom1_serNum": 1059, "atom2_serNum": 1080, "donAcc_type": "standard", "distance": 3.022, "atom1_id": "///A/128/O", "atom2_id": "///A/131/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 141, "atom1_serNum": 1063, "atom2_serNum": 1070, "donAcc_type": "standard", "distance": 2.820, "atom1_id": "///A/129/N", "atom2_id": "///A/129/OE1", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 142, "atom1_serNum": 1075, "atom2_serNum": 1105, "donAcc_type": "standard", "distance": 3.011, "atom1_id": "///A/130/O", "atom2_id": "///A/134/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 143, "atom1_serNum": 1083, "atom2_serNum": 1114, "donAcc_type": "standard", "distance": 2.975, "atom1_id": "///A/131/O", "atom2_id": "///A/135/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 144, "atom1_serNum": 1091, "atom2_serNum": 1119, "donAcc_type": "acceptable", "distance": 2.955, "atom1_id": "///A/132/O", "atom2_id": "///A/135/OG", "atom_pair": "O:O", "residue_pair": "aa:aa" }, { "index": 145, "atom1_serNum": 1091, "atom2_serNum": 1120, "donAcc_type": "standard", "distance": 2.902, "atom1_id": "///A/132/O", "atom2_id": "///A/136/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 146, "atom1_serNum": 1100, "atom2_serNum": 1131, "donAcc_type": "standard", "distance": 2.903, "atom1_id": "///A/133/O", "atom2_id": "///A/137/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 147, "atom1_serNum": 1108, "atom2_serNum": 1140, "donAcc_type": "standard", "distance": 3.296, "atom1_id": "///A/134/O", "atom2_id": "///A/138/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 148, "atom1_serNum": 1117, "atom2_serNum": 1140, "donAcc_type": "standard", "distance": 2.976, "atom1_id": "///A/135/O", "atom2_id": "///A/138/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 149, "atom1_serNum": 1123, "atom2_serNum": 1151, "donAcc_type": "standard", "distance": 2.855, "atom1_id": "///A/136/O", "atom2_id": "///A/139/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 150, "atom1_serNum": 1134, "atom2_serNum": 1159, "donAcc_type": "standard", "distance": 3.021, "atom1_id": "///A/137/O", "atom2_id": "///A/140/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 151, "atom1_serNum": 1134, "atom2_serNum": 1171, "donAcc_type": "standard", "distance": 3.301, "atom1_id": "///A/137/O", "atom2_id": "///A/141/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 152, "atom1_serNum": 1179, "atom2_serNum": 1217, "donAcc_type": "questionable", "distance": 2.860, "atom1_id": "///B/1/O5'", "atom2_id": "///B/3/OP1", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 153, "atom1_serNum": 1199, "atom2_serNum": 1222, "donAcc_type": "questionable", "distance": 2.435, "atom1_id": "///B/2/OP2", "atom2_id": "///B/3/O4'", "atom_pair": "O:O", "residue_pair": "nt:nt" }, { "index": 154, "atom1_serNum": 1293, "atom2_serNum": 1316, "donAcc_type": "standard", "distance": 2.611, "atom1_id": "///B/6/O2", "atom2_id": "///B/7/N6", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 155, "atom1_serNum": 1342, "atom2_serNum": 1379, "donAcc_type": "standard", "distance": 2.737, "atom1_id": "///B/9/OP2", "atom2_id": "///B/10/N1", "atom_pair": "O:N", "residue_pair": "nt:nt" }, { "index": 156, "atom1_serNum": 1342, "atom2_serNum": 1381, "donAcc_type": "standard", "distance": 3.192, "atom1_id": "///B/9/OP2", "atom2_id": "///B/10/N2", "atom_pair": "O:N", "residue_pair": "nt:nt" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "4hja", "num_aaChains": 1, "aaChains": "A=139", "num_naChains": 1, "naChains": "B=11", "num_atoms": 1540, "num_waters": 138, "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 10, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 3, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 4, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 5, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 6, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 7, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 8, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 9, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 10, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }