ClaRNA

Doublet Group distance statistics: 18356

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Distances from reference structure (by RMSD)

1, 0, 1, 1, 0, 0, 1, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9,

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C6 B 0, 0.460, 0.919, 1.379, 1.908 max_d=1.908 avg_d=0.919 std_dev=0.460
N1 A 0, 0.126, 0.689, 1.253, 1.838 max_d=1.838 avg_d=0.689 std_dev=0.564
C6 A 0, 0.377, 1.104, 1.831, 2.261 max_d=2.261 avg_d=1.104 std_dev=0.727
N1 B 0, 0.168, 1.002, 1.835, 2.618 max_d=2.618 avg_d=1.002 std_dev=0.834
C5 B 0, 0.437, 1.350, 2.263, 2.962 max_d=2.962 avg_d=1.350 std_dev=0.913
C2 A 0, 0.325, 1.261, 2.196, 2.923 max_d=2.923 avg_d=1.261 std_dev=0.935
C2 B 0, 0.719, 1.700, 2.681, 3.232 max_d=3.232 avg_d=1.700 std_dev=0.981
N3 B 0, 0.617, 1.632, 2.647, 2.883 max_d=2.883 avg_d=1.632 std_dev=1.015
C1' A 0, 0.253, 1.350, 2.447, 3.174 max_d=3.174 avg_d=1.350 std_dev=1.097
O4' A 0, 0.733, 1.907, 3.081, 4.004 max_d=4.004 avg_d=1.907 std_dev=1.174
C4 B 0, 0.283, 1.473, 2.663, 3.416 max_d=3.416 avg_d=1.473 std_dev=1.190
C5 A 0, 0.538, 1.826, 3.114, 4.216 max_d=4.216 avg_d=1.826 std_dev=1.288
O2 A 0, 0.494, 1.858, 3.222, 4.054 max_d=4.054 avg_d=1.858 std_dev=1.364
O4' B 0, 0.469, 1.891, 3.313, 4.051 max_d=4.051 avg_d=1.891 std_dev=1.422
N3 A 0, 0.265, 1.731, 3.196, 4.343 max_d=4.343 avg_d=1.731 std_dev=1.466
C1' B 0, 0.357, 1.842, 3.328, 4.325 max_d=4.325 avg_d=1.842 std_dev=1.486
O2 B 0, 1.261, 2.766, 4.271, 4.925 max_d=4.925 avg_d=2.766 std_dev=1.505
C4 A 0, 0.516, 2.135, 3.755, 5.424 max_d=5.424 avg_d=2.135 std_dev=1.620
C4' A 0, 0.986, 2.630, 4.275, 6.798 max_d=6.798 avg_d=2.630 std_dev=1.644
C5' B 0, 0.640, 2.338, 4.036, 6.386 max_d=6.386 avg_d=2.338 std_dev=1.698
O5' B 0, 0.670, 2.399, 4.129, 6.234 max_d=6.234 avg_d=2.399 std_dev=1.729
C4' B 0, 0.659, 2.400, 4.141, 5.661 max_d=5.661 avg_d=2.400 std_dev=1.741
O4 B 0, 0.452, 2.291, 4.131, 5.051 max_d=5.051 avg_d=2.291 std_dev=1.839
C3' B 0, 0.826, 2.673, 4.519, 5.967 max_d=5.967 avg_d=2.673 std_dev=1.846
C2' B 0, 0.598, 2.460, 4.321, 5.733 max_d=5.733 avg_d=2.460 std_dev=1.862
P B 0, 0.587, 2.468, 4.348, 6.493 max_d=6.493 avg_d=2.468 std_dev=1.880
C2' A 0, 0.556, 2.461, 4.366, 5.131 max_d=5.131 avg_d=2.461 std_dev=1.905
OP1 B 0, 1.132, 3.160, 5.188, 7.674 max_d=7.674 avg_d=3.160 std_dev=2.028
OP2 B 0, 1.206, 3.235, 5.263, 6.775 max_d=6.775 avg_d=3.235 std_dev=2.029
C3' A 0, 0.815, 2.897, 4.978, 7.206 max_d=7.206 avg_d=2.897 std_dev=2.082
C5' A 0, 1.526, 3.667, 5.808, 7.996 max_d=7.996 avg_d=3.667 std_dev=2.141
O4 A 0, 0.690, 3.002, 5.315, 7.763 max_d=7.763 avg_d=3.002 std_dev=2.313
O5' A 0, 1.725, 4.062, 6.398, 8.107 max_d=8.107 avg_d=4.062 std_dev=2.336
O2' A 0, 1.221, 3.680, 6.140, 6.902 max_d=6.902 avg_d=3.680 std_dev=2.460
O3' B 0, 0.942, 3.473, 6.004, 8.365 max_d=8.365 avg_d=3.473 std_dev=2.531
O2' B 0, 0.459, 3.137, 5.814, 8.074 max_d=8.074 avg_d=3.137 std_dev=2.677
P A 0, 1.902, 4.713, 7.525, 8.640 max_d=8.640 avg_d=4.713 std_dev=2.812
O3' A 0, 0.921, 3.849, 6.777, 9.773 max_d=9.773 avg_d=3.849 std_dev=2.928
OP1 A 0, 2.019, 5.019, 8.019, 9.479 max_d=9.479 avg_d=5.019 std_dev=3.000
OP2 A 0, 2.165, 5.784, 9.403, 10.906 max_d=10.906 avg_d=5.784 std_dev=3.619

Atoms distances (summary)

atom dist matrix

Atoms distances Chain-A - Chain-A

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3O2O2'O3'O4O4'O5'OP1OP2P
C1' 0.00 0.05 0.00 0.02 0.03 0.02 0.03 0.06 0.03 0.01 0.04 0.09 0.03 0.32 0.04 0.01 0.32 0.44 0.81 0.46
C2 0.05 0.00 0.31 0.37 0.01 0.32 0.02 0.45 0.01 0.01 0.00 0.01 0.35 0.60 0.02 0.32 0.84 0.57 1.30 0.94
C2' 0.00 0.31 0.00 0.01 0.11 0.02 0.29 0.17 0.34 0.06 0.20 0.59 0.01 0.05 0.12 0.04 0.53 0.70 1.02 0.65
C3' 0.02 0.37 0.01 0.00 0.40 0.00 0.54 0.03 0.54 0.24 0.36 0.64 0.04 0.02 0.43 0.02 0.33 0.54 0.55 0.33
C4 0.03 0.01 0.11 0.40 0.00 0.19 0.01 0.41 0.02 0.02 0.01 0.01 0.56 0.48 0.00 0.08 0.71 0.84 1.45 1.08
C4' 0.02 0.32 0.02 0.00 0.19 0.00 0.33 0.01 0.36 0.10 0.26 0.62 0.25 0.05 0.20 0.01 0.04 0.53 0.46 0.22
C5 0.03 0.02 0.29 0.54 0.01 0.33 0.00 0.55 0.01 0.01 0.01 0.02 0.77 0.60 0.02 0.23 0.57 0.96 1.26 1.04
C5' 0.06 0.45 0.17 0.03 0.41 0.01 0.55 0.00 0.53 0.20 0.44 0.81 0.11 0.16 0.46 0.03 0.01 0.33 0.36 0.04
C6 0.03 0.01 0.34 0.54 0.02 0.36 0.01 0.53 0.00 0.00 0.02 0.02 0.74 0.55 0.03 0.30 0.46 0.88 1.04 0.92
N1 0.01 0.01 0.06 0.24 0.02 0.10 0.01 0.20 0.00 0.00 0.02 0.03 0.32 0.32 0.02 0.03 0.48 0.53 0.99 0.72
N3 0.04 0.00 0.20 0.36 0.01 0.26 0.01 0.44 0.02 0.02 0.00 0.01 0.38 0.55 0.02 0.24 0.87 0.72 1.49 1.08
O2 0.09 0.01 0.59 0.64 0.01 0.62 0.02 0.81 0.02 0.03 0.01 0.00 0.66 0.95 0.02 0.57 1.15 0.74 1.47 1.12
O2' 0.03 0.35 0.01 0.04 0.56 0.25 0.77 0.11 0.74 0.32 0.38 0.66 0.00 0.13 0.59 0.17 0.33 0.88 1.08 0.56
O3' 0.32 0.60 0.05 0.02 0.48 0.05 0.60 0.16 0.55 0.32 0.55 0.95 0.13 0.00 0.52 0.20 0.29 0.82 0.39 0.35
O4 0.04 0.02 0.12 0.43 0.00 0.20 0.02 0.46 0.03 0.02 0.02 0.02 0.59 0.52 0.00 0.10 0.78 0.93 1.61 1.17
O4' 0.01 0.32 0.04 0.02 0.08 0.01 0.23 0.03 0.30 0.03 0.24 0.57 0.17 0.20 0.10 0.00 0.26 0.53 0.70 0.48
O5' 0.32 0.84 0.53 0.33 0.71 0.04 0.57 0.01 0.46 0.48 0.87 1.15 0.33 0.29 0.78 0.26 0.00 0.02 0.04 0.01
OP1 0.44 0.57 0.70 0.54 0.84 0.53 0.96 0.33 0.88 0.53 0.72 0.74 0.88 0.82 0.93 0.53 0.02 0.00 0.01 0.01
OP2 0.81 1.30 1.02 0.55 1.45 0.46 1.26 0.36 1.04 0.99 1.49 1.47 1.08 0.39 1.61 0.70 0.04 0.01 0.00 0.01
P 0.46 0.94 0.65 0.33 1.08 0.22 1.04 0.04 0.92 0.72 1.08 1.12 0.56 0.35 1.17 0.48 0.01 0.01 0.01 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3O2O2'O3'O4O4'O5'OP1OP2P
C1' 1.42 1.88 1.45 1.21 1.94 1.20 1.52 0.84 1.18 1.40 2.07 2.12 2.12 1.77 2.22 1.26 0.81 1.06 0.75 0.76
C2 2.21 2.36 2.17 1.62 2.22 1.71 1.74 1.06 1.55 1.97 2.43 2.63 3.06 1.98 2.46 1.85 0.78 0.80 0.74 0.46
C2' 1.69 2.27 1.49 1.18 2.26 1.46 1.91 1.35 1.62 1.79 2.42 2.55 2.03 1.58 2.47 1.73 1.24 1.20 1.24 1.28
C3' 1.52 2.03 1.44 1.21 1.96 1.41 1.59 1.42 1.36 1.57 2.15 2.34 1.94 1.69 2.14 1.60 1.46 1.43 1.64 1.69
C4 2.72 2.78 2.38 1.63 2.51 1.93 2.23 1.24 2.14 2.51 2.70 3.07 3.09 1.57 2.58 2.29 0.87 0.80 0.83 0.37
C4' 1.47 1.85 1.62 1.60 1.84 1.45 1.48 1.28 1.28 1.47 1.98 2.07 2.00 2.14 2.04 1.41 1.39 1.64 1.27 1.46
C5 2.35 2.32 2.01 1.41 2.02 1.79 1.79 1.21 1.78 2.12 2.21 2.54 2.59 1.34 2.05 2.04 0.90 0.80 0.79 0.35
C5' 1.65 1.74 2.08 2.19 1.59 1.78 1.34 1.58 1.35 1.51 1.77 1.96 2.31 2.80 1.72 1.55 1.68 1.79 1.44 1.58
C6 1.89 1.95 1.69 1.24 1.73 1.53 1.43 1.02 1.34 1.69 1.91 2.15 2.27 1.39 1.84 1.64 0.84 0.75 0.67 0.24
N1 1.84 2.03 1.78 1.36 1.90 1.50 1.48 0.96 1.28 1.65 2.10 2.27 2.52 1.75 2.11 1.59 0.79 0.81 0.67 0.44
N3 2.61 2.71 2.42 1.71 2.52 1.89 2.11 1.17 1.96 2.37 2.71 3.01 3.29 1.84 2.71 2.16 0.81 0.75 0.79 0.37
O2 2.14 2.34 2.22 1.70 2.27 1.67 1.72 1.03 1.49 1.90 2.47 2.65 3.15 2.17 2.60 1.78 0.77 0.89 0.80 0.61
O2' 2.09 2.77 1.59 1.28 2.90 1.76 2.58 1.74 2.23 2.33 2.95 2.96 1.88 1.27 3.12 2.20 1.57 1.60 1.65 1.62
O3' 1.80 2.41 1.43 1.14 2.35 1.67 2.00 1.95 1.79 1.96 2.53 2.68 1.79 1.21 2.50 2.01 2.02 1.86 2.43 2.44
O4 2.99 3.16 2.55 1.71 2.86 2.01 2.62 1.31 2.50 2.84 3.05 3.52 3.22 1.54 2.92 2.50 0.91 0.89 0.92 0.47
O4' 1.44 1.65 1.67 1.70 1.70 1.53 1.36 1.32 1.15 1.32 1.80 1.86 2.13 2.26 1.95 1.34 1.47 1.55 1.07 1.28
O5' 1.87 1.74 2.53 2.65 1.52 1.98 1.44 1.67 1.56 1.68 1.68 1.93 2.68 3.27 1.56 1.67 1.65 1.58 1.26 1.35
OP1 2.77 2.51 3.46 3.77 2.31 3.00 2.41 2.89 2.60 2.62 2.39 2.57 3.26 4.10 2.22 2.64 2.80 2.59 2.17 2.32
OP2 3.14 2.83 3.94 3.89 2.47 2.98 2.60 2.45 2.85 2.92 2.63 2.97 4.01 4.33 2.32 2.74 2.16 1.71 1.43 1.55
P 2.83 2.47 3.57 3.77 2.11 2.96 2.19 2.59 2.45 2.56 2.28 2.59 3.56 4.34 2.00 2.60 2.44 2.10 1.66 1.87

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3O2O2'O3'O4O4'O5'OP1OP2P
C1' 0.00 0.04 0.01 0.02 0.06 0.04 0.04 0.06 0.03 0.02 0.05 0.05 0.02 0.17 0.06 0.02 0.37 1.03 0.71 0.55
C2 0.04 0.00 0.26 0.14 0.02 0.22 0.01 0.29 0.01 0.01 0.01 0.01 0.30 0.25 0.03 0.34 0.79 1.50 0.98 1.00
C2' 0.01 0.26 0.00 0.01 0.10 0.03 0.21 0.11 0.26 0.06 0.20 0.45 0.01 0.05 0.11 0.02 0.37 0.75 0.75 0.46
C3' 0.02 0.14 0.01 0.00 0.30 0.01 0.41 0.05 0.39 0.18 0.19 0.22 0.04 0.01 0.32 0.04 0.40 0.67 0.72 0.49
C4 0.06 0.02 0.10 0.30 0.00 0.16 0.01 0.41 0.02 0.04 0.01 0.02 0.29 0.25 0.01 0.09 0.97 1.60 1.76 1.35
C4' 0.04 0.22 0.03 0.01 0.16 0.00 0.37 0.01 0.40 0.08 0.12 0.49 0.17 0.04 0.16 0.01 0.02 0.58 0.40 0.23
C5 0.04 0.01 0.21 0.41 0.01 0.37 0.00 0.77 0.01 0.02 0.01 0.01 0.51 0.34 0.02 0.32 1.17 1.56 2.11 1.55
C5' 0.06 0.29 0.11 0.05 0.41 0.01 0.77 0.00 0.77 0.23 0.20 0.75 0.12 0.14 0.43 0.04 0.01 0.31 0.34 0.04
C6 0.03 0.01 0.26 0.39 0.02 0.40 0.01 0.77 0.00 0.01 0.01 0.01 0.54 0.31 0.03 0.40 1.08 1.37 1.86 1.36
N1 0.02 0.01 0.06 0.18 0.04 0.08 0.02 0.23 0.01 0.00 0.02 0.02 0.16 0.15 0.04 0.05 0.65 1.25 1.16 0.89
N3 0.05 0.01 0.20 0.19 0.01 0.12 0.01 0.20 0.01 0.02 0.00 0.01 0.24 0.23 0.02 0.22 0.86 1.60 1.28 1.15
O2 0.05 0.01 0.45 0.22 0.02 0.49 0.01 0.75 0.01 0.02 0.01 0.00 0.64 0.41 0.02 0.65 1.11 1.65 0.86 1.17
O2' 0.02 0.30 0.01 0.04 0.29 0.17 0.51 0.12 0.54 0.16 0.24 0.64 0.00 0.09 0.31 0.12 0.33 0.73 0.52 0.29
O3' 0.17 0.25 0.05 0.01 0.25 0.04 0.34 0.14 0.31 0.15 0.23 0.41 0.09 0.00 0.27 0.10 0.67 0.94 0.75 0.70
O4 0.06 0.03 0.11 0.32 0.01 0.16 0.02 0.43 0.03 0.04 0.02 0.02 0.31 0.27 0.00 0.09 1.03 1.71 1.87 1.46
O4' 0.02 0.34 0.02 0.04 0.09 0.01 0.32 0.04 0.40 0.05 0.22 0.65 0.12 0.10 0.09 0.00 0.41 0.95 0.53 0.51
O5' 0.37 0.79 0.37 0.40 0.97 0.02 1.17 0.01 1.08 0.65 0.86 1.11 0.33 0.67 1.03 0.41 0.00 0.02 0.02 0.01
OP1 1.03 1.50 0.75 0.67 1.60 0.58 1.56 0.31 1.37 1.25 1.60 1.65 0.73 0.94 1.71 0.95 0.02 0.00 0.01 0.00
OP2 0.71 0.98 0.75 0.72 1.76 0.40 2.11 0.34 1.86 1.16 1.28 0.86 0.52 0.75 1.87 0.53 0.02 0.01 0.00 0.01
P 0.55 1.00 0.46 0.49 1.35 0.23 1.55 0.04 1.36 0.89 1.15 1.17 0.29 0.70 1.46 0.51 0.01 0.00 0.01 0.00