**************************************************************************** Note: By default, each nucleotide/amino-acid is identified by chainId.name#. For example, B.DA1689 means adenosine #1689 on chain B, and C.ARG49 denotes arginine #49 on chain C. Use the --idstr=long option to get strictly delineated id strings. Command: x3dna-dssr snap -i=/data/pdb/pdbfiles/7ray.pdb -o=7ray.out --type=base File name: 7ray.pdb no. of peptide chains: 1 [A=74] no. of DNA/RNA chains: 2 [B=12,C=12] no. of amino acids: 74 no. of nucleotides: 24 no. of atoms: 1119 no. of waters: 72 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 B.5CM6,C.5CM6 **************************************************************************** List of 1 helix Note: a helix is defined by base-stacking interactions, regardless of bp type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[0] bps=12 strand-1 5'-GCCAAcGTTGGC-3' bp-type |||||||||||| strand-2 3'-CGGTTGcAACCG-5' helix-form BB.BBBBB.BB 1 B.DG1 C.DC12 G-C WC 19-XIX cWW cW-W 2 B.DC2 C.DG11 C-G WC 19-XIX cWW cW-W 3 B.DC3 C.DG10 C-G WC 19-XIX cWW cW-W 4 B.DA4 C.DT9 A-T WC 20-XX cWW cW-W 5 B.DA5 C.DT8 A-T WC 20-XX cWW cW-W 6 B.5CM6 C.DG7 c-G WC 19-XIX cWW cW-W 7 B.DG7 C.5CM6 G-c WC 19-XIX cWW cW-W 8 B.DT8 C.DA5 T-A WC 20-XX cWW cW-W 9 B.DT9 C.DA4 T-A WC 20-XX cWW cW-W 10 B.DG10 C.DC3 G-C WC 19-XIX cWW cW-W 11 B.DG11 C.DC2 G-C WC 19-XIX cWW cW-W 12 B.DC12 C.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 10 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7ray C-glu B.5CM6 A.GLU176 -10.25 -172.31 0.16 10.16 1.35 -39.00 -8.40 -171.81 2 7ray C-arg B.5CM6 A.ARG188 9.79 -156.91 -6.42 7.20 1.64 -39.92 38.29 -153.88 3 7ray G-arg B.DG7 A.ARG188 -10.35 173.76 2.63 -9.95 -1.06 20.16 -52.85 172.92 4 7ray A-lys C.DA4 A.LYS186 12.74 -159.82 -7.64 9.41 -3.94 -14.04 76.11 -154.06 5 7ray A-arg C.DA5 A.ARG188 10.79 -144.46 -1.83 10.11 3.30 -3.97 55.64 -139.60 6 7ray C-arg C.5CM6 A.ARG166 11.86 -125.69 -5.69 8.58 5.88 -17.85 -57.18 -116.43 7 7ray C-glu C.5CM6 A.GLU176 11.48 -151.99 -3.64 10.86 0.86 24.54 7.79 -151.25 8 7ray C-tyr C.5CM6 A.TYR178 -12.67 178.47 1.19 -10.17 -7.45 -56.71 -28.99 178.20 9 7ray C-arg C.5CM6 A.ARG188 9.88 -175.14 2.37 9.59 0.21 10.60 49.20 -174.63 10 7ray G-arg C.DG7 A.ARG166 -12.13 -158.36 -4.63 10.69 3.38 -31.09 -47.37 -155.38 **************************************************************************** List of 9 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7ray AT-arg C.DA5 B.DT8 A.ARG188 10.93 -141.09 -1.98 9.89 4.19 1.77 56.03 -135.67 2 7ray AT-lys C.DA4 B.DT9 A.LYS186 12.73 -155.38 -7.80 9.59 -3.05 -7.29 75.38 -148.67 3 7ray GC-arg C.DG7 B.5CM6 A.ARG166 -11.94 -162.37 -4.55 10.49 3.43 -28.66 -52.81 -159.60 4 7ray GC-arg C.DG7 B.5CM6 A.ARG188 -9.84 154.57 -6.27 -7.20 -2.37 -34.54 -42.34 151.31 5 7ray GC-arg B.DG7 C.5CM6 A.ARG166 -11.83 128.63 -5.36 -8.54 -6.20 -13.89 57.32 120.27 6 7ray GC-arg B.DG7 C.5CM6 A.ARG188 -10.12 174.46 2.50 -9.78 -0.63 15.35 -51.09 173.80 7 7ray GC-glu C.DG7 B.5CM6 A.GLU176 10.43 171.76 0.35 -10.27 -1.80 -34.35 3.30 171.37 8 7ray GC-glu B.DG7 C.5CM6 A.GLU176 -11.60 153.22 -3.37 -11.02 -1.32 29.45 -8.57 152.22 9 7ray GC-tyr B.DG7 C.5CM6 A.TYR178 12.87 -177.61 1.13 10.67 7.11 -61.39 30.69 -177.11 **************************************************************************** List of 10 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 7ray OP2@B.DA4 NH2@A.ARG209 2.87 po4:sidechain:salt-bridge 2 7ray OP1@B.5CM6 NH1@A.ARG195 3.01 po4:sidechain:salt-bridge 3 7ray OP2@B.5CM6 OG@A.SER189 2.46 po4:sidechain 4 7ray OP2@B.5CM6 NH2@A.ARG195 3.63 po4:sidechain:salt-bridge 5 7ray OP2@C.DA4 NZ@A.LYS186 2.98 po4:sidechain:salt-bridge 6 7ray OP1@C.5CM6 N@A.LYS167 2.71 po4:backbone 7 7ray OP1@C.5CM6 N.A@A.SER168 2.57 po4:backbone 8 7ray OP1@C.DG7 N.A@A.LEU170 3.24 po4:backbone 9 7ray OP2@C.DG7 N@A.SER171 3.16 po4:backbone 10 7ray OP2@C.DG7 OG@A.SER171 2.72 po4:sidechain **************************************************************************** List of 4 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 7ray N7@B.DG7 NH2@A.ARG188 3.09 base:sidechain 2 7ray O6@B.DG7 NH1@A.ARG188 2.69 base:sidechain 3 7ray N7@C.DG7 NH1@A.ARG166 2.92 base:sidechain 4 7ray O6@C.DG7 NH2@A.ARG166 3.27 base:sidechain **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 7ray G-arg B.DG7 A.ARG188 0.10 10 2 7ray G-arg C.DG7 A.ARG166 0.37 9 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 7ray C-arg B.5CM6 A.ARG188 3.57 3 2 7ray C-arg C.5CM6 A.ARG166 3.53 12 **************************************************************************** List of 3 additional files 1 -- 7ray-baseAA-pairs.pdb 2 -- 7ray-baseAA-stacks.pdb 3 -- 7ray-pairs.pdb