**************************************************************************** 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/6cnq.pdb -o=6cnq.out --type=base File name: 6cnq.pdb no. of peptide chains: 2 [A=68,B=68] no. of DNA/RNA chains: 4 [C=12,D=12,E=12,F=12] no. of amino acids: 136 no. of nucleotides: 48 no. of atoms: 2048 no. of waters: 29 no. of metals: 0 **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5CM-c 4 D.5CM6,C.5CM6,E.5CM6,F.5CM6 **************************************************************************** List of 2 helices 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.BBBBBBBB 1 D.DG1 C.DC12 G-C WC 19-XIX cWW cW-W 2 D.DC2 C.DG11 C-G WC 19-XIX cWW cW-W 3 D.DC3 C.DG10 C-G WC 19-XIX cWW cW-W 4 D.DA4 C.DT9 A-T WC 20-XX cWW cW-W 5 D.DA5 C.DT8 A-T WC 20-XX cWW cW-W 6 D.5CM6 C.DG7 c-G WC 19-XIX cWW cW-W 7 D.DG7 C.5CM6 G-c WC 19-XIX cWW cW-W 8 D.DT8 C.DA5 T-A WC 20-XX cWW cW-W 9 D.DT9 C.DA4 T-A WC 20-XX cWW cW-W 10 D.DG10 C.DC3 G-C WC 19-XIX cWW cW-W 11 D.DG11 C.DC2 G-C WC 19-XIX cWW cW-W 12 D.DC12 C.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=12 strand-1 5'-GCCAAcGTTGGC-3' bp-type |||||||||||| strand-2 3'-CGGTTGcAACCG-5' helix-form BB.BBBBB.BB 1 E.DG1 F.DC12 G-C WC 19-XIX cWW cW-W 2 E.DC2 F.DG11 C-G WC 19-XIX cWW cW-W 3 E.DC3 F.DG10 C-G WC 19-XIX cWW cW-W 4 E.DA4 F.DT9 A-T WC 20-XX cWW cW-W 5 E.DA5 F.DT8 A-T WC 20-XX cWW cW-W 6 E.5CM6 F.DG7 c-G WC 19-XIX cWW cW-W 7 E.DG7 F.5CM6 G-c WC 19-XIX cWW cW-W 8 E.DT8 F.DA5 T-A WC 20-XX cWW cW-W 9 E.DT9 F.DA4 T-A WC 20-XX cWW cW-W 10 E.DG10 F.DC3 G-C WC 19-XIX cWW cW-W 11 E.DG11 F.DC2 G-C WC 19-XIX cWW cW-W 12 E.DC12 F.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 24 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6cnq A-arg D.DA5 A.ARG166 12.63 -174.48 3.84 11.97 -1.20 36.12 -47.59 -173.63 2 6cnq C-arg D.5CM6 A.ARG166 11.36 167.29 -4.85 -9.93 -2.61 -29.22 64.80 164.36 3 6cnq C-asp D.5CM6 A.ASP176 -9.06 -178.80 -0.19 8.38 3.44 -52.81 -19.21 -178.64 4 6cnq C-arg D.5CM6 A.ARG188 9.96 -159.97 -7.08 6.85 1.41 -41.79 32.41 -157.60 5 6cnq G-arg D.DG7 A.ARG188 -10.41 169.59 2.82 -9.92 -1.36 27.93 -51.61 168.05 6 6cnq A-tyr C.DA5 A.TYR178 13.20 -151.56 -4.76 11.30 -4.89 50.85 56.82 -143.61 7 6cnq A-arg C.DA5 A.ARG188 10.86 -141.80 -1.35 10.32 3.09 -0.97 59.76 -135.66 8 6cnq C-arg C.5CM6 A.ARG166 11.77 -127.96 -6.19 7.96 6.06 -9.46 -58.80 -119.28 9 6cnq C-asp C.5CM6 A.ASP176 10.28 -149.58 -3.41 9.66 -0.81 48.65 10.51 -146.38 10 6cnq C-tyr C.5CM6 A.TYR178 12.78 -175.86 -0.80 10.40 -7.38 68.05 36.31 -174.70 11 6cnq C-arg C.5CM6 A.ARG188 9.96 -169.62 2.53 9.63 0.16 19.24 53.86 -168.17 12 6cnq G-arg C.DG7 A.ARG166 -11.90 -157.91 -4.88 10.56 2.50 -35.21 -51.66 -154.10 13 6cnq G-ser C.DG7 A.SER171 10.32 -115.10 -4.74 9.13 0.90 18.78 -10.28 -113.81 14 6cnq C-arg E.5CM6 B.ARG166 11.26 165.16 -4.78 -9.84 -2.68 -29.02 66.36 161.58 15 6cnq C-asp E.5CM6 B.ASP176 -8.87 -175.18 0.30 8.11 3.57 -53.69 -17.63 -174.53 16 6cnq C-arg E.5CM6 B.ARG188 9.95 -162.96 -7.24 6.68 1.38 -40.71 33.03 -160.99 17 6cnq G-arg E.DG7 B.ARG188 -10.28 163.99 2.74 -9.82 -1.35 25.30 -49.44 161.89 18 6cnq A-tyr F.DA5 B.TYR178 13.19 -150.46 -4.92 11.23 -4.84 57.29 58.36 -140.59 19 6cnq A-arg F.DA5 B.ARG188 10.79 -136.93 -1.36 10.08 3.59 2.53 58.45 -130.24 20 6cnq C-arg F.5CM6 B.ARG166 11.75 -125.00 -5.95 8.04 6.17 -8.27 -58.31 -115.95 21 6cnq C-asp F.5CM6 B.ASP176 10.13 -153.58 -3.87 9.31 -0.98 47.88 13.80 -150.81 22 6cnq C-tyr F.5CM6 B.TYR178 -12.86 -176.38 -0.98 10.08 -7.93 69.61 39.85 -175.26 23 6cnq C-arg F.5CM6 B.ARG188 10.02 -166.77 2.72 9.64 0.04 17.29 56.01 -164.82 24 6cnq G-arg F.DG7 B.ARG166 -11.82 -158.56 -4.60 10.48 2.95 -32.97 -52.66 -154.92 **************************************************************************** List of 20 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6cnq AT-arg D.DA5 C.DT8 A.ARG166 12.72 -174.17 3.65 12.18 -0.46 42.70 -46.80 -173.15 2 6cnq AT-arg C.DA5 D.DT8 A.ARG188 11.04 -136.06 -1.76 10.09 4.12 6.69 56.01 -129.76 3 6cnq AT-arg F.DA5 E.DT8 B.ARG188 10.99 -133.42 -1.56 9.96 4.38 7.15 56.87 -126.43 4 6cnq AT-tyr C.DA5 D.DT8 A.TYR178 13.33 -146.42 -4.96 11.74 -3.90 58.52 54.95 -135.60 5 6cnq AT-tyr F.DA5 E.DT8 B.TYR178 13.31 -147.66 -5.03 11.62 -4.09 61.91 58.18 -135.63 6 6cnq GC-arg C.DG7 D.5CM6 A.ARG166 -11.63 -162.58 -4.87 10.25 2.55 -32.27 -58.28 -159.12 7 6cnq GC-arg C.DG7 D.5CM6 A.ARG188 -10.12 156.83 -6.98 -6.96 -2.31 -35.62 -37.27 154.23 8 6cnq GC-arg D.DG7 C.5CM6 A.ARG166 -11.71 131.74 -5.83 -7.99 -6.26 -7.71 60.80 123.27 9 6cnq GC-arg D.DG7 C.5CM6 A.ARG188 -10.18 169.61 2.68 -9.79 -0.75 23.61 -52.82 168.12 10 6cnq GC-arg F.DG7 E.5CM6 B.ARG166 -11.54 -161.83 -4.70 10.16 2.81 -31.08 -59.55 -158.14 11 6cnq GC-arg F.DG7 E.5CM6 B.ARG188 -10.06 159.46 -7.13 -6.75 -2.19 -36.32 -38.25 157.05 12 6cnq GC-arg E.DG7 F.5CM6 B.ARG166 -11.69 128.54 -5.84 -8.00 -6.20 -6.81 62.65 118.78 13 6cnq GC-arg E.DG7 F.5CM6 B.ARG188 -10.15 165.36 2.74 -9.75 -0.70 21.35 -52.79 163.34 14 6cnq GC-asp C.DG7 D.5CM6 A.ASP176 -9.38 177.34 0.03 -8.51 -3.94 -47.51 13.04 177.08 15 6cnq GC-asp D.DG7 C.5CM6 A.ASP176 -10.41 150.89 -3.10 -9.93 0.42 52.32 -8.31 147.39 16 6cnq GC-asp F.DG7 E.5CM6 B.ASP176 -9.17 172.59 0.52 -8.28 -3.91 -49.46 11.84 171.79 17 6cnq GC-asp E.DG7 F.5CM6 B.ASP176 -10.20 153.03 -3.71 -9.48 0.69 51.44 -9.98 149.87 18 6cnq GC-ser C.DG7 D.5CM6 A.SER171 10.15 -115.18 -4.95 8.83 0.70 19.70 -18.41 -113.11 19 6cnq GC-tyr D.DG7 C.5CM6 A.TYR178 -12.94 176.10 -0.51 -10.93 6.92 72.28 -34.84 174.90 20 6cnq GC-tyr E.DG7 F.5CM6 B.TYR178 -12.94 174.42 -0.68 -10.58 7.41 73.79 -37.01 172.57 **************************************************************************** List of 21 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6cnq OP2@D.DA4 NE@A.ARG209 3.08 po4:sidechain:salt-bridge 2 6cnq OP2@D.DA4 NH2@A.ARG209 3.38 po4:sidechain:salt-bridge 3 6cnq OP2@D.DA5 N@A.LYS190 3.70 po4:backbone 4 6cnq OP2@D.5CM6 OG@A.SER189 2.45 po4:sidechain 5 6cnq OP2@C.DA4 NZ@A.LYS186 3.13 po4:sidechain:salt-bridge 6 6cnq OP1@C.5CM6 N@A.SER168 2.82 po4:backbone 7 6cnq OP1@C.5CM6 OG@A.SER168 2.79 po4:sidechain 8 6cnq OP2@C.5CM6 N@A.LYS167 3.10 po4:backbone 9 6cnq OP1@C.DG7 N@A.LEU170 3.13 po4:backbone 10 6cnq OP2@C.DG7 N@A.SER171 2.99 po4:backbone 11 6cnq OP2@C.DG7 OG@A.SER171 2.48 po4:sidechain 12 6cnq OP2@E.DA4 NE@B.ARG209 2.95 po4:sidechain:salt-bridge 13 6cnq OP2@E.DA5 N@B.LYS190 3.29 po4:backbone 14 6cnq OP2@E.5CM6 OG@B.SER189 2.52 po4:sidechain 15 6cnq OP2@F.DA4 NZ@B.LYS186 2.77 po4:sidechain:salt-bridge 16 6cnq OP1@F.5CM6 N@B.SER168 2.75 po4:backbone 17 6cnq OP1@F.5CM6 OG@B.SER168 2.95 po4:sidechain 18 6cnq OP2@F.5CM6 N@B.LYS167 3.07 po4:backbone 19 6cnq OP1@F.DG7 N@B.LEU170 3.10 po4:backbone 20 6cnq OP2@F.DG7 N@B.SER171 2.99 po4:backbone 21 6cnq OP2@F.DG7 OG@B.SER171 2.57 po4:sidechain **************************************************************************** List of 8 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6cnq N7.A@D.DG7 NH2@A.ARG188 3.20 base:sidechain 2 6cnq O6.A@D.DG7 NH1@A.ARG188 2.87 base:sidechain 3 6cnq N7@C.DG7 NH1@A.ARG166 2.94 base:sidechain 4 6cnq O6@C.DG7 NH2@A.ARG166 3.10 base:sidechain 5 6cnq N7@E.DG7 NH2@B.ARG188 3.19 base:sidechain 6 6cnq O6@E.DG7 NH1@B.ARG188 2.74 base:sidechain 7 6cnq N7@F.DG7 NH1@B.ARG166 2.82 base:sidechain 8 6cnq O6@F.DG7 NH2@B.ARG166 2.91 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6cnq G-arg D.DG7 A.ARG188 0.03 6 2 6cnq G-arg C.DG7 A.ARG166 0.48 23 3 6cnq G-arg E.DG7 B.ARG188 0.01 6 4 6cnq G-arg F.DG7 B.ARG166 0.68 21 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6cnq C-arg D.5CM6 A.ARG188 3.44 10 2 6cnq C-arg C.5CM6 A.ARG166 3.78 16 3 6cnq C-arg E.5CM6 B.ARG188 3.51 6 4 6cnq C-arg F.5CM6 B.ARG166 3.85 17 **************************************************************************** List of 3 additional files 1 -- 6cnq-baseAA-pairs.pdb 2 -- 6cnq-baseAA-stacks.pdb 3 -- 6cnq-pairs.pdb