**************************************************************************** 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/6ogk.pdb -o=6ogk.out --type=base File name: 6ogk.pdb no. of peptide chains: 1 [A=76] no. of DNA/RNA chains: 2 [C=12,D=12] no. of amino acids: 76 no. of nucleotides: 24 no. of atoms: 1146 no. of waters: 56 no. of metals: 1 [Ca=1] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 5CM-c 1 D.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'-GCCTAcACTCCG-3' bp-type |||||||||||| strand-2 3'-CGGATGTGAGGC-5' helix-form BBBBBBBBB.. 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.DT4 C.DA9 T-A 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.DA7 C.DT6 A-T WC 20-XX cWW cW-W 8 D.DC8 C.DG5 C-G WC 19-XIX cWW cW-W 9 D.DT9 C.DA4 T-A WC 20-XX cWW cW-W 10 D.DC10 C.DG3 C-G WC 19-XIX cWW cW-W 11 D.DC11 C.DG2 C-G WC 19-XIX cWW cW-W 12 D.DG12 C.DC1 G-C 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 6ogk C-arg D.5CM6 A.ARG111 11.36 168.87 -4.54 -10.03 -2.79 -27.37 51.38 167.25 2 6ogk C-asp D.5CM6 A.ASP121 -8.82 -167.71 0.21 8.09 3.50 -60.76 -16.36 -165.58 3 6ogk C-arg D.5CM6 A.ARG133 9.86 -154.93 -6.88 6.58 2.55 -59.84 55.69 -146.65 4 6ogk A-arg D.DA7 A.ARG133 -9.87 168.65 1.53 -9.73 -0.68 34.82 -77.48 164.59 5 6ogk G-tyr C.DG5 A.TYR123 13.19 119.15 7.02 -2.63 10.85 -11.03 75.02 100.14 6 6ogk G-arg C.DG5 A.ARG133 10.57 174.58 1.07 -10.04 3.11 -27.92 84.98 172.37 7 6ogk T-arg C.DT6 A.ARG111 11.39 -126.36 -6.16 7.47 5.99 -7.58 -55.61 -118.49 8 6ogk T-asp C.DT6 A.ASP121 10.08 -153.00 -3.61 9.39 -0.54 58.58 10.53 -148.81 9 6ogk T-arg C.DT6 A.ARG133 9.99 -172.32 1.58 9.86 -0.12 29.46 75.54 -169.89 10 6ogk G-arg C.DG7 A.ARG111 -11.72 -161.16 -4.78 10.34 2.73 -32.31 -41.37 -158.97 **************************************************************************** List of 8 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6ogk AT-arg D.DA7 C.DT6 A.ARG111 -11.28 127.78 -6.13 -7.20 -6.14 -4.45 56.28 120.07 2 6ogk AT-arg D.DA7 C.DT6 A.ARG133 -9.93 170.48 1.55 -9.80 -0.28 32.14 -76.53 167.27 3 6ogk AT-asp D.DA7 C.DT6 A.ASP121 -9.96 153.08 -3.56 -9.30 0.23 61.91 -10.85 148.34 4 6ogk GC-arg C.DG7 D.5CM6 A.ARG111 -11.54 -165.01 -4.66 10.19 2.75 -29.84 -46.38 -163.07 5 6ogk GC-arg C.DG7 D.5CM6 A.ARG133 -9.90 151.48 -6.72 -6.45 -3.34 -54.67 -59.04 142.36 6 6ogk GC-arg C.DG5 D.DC8 A.ARG133 10.56 -150.25 -2.71 9.83 2.75 10.37 85.62 -138.82 7 6ogk GC-asp C.DG7 D.5CM6 A.ASP121 8.98 166.68 0.49 -8.09 -3.86 -56.17 11.61 164.81 8 6ogk GC-tyr C.DG5 D.DC8 A.TYR123 13.16 114.66 6.62 -2.04 11.19 -16.33 73.19 94.26 **************************************************************************** List of 9 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6ogk OP1@D.DA5 NH1@A.ARG162 2.99 po4:sidechain:salt-bridge 2 6ogk OP1@D.DA5 NH2@A.ARG162 3.08 po4:sidechain:salt-bridge 3 6ogk OP2@D.5CM6 N@A.VAL136 3.83 po4:backbone 4 6ogk OP2.A@C.DG5 NZ@A.LYS109 2.45 po4:sidechain:salt-bridge 5 6ogk OP1@C.DT6 N@A.LYS112 2.76 po4:backbone 6 6ogk OP1@C.DT6 N@A.SER113 3.14 po4:backbone 7 6ogk OP1@C.DG7 N@A.ARG115 3.19 po4:backbone 8 6ogk OP2@C.DG7 N@A.SER116 3.11 po4:backbone 9 6ogk OP2@C.DG7 OG@A.SER116 2.58 po4:sidechain **************************************************************************** List of 5 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6ogk O6@C.DG5 NH2@A.ARG133 3.09 base:sidechain 2 6ogk O4@C.DT6 NH1@A.ARG133 2.84 base:sidechain 3 6ogk O4@C.DT6 NH2@A.ARG133 3.02 base:sidechain 4 6ogk N7@C.DG7 NH1@A.ARG111 2.76 base:sidechain 5 6ogk O6@C.DG7 NH2@A.ARG111 2.87 base:sidechain **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6ogk T-arg C.DT6 A.ARG133 0.10 61 2 6ogk G-arg C.DG7 A.ARG111 0.25 18 **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6ogk T-arg C.DT6 A.ARG111 3.62 9 **************************************************************************** List of 3 additional files 1 -- 6ogk-baseAA-pairs.pdb 2 -- 6ogk-baseAA-stacks.pdb 3 -- 6ogk-pairs.pdb