**************************************************************************** File name: 7cd6.pdb1 no. of peptide chains: 2 [1.A=277,2.A=277] no. of DNA/RNA chains: 2 [1.B=9,2.B=9] no. of amino acids: 554 no. of nucleotides: 18 no. of atoms: 4838 no. of waters: 54 no. of metals: 0 **************************************************************************** List of 1 helix Note: A helix is defined by base-stacking interactions, regardless of pair 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=6 strand-1 5'-GTATAC-3' bp-type |||||| strand-2 3'-CATATG-5' helix-form B.x.B 1 1:B.DG3 2:B.DC9 G-C WC 19-XIX cWW cW-W 2 1:B.DT4 2:B.DA8 T-A WC 20-XX cWW cW-W 3 1:B.DA5 2:B.DT7 A-T WC 20-XX cWW cW-W 4 1:B.DT7 2:B.DA5 T-A WC 20-XX cWW cW-W 5 1:B.DA8 2:B.DT4 A-T WC 20-XX cWW cW-W 6 1:B.DC9 2:B.DG3 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 14 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7cd6 G-arg 1:B.DG1 2:A.ARG176 4.66 -110.55 4.49 -1.05 -0.64 62.27 -30.72 -92.26 2 7cd6 C-arg 1:B.DC2 2:A.ARG176 -8.05 109.75 -5.94 -5.35 -0.95 77.75 43.74 72.18 3 7cd6 C-met 1:B.DC2 2:A.MET269 9.69 159.61 4.30 8.68 -0.13 44.95 34.03 156.83 4 7cd6 G-tyr 1:B.DG3 2:A.TYR268 -7.81 179.76 3.73 6.76 1.21 -73.15 -9.85 179.69 5 7cd6 G-met 1:B.DG3 2:A.MET269 -7.73 150.40 5.05 4.01 -4.27 12.49 26.92 149.36 6 7cd6 A-lys 1:B.DA5 2:A.LYS97 11.35 72.07 -10.15 4.00 3.13 -67.73 20.15 15.20 7 7cd6 C-arg 1:B.DC9 1:A.ARG176 10.06 99.59 9.69 2.51 0.98 -21.92 -46.55 88.45 8 7cd6 G-arg 2:B.DG1 1:A.ARG176 4.66 -110.54 4.49 -1.05 -0.64 62.27 -30.73 -92.25 9 7cd6 C-arg 2:B.DC2 1:A.ARG176 -8.05 109.75 -5.94 -5.35 -0.95 77.75 43.73 72.17 10 7cd6 C-met 2:B.DC2 1:A.MET269 9.69 159.60 4.30 8.68 -0.14 44.96 34.01 156.82 11 7cd6 G-tyr 2:B.DG3 1:A.TYR268 -7.81 179.74 3.72 6.76 1.21 -73.14 -9.84 179.67 12 7cd6 G-met 2:B.DG3 1:A.MET269 -7.73 150.41 5.05 4.01 -4.27 12.49 26.91 149.36 13 7cd6 A-lys 2:B.DA5 1:A.LYS97 11.35 72.06 -10.15 4.00 3.13 -67.72 20.16 15.19 14 7cd6 C-arg 2:B.DC9 2:A.ARG176 10.06 99.58 9.69 2.51 0.98 -21.92 -46.55 88.45 **************************************************************************** List of 8 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7cd6 GC-arg 1:B.DG3 2:B.DC9 2:A.ARG176 -10.18 99.83 -2.80 -9.70 -1.24 50.60 21.20 86.98 2 7cd6 GC-tyr 1:B.DG3 2:B.DC9 2:A.TYR268 -7.91 -175.30 -3.47 -7.02 1.12 75.62 11.46 -174.02 3 7cd6 GC-met 1:B.DG3 2:B.DC9 2:A.MET269 -7.75 154.01 4.83 4.23 -4.35 8.13 28.17 153.12 4 7cd6 AT-lys 1:B.DA5 2:B.DT7 2:A.LYS97 -11.39 67.43 -9.98 5.32 1.26 -65.72 15.09 0.55 5 7cd6 GC-arg 2:B.DG3 1:B.DC9 1:A.ARG176 -10.18 99.83 -2.80 -9.70 -1.24 50.61 21.20 86.98 6 7cd6 GC-tyr 2:B.DG3 1:B.DC9 1:A.TYR268 -7.91 -175.32 -3.47 -7.02 1.12 75.62 11.45 -174.04 7 7cd6 GC-met 2:B.DG3 1:B.DC9 1:A.MET269 -7.75 154.01 4.83 4.23 -4.35 8.13 28.16 153.12 8 7cd6 AT-lys 2:B.DA5 1:B.DT7 1:A.LYS97 -11.39 67.42 -9.98 5.32 1.26 -65.71 15.10 0.54 **************************************************************************** List of 16 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 7cd6 OP1@1:B.DG3 N@2:A.MET270 2.99 po4:backbone 2 7cd6 OP1@1:B.DA5 NZ@2:A.LYS77 2.95 po4:sidechain:salt-bridge 3 7cd6 OP1@1:B.DA6 N@2:A.ARG72 3.20 po4:backbone 4 7cd6 OP1@1:B.DA6 N@2:A.ALA73 2.82 po4:backbone 5 7cd6 OP1@1:B.DT7 NH1@2:A.ARG72 2.86 po4:sidechain:salt-bridge 6 7cd6 OP1@1:B.DT7 NZ@2:A.LYS102 3.02 po4:sidechain:salt-bridge 7 7cd6 O3'@1:B.DA6 NH1@2:A.ARG72 2.89 po4:sidechain 8 7cd6 OP1@1:B.DC9 OH@1:A.TYR127 2.99 po4:sidechain 9 7cd6 OP1@2:B.DG3 N@1:A.MET270 2.99 po4:backbone 10 7cd6 OP1@2:B.DA5 NZ@1:A.LYS77 2.95 po4:sidechain:salt-bridge 11 7cd6 OP1@2:B.DA6 N@1:A.ARG72 3.20 po4:backbone 12 7cd6 OP1@2:B.DA6 N@1:A.ALA73 2.83 po4:backbone 13 7cd6 OP1@2:B.DT7 NH1@1:A.ARG72 2.86 po4:sidechain:salt-bridge 14 7cd6 OP1@2:B.DT7 NZ@1:A.LYS102 3.02 po4:sidechain:salt-bridge 15 7cd6 O3'@2:B.DA6 NH1@1:A.ARG72 2.89 po4:sidechain 16 7cd6 OP1@2:B.DC9 OH@2:A.TYR127 2.99 po4:sidechain **************************************************************************** List of 4 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 7cd6 N3@1:B.DC2 NH2@2:A.ARG176 3.63 base:sidechain 2 7cd6 N3@1:B.DA5 NZ@2:A.LYS97 3.86 base:sidechain 3 7cd6 N3@2:B.DC2 NH2@1:A.ARG176 3.63 base:sidechain 4 7cd6 N3@2:B.DA5 NZ@1:A.LYS97 3.86 base:sidechain **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 7cd6 C-arg 1:B.DC2 2:A.ARG176 0.03 26 2 7cd6 C-arg 2:B.DC2 1:A.ARG176 0.03 26 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 7cd6 G-arg 1:B.DG1 2:A.ARG176 3.65 49 2 7cd6 C-arg 1:B.DC9 1:A.ARG176 3.57 16 3 7cd6 G-arg 2:B.DG1 1:A.ARG176 3.65 49 4 7cd6 C-arg 2:B.DC9 2:A.ARG176 3.57 16 **************************************************************************** List of 3 additional files 1 -- 7cd6-baseAA-pairs.pdb 2 -- 7cd6-baseAA-stacks.pdb 3 -- 7cd6-pairs.pdb