**************************************************************************** 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/6cc8.pdb -o=6cc8.out --type=base File name: 6cc8.pdb no. of peptide chains: 2 [A=71,B=71] no. of DNA/RNA chains: 4 [C=12,D=12,E=12,F=12] no. of amino acids: 142 no. of nucleotides: 48 no. of atoms: 2178 no. of waters: 64 no. of metals: 0 **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5CM-c 4 C.5CM6,D.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 C.DG1 D.DC12 G-C WC 19-XIX cWW cW-W 2 C.DC2 D.DG11 C-G WC 19-XIX cWW cW-W 3 C.DC3 D.DG10 C-G WC 19-XIX cWW cW-W 4 C.DA4 D.DT9 A-T WC 20-XX cWW cW-W 5 C.DA5 D.DT8 A-T WC 20-XX cWW cW-W 6 C.5CM6 D.DG7 c-G WC 19-XIX cWW cW-W 7 C.DG7 D.5CM6 G-c WC 19-XIX cWW cW-W 8 C.DT8 D.DA5 T-A WC 20-XX cWW cW-W 9 C.DT9 D.DA4 T-A WC 20-XX cWW cW-W 10 C.DG10 D.DC3 G-C WC 19-XIX cWW cW-W 11 C.DG11 D.DC2 G-C WC 19-XIX cWW cW-W 12 C.DC12 D.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.BBBBBBBB 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 18 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6cc8 A-arg C.DA5 A.ARG44 10.88 -153.02 -1.80 10.61 1.63 12.29 68.65 -146.96 2 6cc8 C-arg C.5CM6 A.ARG22 11.73 -122.12 -6.58 8.08 5.39 -5.42 -54.63 -113.91 3 6cc8 C-asp C.5CM6 A.ASP32 10.61 -152.64 -4.41 9.54 -1.48 52.23 15.15 -149.16 4 6cc8 C-arg C.5CM6 A.ARG44 10.34 -172.41 1.63 10.15 -1.09 27.43 57.76 -171.05 5 6cc8 G-arg C.DG7 A.ARG22 -11.74 -160.24 -4.98 10.41 2.18 -28.64 -47.80 -157.62 6 6cc8 C-arg D.5CM6 A.ARG22 11.44 165.53 -4.88 -10.16 -1.97 -24.62 57.81 163.02 7 6cc8 C-arg D.5CM6 A.ARG44 10.11 -154.24 -6.74 6.93 2.96 -53.23 35.54 -149.53 8 6cc8 G-arg D.DG7 A.ARG44 -10.54 175.26 2.18 -10.30 0.56 34.17 -57.68 174.31 9 6cc8 T-arg D.DT8 A.ARG44 -10.97 147.00 -2.22 -10.49 -2.31 15.50 -62.10 140.87 10 6cc8 A-arg E.DA5 B.ARG44 10.92 -155.72 -2.04 10.64 1.42 12.13 70.41 -149.98 11 6cc8 C-arg E.5CM6 B.ARG22 11.72 -123.82 -6.34 8.07 5.66 -7.47 -55.66 -115.49 12 6cc8 C-asp E.5CM6 B.ASP32 10.55 -151.86 -4.04 9.67 -1.23 52.69 11.96 -148.33 13 6cc8 C-arg E.5CM6 B.ARG44 10.27 -175.00 1.58 10.11 -0.97 30.71 58.50 -174.03 14 6cc8 G-arg E.DG7 B.ARG22 -11.76 -159.38 -4.79 10.48 2.35 -31.46 -46.90 -156.55 15 6cc8 C-arg F.5CM6 B.ARG22 11.41 164.05 -4.76 -10.15 -2.13 -27.58 56.94 161.24 16 6cc8 C-arg F.5CM6 B.ARG44 10.08 -152.88 -6.60 7.00 3.00 -53.65 36.58 -147.73 17 6cc8 G-arg F.DG7 B.ARG44 -10.58 177.06 2.00 -10.37 0.61 35.01 -59.32 176.43 18 6cc8 T-arg F.DT8 B.ARG44 -10.82 147.41 -2.69 -10.30 -1.96 15.18 -60.52 141.70 **************************************************************************** List of 12 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6cc8 AT-arg C.DA5 D.DT8 A.ARG44 10.93 -150.01 -2.01 10.56 1.98 13.88 65.37 -143.88 2 6cc8 AT-arg E.DA5 F.DT8 B.ARG44 10.87 -151.57 -2.36 10.47 1.71 13.62 65.46 -145.77 3 6cc8 GC-arg D.DG7 C.5CM6 A.ARG22 -11.66 125.47 -6.24 -8.17 -5.50 -4.67 54.96 117.77 4 6cc8 GC-arg D.DG7 C.5CM6 A.ARG44 -10.44 173.85 1.90 -10.23 0.83 30.79 -57.79 172.69 5 6cc8 GC-arg C.DG7 D.5CM6 A.ARG22 -11.59 -162.87 -4.94 10.28 2.07 -26.66 -52.82 -160.28 6 6cc8 GC-arg C.DG7 D.5CM6 A.ARG44 -10.09 151.25 -6.54 -6.82 -3.53 -49.05 -38.77 146.23 7 6cc8 GC-arg F.DG7 E.5CM6 B.ARG22 -11.66 125.89 -6.02 -8.15 -5.77 -6.83 55.43 118.03 8 6cc8 GC-arg F.DG7 E.5CM6 B.ARG44 -10.43 176.04 1.78 -10.24 0.79 32.85 -58.94 175.24 9 6cc8 GC-arg E.DG7 F.5CM6 B.ARG22 -11.58 -161.69 -4.78 10.31 2.23 -29.57 -51.95 -158.85 10 6cc8 GC-arg E.DG7 F.5CM6 B.ARG44 -10.07 149.62 -6.42 -6.87 -3.59 -49.71 -39.56 144.09 11 6cc8 GC-asp D.DG7 C.5CM6 A.ASP32 -10.63 155.09 -4.08 -9.73 1.27 54.81 -14.14 151.64 12 6cc8 GC-asp F.DG7 E.5CM6 B.ASP32 -10.61 153.66 -3.76 -9.86 1.07 54.37 -11.69 150.15 **************************************************************************** List of 20 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6cc8 OP2@C.DA4 NZ@A.LYS42 2.67 po4:sidechain:salt-bridge 2 6cc8 OP2@C.DA5 NH2@A.ARG3 3.18 po4:sidechain:salt-bridge 3 6cc8 OP1@C.5CM6 N@A.SER24 2.94 po4:backbone 4 6cc8 OP1@C.5CM6 OG@A.SER24 2.72 po4:sidechain 5 6cc8 OP2@C.5CM6 N@A.ARG23 3.43 po4:backbone 6 6cc8 OP1@C.DG7 N@A.LEU26 3.09 po4:backbone 7 6cc8 OP2@C.DG7 N@A.SER27 3.13 po4:backbone 8 6cc8 OP2@C.DG7 OG@A.SER27 2.66 po4:sidechain 9 6cc8 OP2@D.DA4 NE.A@A.ARG65 3.24 po4:sidechain:salt-bridge 10 6cc8 OP2@D.5CM6 OG@A.SER45 2.63 po4:sidechain 11 6cc8 OP2@E.DA4 NZ@B.LYS42 2.65 po4:sidechain:salt-bridge 12 6cc8 OP2@E.DA5 NH2@B.ARG3 2.76 po4:sidechain:salt-bridge 13 6cc8 OP1@E.5CM6 N@B.SER24 2.88 po4:backbone 14 6cc8 OP2@E.5CM6 N@B.ARG23 3.29 po4:backbone 15 6cc8 OP1@E.DG7 N@B.LEU26 3.17 po4:backbone 16 6cc8 OP2@E.DG7 N@B.SER27 3.13 po4:backbone 17 6cc8 OP2@E.DG7 OG@B.SER27 2.68 po4:sidechain 18 6cc8 OP2@F.DA4 NE@B.ARG65 3.14 po4:sidechain:salt-bridge 19 6cc8 OP2@F.DA5 N@B.LYS46 3.93 po4:backbone 20 6cc8 OP2@F.5CM6 OG@B.SER45 2.62 po4:sidechain **************************************************************************** List of 8 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6cc8 N7@C.DG7 NH1@A.ARG22 2.73 base:sidechain 2 6cc8 O6@C.DG7 NH2@A.ARG22 2.85 base:sidechain 3 6cc8 N7@D.DG7 NH2@A.ARG44 2.92 base:sidechain 4 6cc8 O6@D.DG7 NH1@A.ARG44 2.72 base:sidechain 5 6cc8 N7@E.DG7 NH1@B.ARG22 2.74 base:sidechain 6 6cc8 O6@E.DG7 NH2@B.ARG22 2.84 base:sidechain 7 6cc8 N7@F.DG7 NH2@B.ARG44 3.05 base:sidechain 8 6cc8 O6@F.DG7 NH1@B.ARG44 2.73 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6cc8 G-arg C.DG7 A.ARG22 0.29 17 2 6cc8 G-arg D.DG7 A.ARG44 0.06 11 3 6cc8 G-arg E.DG7 B.ARG22 0.39 20 4 6cc8 G-arg F.DG7 B.ARG44 0.02 14 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6cc8 C-arg C.5CM6 A.ARG22 3.59 14 2 6cc8 C-arg D.5CM6 A.ARG44 3.48 3 3 6cc8 C-arg E.5CM6 B.ARG22 3.63 15 4 6cc8 C-arg F.5CM6 B.ARG44 3.42 7 **************************************************************************** List of 3 additional files 1 -- 6cc8-baseAA-pairs.pdb 2 -- 6cc8-baseAA-stacks.pdb 3 -- 6cc8-pairs.pdb