**************************************************************************** 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/6a5n.pdb -o=6a5n.out --type=base File name: 6a5n.pdb no. of peptide chains: 1 [A=502] no. of DNA/RNA chains: 2 [C=13,D=13] no. of amino acids: 502 no. of nucleotides: 26 no. of atoms: 4515 no. of waters: 40 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 5CM-c 1 C.5CM8 **************************************************************************** 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'-AGTACTAGCAGT-3' bp-type |||||||||||| strand-2 3'-TCATGATCGTCA-5' helix-form .BB.BxBBBB. 1 C.DA2 D.DT14 A-T WC 20-XX cWW cW-W 2 C.DG3 D.DC13 G-C WC 19-XIX cWW cW-W 3 C.DT4 D.DA12 T-A WC 20-XX cWW cW-W 4 C.DA5 D.DT11 A-T WC 20-XX cWW cW-W 5 C.DC6 D.DG10 C-G WC 19-XIX cWW cW-W 6 C.DT7 D.DA9 T-A WC 20-XX cWW cW-W 7 C.DA9 D.DT7 A-T WC 20-XX cWW cW-W 8 C.DG10 D.DC6 G-C WC 19-XIX cWW cW-W 9 C.DC11 D.DG5 C-G WC 19-XIX cWW cW-W 10 C.DA12 D.DT4 A-T WC 20-XX cWW cW-W 11 C.DG13 D.DC3 G-C WC 19-XIX cWW cW-W 12 C.DT14 D.DA2 T-A WC 20-XX cWW cW-W **************************************************************************** List of 20 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6a5n T-gln C.DT7 A.GLN357 7.48 24.16 -6.07 3.84 2.08 22.34 5.24 7.60 2 6a5n C-gly C.5CM8 A.GLY359 7.99 -87.54 -4.47 5.52 3.66 -45.68 66.23 -37.88 3 6a5n C-val C.5CM8 A.VAL375 7.22 131.81 3.30 2.51 5.90 -17.34 -8.16 131.08 4 6a5n C-ala C.5CM8 A.ALA376 4.13 -86.14 -0.73 1.76 3.67 55.08 -46.87 -50.39 5 6a5n C-ser C.5CM8 A.SER377 5.63 110.74 -1.80 4.77 2.39 -18.83 -7.68 109.47 6 6a5n C-gly C.5CM8 A.GLY378 -4.76 -154.01 0.58 -4.25 -2.06 -13.02 61.22 -149.49 7 6a5n C-gly C.5CM8 A.GLY379 -5.53 122.48 1.15 0.95 -5.32 74.56 41.10 98.42 8 6a5n C-tyr C.5CM8 A.TYR380 -4.52 53.73 -0.32 -0.94 -4.41 42.80 -13.74 30.23 9 6a5n C-asp C.5CM8 A.ASP382 -3.70 118.88 -1.46 -3.38 0.42 0.43 -87.80 90.25 10 6a5n C-tyr C.5CM8 A.TYR392 5.47 93.33 4.24 -3.38 -0.74 -6.31 -76.87 57.27 11 6a5n C-thr C.5CM8 A.THR393 -5.62 159.80 2.59 -4.42 -2.31 -51.86 52.75 154.63 12 6a5n C-gly C.5CM8 A.GLY394 -8.15 21.88 7.48 3.20 -0.40 13.12 13.33 11.41 13 6a5n C-gln C.5CM8 A.GLN395 -9.17 121.49 4.75 1.05 -7.78 -6.97 -86.72 95.30 14 6a5n A-arg C.DA9 A.ARG306 11.83 -72.50 -11.78 0.82 -0.77 -25.67 67.76 -2.62 15 6a5n A-gln C.DA9 A.GLN357 -8.25 -62.11 -6.02 2.69 -4.95 9.37 -17.32 -59.21 16 6a5n G-arg C.DG10 A.ARG306 -11.51 -59.81 -9.60 3.17 -5.50 -8.82 53.28 -26.73 17 6a5n A-thr C.DA12 A.THR444 8.20 -163.01 -1.70 7.87 1.52 6.37 3.48 -162.97 18 6a5n G-gln D.DG8 A.GLN357 9.39 -46.25 -9.18 -0.44 1.94 40.14 19.94 -11.73 19 6a5n A-ser D.DA9 A.SER356 -7.20 87.36 -5.67 3.83 2.27 -75.07 -16.96 45.02 20 6a5n A-gln D.DA9 A.GLN357 -6.73 -37.41 -5.68 -3.10 -1.87 35.76 1.59 -11.06 **************************************************************************** List of 6 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6a5n AT-arg C.DA9 D.DT7 A.ARG306 11.40 -58.51 -11.20 0.88 -1.90 -20.01 54.88 -3.42 2 6a5n AT-gln D.DA9 C.DT7 A.GLN357 -7.11 -30.52 -5.88 -3.46 -1.99 29.04 -1.81 -9.31 3 6a5n AT-gln C.DA9 D.DT7 A.GLN357 -8.13 -68.75 -5.19 3.36 -5.28 19.91 -26.49 -61.11 4 6a5n AT-ser D.DA9 C.DT7 A.SER356 -7.51 94.47 -6.05 4.00 1.95 -82.57 -17.77 47.02 5 6a5n AT-thr C.DA12 D.DT4 A.THR444 8.57 -165.20 -1.40 8.09 2.47 15.90 8.67 -165.01 6 6a5n GC-arg C.DG10 D.DC6 A.ARG306 -11.64 -57.62 -9.76 3.22 -5.47 -5.11 52.15 -24.87 **************************************************************************** List of 20 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6a5n OP1@C.5CM8 N@A.GLY359 2.74 po4:backbone 2 6a5n OP2@C.5CM8 OH@A.TYR380 2.84 po4:sidechain 3 6a5n OP1@C.DA9 NH1@A.ARG344 3.17 po4:sidechain:salt-bridge 4 6a5n OP1@C.DA9 OG@A.SER377 2.32 po4:sidechain 5 6a5n OP1@C.DA9 OH@A.TYR453 3.62 po4:sidechain 6 6a5n OP2@C.DA9 NZ@A.LYS442 2.41 po4:sidechain:salt-bridge 7 6a5n O5'@C.DA9 NH1@A.ARG344 2.93 po4:sidechain 8 6a5n OP1@C.DG10 N@A.ARG344 2.84 po4:backbone 9 6a5n OP2@C.DG10 OH@A.TYR453 2.45 po4:sidechain 10 6a5n OP1@C.DC11 OH@A.TYR343 3.54 po4:sidechain 11 6a5n OP2@C.DC11 NZ@A.LYS449 2.48 po4:sidechain:salt-bridge 12 6a5n OP1@C.DA12 N@A.GLY302 2.71 po4:backbone 13 6a5n OP1@C.DA12 N@A.GLY304 2.76 po4:backbone 14 6a5n OP1@C.DA12 N@A.LEU305 3.55 po4:backbone 15 6a5n OP1@D.DG10 OG@A.SER312 3.44 po4:sidechain 16 6a5n OP1@D.DG10 NZ@A.LYS316 3.09 po4:sidechain:salt-bridge 17 6a5n OP1@D.DT11 ND2@A.ASN348 3.56 po4:sidechain 18 6a5n O3'@D.DG10 ND2@A.ASN348 3.60 po4:sidechain 19 6a5n OP1@D.DC13 NZ@A.LYS369 2.80 po4:sidechain:salt-bridge 20 6a5n O3'@D.DA12 OH@A.TYR362 3.60 po4:sidechain **************************************************************************** List of 9 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6a5n O2@C.5CM8 N@A.SER377 2.70 base:backbone 2 6a5n O2@C.5CM8 N@A.GLY378 3.24 base:backbone 3 6a5n O2@C.5CM8 N@A.GLY379 3.16 base:backbone 4 6a5n N4@C.5CM8 OD1@A.ASP382 2.81 base:sidechain 5 6a5n N4@C.5CM8 OD2@A.ASP382 3.14 base:sidechain 6 6a5n N4@C.5CM8 O@A.THR393 2.84 base:backbone 7 6a5n N3@C.DA9 NH1@A.ARG306 3.64 base:sidechain 8 6a5n N2@D.DG8 OE1@A.GLN357 2.41 base:sidechain 9 6a5n N3@D.DA9 OG@A.SER356 2.57 base:sidechain **************************************************************************** List of 3 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6a5n C-asp C.5CM8 A.ASP382 0.41 10 2 6a5n A-arg C.DA9 A.ARG306 0.17 64 3 6a5n G-gln D.DG8 A.GLN357 0.12 36 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6a5n T-gln C.DT7 A.GLN357 4.21 8 2 6a5n C-tyr C.5CM8 A.TYR380 3.04 44 3 6a5n C-tyr C.5CM8 A.TYR392 3.19 5 4 6a5n A-gln C.DA9 A.GLN357 3.66 23 **************************************************************************** List of 1 interface stacks with 3+ planar moieties Note: an interface stack is an ordered list of three and more nucleobases and planar moieties of amino acids, assembled together via stacking interactions (nucleobases within to a stem are excluded by default). 1 size=3 TQA C.DT7,A.GLN357,C.DA9 **************************************************************************** List of 3 additional files 1 -- 6a5n-baseAA-pairs.pdb 2 -- 6a5n-baseAA-stacks.pdb 3 -- 6a5n-pairs.pdb