**************************************************************************** File name: 4nig.pdb no. of peptide chains: 1 [A=202] no. of DNA/RNA chains: 2 [B=12,C=13] no. of amino acids: 202 no. of nucleotides: 25 no. of atoms: 2432 no. of waters: 334 no. of metals: 1 [Mn=1] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 2YR-c 1 B.2YR10 2 6MA-a 1 B.6MA8 **************************************************************************** List of 2 helices 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=5 strand-1 5'-AGGTA-3' bp-type ||||| strand-2 3'-TCCAT-5' helix-form BBBB 1 B.DA2 C.DT13 A-T WC 20-XX cWW cW-W 2 B.DG3 C.DC12 G-C WC 19-XIX cWW cW-W 3 B.DG4 C.DC11 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA10 T-A WC 20-XX cWW cW-W 5 B.DA6 C.DT9 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=5 strand-1 5'-AcCGT-3' bp-type ||||| strand-2 3'-TGGCA-5' helix-form .BBB 1 B.DA9 C.DT6 A-T WC 20-XX cWW cW-W 2 B.2YR10 C.DG5 c-G WC 19-XIX cWW cW-W 3 B.DC11 C.DG4 C-G WC 19-XIX cWW cW-W 4 B.DG12 C.DC3 G-C WC 19-XIX cWW cW-W 5 B.DT13 C.DA2 T-A WC 20-XX cWW cW-W **************************************************************************** List of 17 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4nig A-met B.6MA8 A.MET61 10.52 26.69 -9.45 0.34 4.62 4.26 6.69 25.50 2 4nig A-trp B.6MA8 A.TRP69 6.54 161.51 -2.91 -3.92 4.34 -75.82 1.99 156.49 3 4nig A-tyr B.6MA8 A.TYR76 8.35 -85.41 6.80 2.78 3.97 -23.61 -80.28 -18.91 4 4nig A-tyr B.6MA8 A.TYR78 9.25 -64.64 1.30 -2.24 8.87 -3.19 50.54 -41.58 5 4nig A-leu B.6MA8 A.LEU118 7.88 -126.77 3.37 -7.05 1.07 -24.59 10.03 -125.18 6 4nig A-leu B.6MA8 A.LEU128 -9.82 106.70 -0.31 9.49 -2.48 -13.52 -13.57 105.50 7 4nig A-his B.6MA8 A.HIS131 -7.80 93.54 4.85 6.07 -0.67 -58.25 41.22 65.04 8 4nig A-gln B.6MA8 A.GLN132 -7.20 20.40 4.40 2.48 -5.13 6.96 7.22 17.78 9 4nig A-asp B.6MA8 A.ASP133 -5.02 81.99 1.73 0.09 -4.71 -46.20 -44.78 53.83 10 4nig A-lys B.6MA8 A.LYS134 -7.20 72.11 5.59 -3.75 -2.56 2.92 -20.59 69.43 11 4nig A-arg B.6MA8 A.ARG210 -9.51 91.38 -4.38 -8.41 0.79 23.73 -10.56 88.41 12 4nig A-cys B.DA9 A.CYS129 8.28 28.04 6.45 4.93 1.64 1.64 -6.07 27.34 13 4nig A-arg B.DA9 A.ARG161 -10.01 -178.49 3.93 9.17 -0.79 1.10 63.57 -178.23 14 4nig C-cys B.2YR10 A.CYS129 -9.14 15.51 7.92 4.28 -1.61 -12.84 -7.59 4.25 15 4nig G-arg C.DG4 A.ARG161 11.86 71.56 4.72 9.81 4.72 36.34 38.18 50.25 16 4nig G-arg C.DG5 A.ARG161 11.28 54.27 8.68 6.73 2.58 47.24 18.76 19.70 17 4nig T-arg C.DT6 A.ARG161 10.11 -36.77 9.35 3.84 -0.29 35.95 3.93 -6.77 **************************************************************************** List of 5 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4nig AT-cys B.DA9 C.DT6 A.CYS129 8.28 32.09 6.41 5.18 0.82 -12.26 -5.19 29.27 2 4nig AT-arg B.DA9 C.DT6 A.ARG161 -10.06 -176.06 3.91 9.27 -0.25 2.42 49.75 -175.65 3 4nig GC-arg C.DG4 B.DC11 A.ARG161 11.84 71.11 4.26 9.88 4.95 35.63 33.79 53.12 4 4nig GC-cys C.DG5 B.2YR10 A.CYS129 9.22 176.80 -4.16 -8.06 1.67 7.44 13.89 176.77 5 4nig GC-arg C.DG5 B.2YR10 A.ARG161 11.18 54.78 8.62 6.61 2.63 48.37 18.18 18.84 **************************************************************************** List of 9 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4nig OP1@B.DA6 N@A.TYR76 3.00 po4:backbone 2 4nig OP2@B.DA7 N@A.GLY53 2.84 po4:backbone 3 4nig OP1@B.6MA8 OH@A.TYR76 2.70 po4:sidechain 4 4nig OP2@B.6MA8 O@A.LEU130 3.37 po4:backbone 5 4nig OP2@B.DA9 N@A.CYS129 2.79 po4:backbone 6 4nig OP2@B.2YR10 NZ@A.LYS127 3.03 po4:sidechain:salt-bridge 7 4nig OP2@C.DC3 NH1@A.ARG167 2.68 po4:sidechain:salt-bridge 8 4nig OP2@C.DC3 NH2@A.ARG167 3.10 po4:sidechain:salt-bridge 9 4nig OP2@C.DG5 ND2@A.ASN162 3.37 po4:sidechain **************************************************************************** List of 4 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4nig N6@B.6MA8 O@A.GLN132 3.92 base:backbone 2 4nig N7@C.DG5 NH1@A.ARG161 2.85 base:sidechain 3 4nig O6@C.DG5 NH2@A.ARG161 2.86 base:sidechain 4 4nig O4@C.DT6 NH1@A.ARG161 3.20 base:sidechain **************************************************************************** List of 1 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4nig G-arg C.DG5 A.ARG161 0.51 18 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4nig A-trp B.6MA8 A.TRP69 3.62 16 2 4nig A-his B.6MA8 A.HIS131 3.69 18 3 4nig A-asp B.6MA8 A.ASP133 3.93 25 4 4nig G-arg C.DG4 A.ARG161 3.63 11 **************************************************************************** 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 WAH A.TRP69,B.6MA8,A.HIS131 **************************************************************************** List of 3 additional files 1 -- 4nig-baseAA-pairs.pdb 2 -- 4nig-baseAA-stacks.pdb 3 -- 4nig-pairs.pdb