**************************************************************************** File name: 4e68.pdb1 no. of peptide chains: 2 [1.A=559,2.A=559] no. of DNA/RNA chains: 2 [1.B=18,2.B=18] no. of amino acids: 1118 no. of nucleotides: 36 no. of atoms: 9996 no. of waters: 278 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=17 strand-1 5'-GCATTTCCCGTAAATCT-3' bp-type ..||||.|.|.||||.. strand-2 3'-TCTAAATGCCCTTTACG-5' helix-form .BBBBB....BBBBB. 1 1:B.DG1002 2:B.DT1018 G-T -- -- cWW cW-W 2 1:B.DC1003 2:B.DC1017 C-C -- -- cWW cW-W 3 1:B.DA1004 2:B.DT1016 A-T WC 20-XX cWW cW-W 4 1:B.DT1005 2:B.DA1015 T-A WC 20-XX cWW cW-W 5 1:B.DT1006 2:B.DA1014 T-A WC 20-XX cWW cW-W 6 1:B.DT1007 2:B.DA1013 T-A WC 20-XX cWW cW-W 7 1:B.DC1008 2:B.DT1012 C-T -- -- cWW cW-W 8 1:B.DC1009 2:B.DG1011 C-G WC 19-XIX cWW cW-W 9 1:B.DC1010 2:B.DC1010 C-C -- -- cWW cW-W 10 1:B.DG1011 2:B.DC1009 G-C WC 19-XIX cWW cW-W 11 1:B.DT1012 2:B.DC1008 T-C -- -- cWW cW-W 12 1:B.DA1013 2:B.DT1007 A-T WC 20-XX cWW cW-W 13 1:B.DA1014 2:B.DT1006 A-T WC 20-XX cWW cW-W 14 1:B.DA1015 2:B.DT1005 A-T WC 20-XX cWW cW-W 15 1:B.DT1016 2:B.DA1004 T-A WC 20-XX cWW cW-W 16 1:B.DC1017 2:B.DC1003 C-C -- -- cWW cW-W 17 1:B.DT1018 2:B.DG1002 T-G -- -- cWW cW-W **************************************************************************** List of 24 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4e68 T-ser 1:B.DT1006 1:A.SER465 9.97 -83.88 2.37 5.98 7.62 -61.30 -55.15 -17.03 2 4e68 T-asn 1:B.DT1006 1:A.ASN466 8.71 91.66 8.02 3.05 1.47 -20.19 -64.60 65.95 3 4e68 T-gln 1:B.DT1006 1:A.GLN469 11.78 150.05 8.94 -5.99 4.80 -8.34 33.00 148.64 4 4e68 T-ser 1:B.DT1007 1:A.SER465 -9.86 -93.91 3.46 7.72 5.06 -78.87 -29.69 -46.01 5 4e68 T-asn 1:B.DT1007 1:A.ASN466 7.90 69.42 7.44 2.06 -1.69 -37.98 -48.73 33.35 6 4e68 C-asn 1:B.DC1008 1:A.ASN466 -8.32 -64.98 7.17 2.09 -3.67 -48.28 -43.33 -3.95 7 4e68 C-lys 1:B.DC1010 2:A.LYS340 14.24 47.56 9.90 9.83 2.82 -32.34 -15.97 31.53 8 4e68 G-lys 1:B.DG1011 2:A.LYS340 -12.08 -45.94 10.43 6.09 0.31 -42.63 -11.74 -12.82 9 4e68 G-asn 1:B.DG1011 2:A.ASN466 8.22 -145.04 0.41 5.96 5.65 -34.12 -67.45 -135.32 10 4e68 G-ile 1:B.DG1011 2:A.ILE467 9.06 179.23 7.68 -4.79 -0.25 -51.40 16.82 179.13 11 4e68 T-asn 1:B.DT1012 2:A.ASN466 8.69 -166.38 0.21 7.79 3.84 -45.42 -65.38 -162.24 12 4e68 A-asn 1:B.DA1013 2:A.ASN466 -7.40 155.86 -1.73 -7.17 0.60 62.10 45.15 149.05 13 4e68 T-ser 2:B.DT1006 2:A.SER465 9.97 -83.88 2.37 5.98 7.62 -61.30 -55.15 -17.03 14 4e68 T-asn 2:B.DT1006 2:A.ASN466 8.71 91.66 8.02 3.05 1.47 -20.19 -64.60 65.95 15 4e68 T-gln 2:B.DT1006 2:A.GLN469 11.78 150.05 8.94 -5.99 4.80 -8.34 33.00 148.64 16 4e68 T-ser 2:B.DT1007 2:A.SER465 -9.86 -93.91 3.46 7.72 5.06 -78.87 -29.69 -46.01 17 4e68 T-asn 2:B.DT1007 2:A.ASN466 7.90 69.42 7.44 2.06 -1.69 -37.98 -48.73 33.35 18 4e68 C-asn 2:B.DC1008 2:A.ASN466 -8.32 -64.98 7.17 2.09 -3.67 -48.28 -43.33 -3.95 19 4e68 C-lys 2:B.DC1010 1:A.LYS340 14.24 47.56 9.90 9.83 2.82 -32.34 -15.97 31.53 20 4e68 G-lys 2:B.DG1011 1:A.LYS340 -12.08 -45.94 10.43 6.09 0.31 -42.63 -11.74 -12.82 21 4e68 G-asn 2:B.DG1011 1:A.ASN466 8.22 -145.04 0.41 5.96 5.65 -34.12 -67.45 -135.32 22 4e68 G-ile 2:B.DG1011 1:A.ILE467 9.06 179.23 7.68 -4.79 -0.25 -51.40 16.82 179.13 23 4e68 T-asn 2:B.DT1012 1:A.ASN466 8.69 -166.38 0.21 7.79 3.84 -45.42 -65.38 -162.24 24 4e68 A-asn 2:B.DA1013 1:A.ASN466 -7.40 155.86 -1.73 -7.17 0.60 62.10 45.15 149.05 **************************************************************************** List of 20 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4e68 CT-asn 1:B.DC1008 2:B.DT1012 1:A.ASN466 -8.50 -72.94 7.51 1.18 -3.78 -56.66 -44.82 -10.85 2 4e68 CC-lys 1:B.DC1010 2:B.DC1010 1:A.LYS340 -13.95 157.12 -9.04 -10.10 -3.31 22.12 34.87 155.53 3 4e68 CC-lys 1:B.DC1010 2:B.DC1010 2:A.LYS340 13.95 47.72 10.10 9.04 3.31 -34.87 -22.12 24.47 4 4e68 GC-lys 1:B.DG1011 2:B.DC1009 2:A.LYS340 -11.93 -47.01 10.33 5.96 0.18 -43.53 -12.25 -13.21 5 4e68 GC-asn 1:B.DG1011 2:B.DC1009 2:A.ASN466 8.02 -145.79 0.38 5.82 5.50 -34.22 -68.40 -136.01 6 4e68 GC-ile 1:B.DG1011 2:B.DC1009 2:A.ILE467 8.88 179.35 7.55 -4.65 -0.36 -51.90 17.81 179.26 7 4e68 TC-asn 1:B.DT1012 2:B.DC1008 2:A.ASN466 8.50 -171.24 1.18 7.51 3.78 -44.82 -56.66 -169.15 8 4e68 AT-ser 1:B.DA1013 2:B.DT1007 2:A.SER465 -9.62 -141.60 7.27 3.06 -5.50 -35.60 -77.50 -126.88 9 4e68 AT-asn 1:B.DA1013 2:B.DT1007 2:A.ASN466 -7.65 153.63 -1.89 -7.32 1.14 55.42 41.57 147.80 10 4e68 AT-ser 1:B.DA1014 2:B.DT1006 2:A.SER465 -9.93 -164.65 5.75 2.03 -7.84 -60.24 -61.59 -158.93 11 4e68 AT-asn 1:B.DA1014 2:B.DT1006 2:A.ASN466 -8.69 127.05 -3.07 -7.94 -1.74 69.08 23.64 112.63 12 4e68 AT-gln 1:B.DA1014 2:B.DT1006 2:A.GLN469 -11.74 47.83 5.82 -8.75 -5.24 -32.10 13.81 33.18 13 4e68 GC-lys 2:B.DG1011 1:B.DC1009 1:A.LYS340 -11.93 -47.01 10.33 5.96 0.18 -43.53 -12.25 -13.21 14 4e68 GC-asn 2:B.DG1011 1:B.DC1009 1:A.ASN466 8.02 -145.79 0.38 5.82 5.50 -34.22 -68.40 -136.01 15 4e68 GC-ile 2:B.DG1011 1:B.DC1009 1:A.ILE467 8.88 179.35 7.55 -4.65 -0.36 -51.90 17.81 179.26 16 4e68 AT-ser 2:B.DA1013 1:B.DT1007 1:A.SER465 -9.62 -141.60 7.27 3.06 -5.50 -35.60 -77.50 -126.88 17 4e68 AT-asn 2:B.DA1013 1:B.DT1007 1:A.ASN466 -7.65 153.63 -1.89 -7.32 1.14 55.42 41.57 147.80 18 4e68 AT-ser 2:B.DA1014 1:B.DT1006 1:A.SER465 -9.93 -164.65 5.75 2.03 -7.84 -60.24 -61.59 -158.93 19 4e68 AT-asn 2:B.DA1014 1:B.DT1006 1:A.ASN466 -8.69 127.05 -3.07 -7.94 -1.74 69.08 23.64 112.63 20 4e68 AT-gln 2:B.DA1014 1:B.DT1006 1:A.GLN469 -11.74 47.83 5.82 -8.75 -5.24 -32.10 13.81 33.18 **************************************************************************** List of 22 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4e68 OP1@1:B.DT1005 N@1:A.VAL432 2.83 po4:backbone 2 4e68 OP1@1:B.DT1006 NH1@1:A.ARG382 2.79 po4:sidechain:salt-bridge 3 4e68 OP2@1:B.DT1006 OG@1:A.SER465 2.64 po4:sidechain 4 4e68 OP2@1:B.DT1006 NE2@1:A.GLN469 2.84 po4:sidechain 5 4e68 O5'@1:B.DT1006 OG@1:A.SER465 3.02 po4:sidechain 6 4e68 OP1@1:B.DC1008 NE2@2:A.GLN344 2.96 po4:sidechain 7 4e68 OP2@1:B.DC1009 N@2:A.GLN344 2.95 po4:backbone 8 4e68 OP1@1:B.DC1010 NE2@2:A.HIS332 2.66 po4:sidechain:salt-bridge 9 4e68 OP2@1:B.DC1010 NZ@2:A.LYS340 2.79 po4:sidechain:salt-bridge 10 4e68 OP1@1:B.DG1011 NZ@2:A.LYS574 2.83 po4:sidechain:salt-bridge 11 4e68 O5'@1:B.DT1018 NE@2:A.ARG423 3.30 po4:sidechain 12 4e68 OP1@2:B.DT1005 N@2:A.VAL432 2.83 po4:backbone 13 4e68 OP1@2:B.DT1006 NH1@2:A.ARG382 2.79 po4:sidechain:salt-bridge 14 4e68 OP2@2:B.DT1006 OG@2:A.SER465 2.64 po4:sidechain 15 4e68 OP2@2:B.DT1006 NE2@2:A.GLN469 2.84 po4:sidechain 16 4e68 O5'@2:B.DT1006 OG@2:A.SER465 3.02 po4:sidechain 17 4e68 OP1@2:B.DC1008 NE2@1:A.GLN344 2.96 po4:sidechain 18 4e68 OP2@2:B.DC1009 N@1:A.GLN344 2.95 po4:backbone 19 4e68 OP1@2:B.DC1010 NE2@1:A.HIS332 2.66 po4:sidechain:salt-bridge 20 4e68 OP2@2:B.DC1010 NZ@1:A.LYS340 2.79 po4:sidechain:salt-bridge 21 4e68 OP1@2:B.DG1011 NZ@1:A.LYS574 2.83 po4:sidechain:salt-bridge 22 4e68 O5'@2:B.DT1018 NE@1:A.ARG423 3.30 po4:sidechain **************************************************************************** List of 4 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4e68 O4@1:B.DT1007 ND2@1:A.ASN466 2.75 base:sidechain 2 4e68 O4@1:B.DT1012 ND2@2:A.ASN466 3.10 base:sidechain 3 4e68 O4@2:B.DT1007 ND2@2:A.ASN466 2.75 base:sidechain 4 4e68 O4@2:B.DT1012 ND2@1:A.ASN466 3.10 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4e68 T-asn 1:B.DT1007 1:A.ASN466 0.95 30 2 4e68 T-asn 1:B.DT1012 2:A.ASN466 0.17 26 3 4e68 T-asn 2:B.DT1007 2:A.ASN466 0.95 30 4 4e68 T-asn 2:B.DT1012 1:A.ASN466 0.17 26 **************************************************************************** List of 2 additional files 1 -- 4e68-baseAA-pairs.pdb 2 -- 4e68-pairs.pdb