**************************************************************************** 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/7cy8.pdb -o=7cy8.out --type=base File name: 7cy8.pdb no. of peptide chains: 1 [A=858] no. of DNA/RNA chains: 2 [C=9,D=8] no. of amino acids: 858 no. of nucleotides: 17 no. of atoms: 6940 no. of waters: 198 no. of metals: 1 [Fe=1] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 C.5CM3,D.5CM3 **************************************************************************** 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=7 strand-1 5'-cGCGCGG-3' bp-type ||||||| strand-2 3'-GCGCGCC-5' helix-form .BBBx. 1 C.5CM3 D.DG8 c-G WC 19-XIX cWW cW-W 2 C.DG4 D.DC7 G-C WC 19-XIX cWW cW-W 3 C.DC5 D.DG6 C-G WC 19-XIX cWW cW-W 4 C.DG6 D.DC5 G-C WC 19-XIX cWW cW-W 5 C.DC7 D.DG4 C-G WC 19-XIX cWW cW-W 6 C.DG9 D.DC2 G-C WC 19-XIX cWW cW-W 7 C.DG10 D.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 12 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7cy8 G-asn C.DG8 A.ASN261 9.28 -80.87 -9.19 -1.26 -0.23 -12.87 34.93 -73.14 2 7cy8 G-asn C.DG9 A.ASN261 -6.54 -71.19 -5.24 1.00 -3.79 -7.04 12.74 -69.88 3 7cy8 A-lys C.DA11 A.LYS472 -12.40 -138.70 -2.50 11.97 -2.03 -50.37 23.35 -133.03 4 7cy8 C-arg D.5CM3 A.ARG244 10.17 -42.67 -5.35 6.79 5.35 -23.86 35.10 -4.48 5 7cy8 C-met D.5CM3 A.MET253 -10.74 -148.88 -7.43 2.93 -7.19 -38.82 30.73 -145.64 6 7cy8 C-ser D.5CM3 A.SER335 -9.54 -152.62 -6.89 6.60 0.40 -89.81 -0.34 -140.97 7 7cy8 C-asp D.5CM3 A.ASP347 6.08 109.16 0.32 -5.80 1.80 -69.88 24.46 86.92 8 7cy8 C-asp D.5CM3 A.ASP350 -4.78 93.12 -0.62 -4.48 1.54 66.53 27.17 63.76 9 7cy8 C-ser D.5CM3 A.SER414 -9.43 -156.39 -3.70 8.66 0.46 -58.08 7.83 -152.87 10 7cy8 C-phe D.5CM3 A.PHE416 -7.09 172.65 0.56 -6.94 -1.33 73.96 4.23 170.79 11 7cy8 C-arg D.5CM3 A.ARG418 -5.36 128.55 -1.87 -1.49 -4.79 21.38 26.13 126.05 12 7cy8 G-asn D.DG4 A.ASN261 -8.23 33.37 -6.55 4.05 -2.90 -23.78 -17.92 15.24 **************************************************************************** List of 2 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7cy8 GC-asn D.DG4 C.DC7 A.ASN261 -8.43 36.36 -6.61 4.01 -3.35 -23.97 -22.86 15.21 2 7cy8 GC-asn C.DG9 D.DC2 A.ASN261 -6.87 -70.96 -4.92 0.96 -4.69 -6.47 1.05 -70.69 **************************************************************************** List of 11 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 7cy8 OP1@C.DG9 OG@A.SER465 3.18 po4:sidechain 2 7cy8 OP1@C.DG10 NH2@A.ARG471 2.88 po4:sidechain:salt-bridge 3 7cy8 OP2@C.DG10 NZ@A.LYS472 3.66 po4:sidechain:salt-bridge 4 7cy8 OP2@D.5CM3 N@A.PHE245 2.88 po4:backbone 5 7cy8 OP2@D.DG4 OH@A.TYR270 2.58 po4:sidechain 6 7cy8 OP2@D.DG4 NH1@A.ARG418 2.80 po4:sidechain:salt-bridge 7 7cy8 OP2@D.DG4 NH2@A.ARG418 3.10 po4:sidechain:salt-bridge 8 7cy8 OP1@D.DC5 N@A.ALA271 2.88 po4:backbone 9 7cy8 OP1@D.DG6 NZ@A.LYS264 2.88 po4:sidechain:salt-bridge 10 7cy8 OP1@D.DG6 NE@A.ARG275 3.98 po4:sidechain:salt-bridge 11 7cy8 OP2@D.DG6 NH2@A.ARG275 2.57 po4:sidechain:salt-bridge **************************************************************************** List of 2 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 7cy8 O2@D.5CM3 NH1@A.ARG418 2.98 base:sidechain 2 7cy8 N4@D.5CM3 OD2@A.ASP350 2.76 base:sidechain **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 7cy8 C-asp D.5CM3 A.ASP350 0.32 41 2 7cy8 C-arg D.5CM3 A.ARG418 0.77 58 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 7cy8 G-asn C.DG9 A.ASN261 3.42 18 2 7cy8 C-arg D.5CM3 A.ARG244 3.42 4 3 7cy8 C-phe D.5CM3 A.PHE416 3.13 17 4 7cy8 G-asn D.DG4 A.ASN261 2.93 27 **************************************************************************** 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 RCF A.ARG244,D.5CM3,A.PHE416 **************************************************************************** List of 3 additional files 1 -- 7cy8-baseAA-pairs.pdb 2 -- 7cy8-baseAA-stacks.pdb 3 -- 7cy8-pairs.pdb