**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=5i2v.pdb -o=5i2v.out File name: 5i2v.pdb no. of DNA/RNA chains: 1 [A=22] no. of nucleotides: 22 no. of atoms: 714 no. of waters: 0 no. of metals: 2 [K=2] **************************************************************************** List of 13 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG2 A.DG6 G+G -- 06-VI cWH cW+M 2 A.DG2 A.DG18 G+G -- 06-VI cHW cM+W 3 A.DG3 A.DG7 G+G -- 06-VI cWH cW+M 4 A.DG3 A.DG19 G+G -- 06-VI cHW cM+W 5 A.DG4 A.DG9 G+G -- 06-VI cWH cW+M 6 A.DG4 A.DG20 G+G -- 06-VI cHW cM+W 7 A.DG6 A.DG11 G+G -- 06-VI cWH cW+M 8 A.DG7 A.DG12 G+G -- 06-VI cWH cW+M 9 A.DG9 A.DG13 G+G -- 06-VI cWH cW+M 10 A.DG11 A.DG18 G+G -- 06-VI cWH cW+M 11 A.DG12 A.DG19 G+G -- 06-VI cWH cW+M 12 A.DG13 A.DG20 G+G -- 06-VI cWH cW+M 13 A.DG20 A.DA21 G+A Platform -- cSH cm+M **************************************************************************** List of 3 multiplets 1 nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 2 nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3 nts=5 GGGGA A.DG4,A.DG9,A.DG13,A.DG20,A.DA21 **************************************************************************** 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=3 strand-1 5'-GGG-3' bp-type ... strand-2 5'-GGG-3' helix-form .x 1 A.DG2 A.DG6 G+G -- 06-VI cWH cW+M 2 A.DG3 A.DG7 G+G -- 06-VI cWH cW+M 3 A.DG4 A.DG9 G+G -- 06-VI cWH cW+M -------------------------------------------------------------------------- helix#2[0] bps=3 parallel strand-1 5'-GGG-3' bp-type ... strand-2 5'-GGG-3' helix-form .. 1 A.DG11 A.DG18 G+G -- 06-VI cWH cW+M 2 A.DG12 A.DG19 G+G -- 06-VI cWH cW+M 3 A.DG13 A.DG20 G+G -- 06-VI cWH cW+M **************************************************************************** List of 4 base stacks Note: a stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=3 GGG A.DG6,A.DG7,A.DG9 2 nts=3 GGG A.DG11,A.DG12,A.DG13 3 nts=3 GGG A.DG18,A.DG19,A.DG20 4 nts=4 AGGG A.DA1,A.DG2,A.DG3,A.DG4 **************************************************************************** Nucleotides not involved in stacking interactions nts=9 CTTAATAAA A.DC5,A.DT8,A.DT10,A.DA14,A.DA15,A.DT16,A.DA17,A.DA21,A.DA22 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=22 AGGGCGGTGTGGGAATAGGGAA A.DA1,A.DG2,A.DG3,A.DG4,A.DC5,A.DG6,A.DG7,A.DT8,A.DG9,A.DT10,A.DG11,A.DG12,A.DG13,A.DA14,A.DA15,A.DT16,A.DA17,A.DG18,A.DG19,A.DG20,A.DA21,A.DA22 **************************************************************************** List of 3 G-tetrads 1 glyco-bond=---- sugar=---. groove=---- planarity=0.172 type=other nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG18 2 glyco-bond=---- sugar=-3-- groove=---- planarity=0.253 type=other nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG19 3 glyco-bond=---- sugar=---- groove=---- planarity=0.260 type=other nts=4 GGGG A.DG4,A.DG9,A.DG13,A.DG20 **************************************************************************** List of 5 splayed-apart dinucleotides 1 A.DG4 A.DC5 angle=106 distance=17.6 ratio=0.80 2 A.DC5 A.DG6 angle=120 distance=15.8 ratio=0.87 3 A.DG7 A.DT8 angle=155 distance=19.3 ratio=0.98 4 A.DT8 A.DG9 angle=136 distance=19.2 ratio=0.93 5 A.DG13 A.DA14 angle=105 distance=13.8 ratio=0.80 ---------------------------------------------------------------- Summary of 3 splayed-apart units 1 nts=3 GCG A.DG4,A.DC5,A.DG6 2 nts=3 GTG A.DG7,A.DT8,A.DG9 3 nts=2 GA A.DG13,A.DA14 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5i2v nts=22 [whole] AGGGCGGTGTGGGAATAGGGAA ...................... >5i2v-A #1 nts=22 0.03(2.83) [chain] DNA AGGGCGGTGTGGGAATAGGGAA ...................... **************************************************************************** Summary of structural features of 22 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 A . A.DA1 0.033 syn,~C2'-endo,non-pair-contact,ss-non-loop 2 G . A.DG2 0.027 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 3 G . A.DG3 0.027 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 4 G . A.DG4 0.029 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 5 C . A.DC5 0.017 turn,anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 6 G . A.DG6 0.024 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 7 G . A.DG7 0.023 anti,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,splayed-apart 8 T . A.DT8 0.029 turn,anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 9 G . A.DG9 0.029 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 10 T . A.DT10 0.045 anti,~C3'-endo,BII,non-stack,non-pair-contact,ss-non-loop 11 G . A.DG11 0.028 turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 12 G . A.DG12 0.021 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 13 G . A.DG13 0.032 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,phosphate,splayed-apart 14 A . A.DA14 0.031 anti,BI,non-stack,non-pair-contact,ss-non-loop,splayed-apart 15 A . A.DA15 0.034 anti,~C2'-endo,BII,non-stack,ss-non-loop 16 T . A.DT16 0.037 anti,~C2'-endo,non-stack,ss-non-loop 17 A . A.DA17 0.029 anti,~C2'-endo,BI,non-stack,ss-non-loop 18 G . A.DG18 0.027 anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 19 G . A.DG19 0.027 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 20 G . A.DG20 0.028 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 21 A . A.DA21 0.034 ~C2'-endo,BII,non-stack,non-canonical,multiplet,ss-non-loop 22 A . A.DA22 0.031 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop **************************************************************************** List of 9 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks