**************************************************************************** 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=1a8n.pdb -o=1a8n.out File name: 1a8n.pdb no. of DNA/RNA chains: 2 [A=12,B=12] no. of nucleotides: 24 no. of atoms: 770 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 17 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG1 A.DC12 G-C WC 19-XIX cWW cW-W 2 A.DG1 B.DC4 G-C -- -- cHH cM-M 3 A.DG2 A.DG11 G+G -- 06-VI cHW cM+W 4 A.DG2 B.DG3 G+G -- 06-VI cWH cW+M 5 A.DG3 A.DG10 G+G -- 06-VI cWH cW+M 6 A.DG3 B.DG2 G+G -- 06-VI cHW cM+W 7 A.DC4 A.DG9 C-G WC 19-XIX cWW cW-W 8 A.DC4 B.DG1 C-G -- -- cHH cM-M 9 A.DG9 B.DG1 G+G -- -- tH. tM+. 10 A.DG9 B.DC12 G-C -- -- cHH cM-M 11 A.DG10 B.DG11 G+G -- 06-VI cWH cW+M 12 A.DG11 B.DG10 G+G -- 06-VI cHW cM+W 13 A.DC12 B.DG9 C-G -- -- cHH cM-M 14 B.DG1 B.DC12 G-C WC 19-XIX cWW cW-W 15 B.DG2 B.DG11 G+G -- 06-VI cHW cM+W 16 B.DG3 B.DG10 G+G -- 06-VI cWH cW+M 17 B.DC4 B.DG9 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 4 multiplets 1 nts=4 GCCG A.DG1,A.DC12,B.DC4,B.DG9 2 nts=4 GGGG A.DG2,A.DG11,B.DG3,B.DG10 3 nts=4 GGGG A.DG3,A.DG10,B.DG2,B.DG11 4 nts=4 CGGC A.DC4,A.DG9,B.DG1,B.DC12 **************************************************************************** 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=6 strand-1 5'-GGGGGC-3' bp-type ..|..| strand-2 3'-GGCGGG-5' helix-form .xx.x 1 A.DG2 B.DG3 G+G -- 06-VI cWH cW+M 2 A.DG3 B.DG2 G+G -- 06-VI cHW cM+W 3 A.DG9 A.DC4 G-C WC 19-XIX cWW cW-W 4 A.DG10 B.DG11 G+G -- 06-VI cWH cW+M 5 A.DG11 B.DG10 G+G -- 06-VI cHW cM+W 6 B.DC4 B.DG9 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 4 isolated WC/wobble pairs Note: isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- -- -1 A.DG1 A.DC12 G-C WC 19-XIX cWW cW-W [#1] -2 A.DC4 A.DG9 C-G WC 19-XIX cWW cW-W -- -3 B.DG1 B.DC12 G-C WC 19-XIX cWW cW-W [#1] -4 B.DC4 B.DG9 C-G WC 19-XIX cWW cW-W **************************************************************************** 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=5 GGGCT A.DG1,A.DG2,A.DG3,A.DC4,A.DT5 2 nts=5 TCGGG A.DT8,B.DC12,B.DG11,B.DG10,B.DG9 3 nts=5 GGGCT A.DG9,A.DG10,A.DG11,A.DC12,B.DT8 4 nts=5 GGGCT B.DG1,B.DG2,B.DG3,B.DC4,B.DT5 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 TTTT A.DT6,A.DT7,B.DT6,B.DT7 **************************************************************************** Note: for the various types of loops listed below, numbers within the first set of brackets are the number of loop nts, and numbers in the second set of brackets are the identities of the stems (positive number) or isolated WC/wobble pairs (negative numbers) to which they are linked. **************************************************************************** List of 2 hairpin loops 1 hairpin loop: nts=6; [4]; linked by [#-2] summary: [1] 4 [A.4 A.9] 1 nts=6 CTTTTG A.DC4,A.DT5,A.DT6,A.DT7,A.DT8,A.DG9 nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8 2 hairpin loop: nts=6; [4]; linked by [#-4] summary: [1] 4 [B.4 B.9] 1 nts=6 CTTTTG B.DC4,B.DT5,B.DT6,B.DT7,B.DT8,B.DG9 nts=4 TTTT B.DT5,B.DT6,B.DT7,B.DT8 **************************************************************************** List of 2 internal loops 1 symmetric internal loop: nts=8; [2,2]; linked by [#-1,#-2] summary: [2] 2 2 [A.1 A.12 A.4 A.9] 1 1 nts=8 GGGCGGGC A.DG1,A.DG2,A.DG3,A.DC4,A.DG9,A.DG10,A.DG11,A.DC12 nts=2 GG A.DG2,A.DG3 nts=2 GG A.DG10,A.DG11 2 symmetric internal loop: nts=8; [2,2]; linked by [#-3,#-4] summary: [2] 2 2 [B.1 B.12 B.4 B.9] 1 1 nts=8 GGGCGGGC B.DG1,B.DG2,B.DG3,B.DC4,B.DG9,B.DG10,B.DG11,B.DC12 nts=2 GG B.DG2,B.DG3 nts=2 GG B.DG10,B.DG11 **************************************************************************** List of 2 G-tetrads 1 glyco-bond=s-s- sugar=.--- groove=wnwn planarity=0.170 type=other nts=4 GGGG A.DG2,A.DG11,B.DG10,B.DG3 2 glyco-bond=-s-s sugar=---. groove=wnwn planarity=0.170 type=other nts=4 GGGG A.DG3,A.DG10,B.DG11,B.DG2 **************************************************************************** List of 4 splayed-apart dinucleotides 1 A.DT7 A.DT8 angle=111 distance=15.3 ratio=0.83 2 A.DT8 A.DG9 angle=90 distance=12.4 ratio=0.71 3 B.DT7 B.DT8 angle=111 distance=15.3 ratio=0.83 4 B.DT8 B.DG9 angle=90 distance=12.4 ratio=0.71 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 TTG A.DT7,A.DT8,A.DG9 2 nts=3 TTG B.DT7,B.DT8,B.DG9 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1a8n nts=24 [whole] GGGCTTTTGGGC&GGGCTTTTGGGC (..(....)..)&(..(....)..) >1a8n-A #1 nts=12 0.63(2.31) [chain] DNA GGGCTTTTGGGC (..(....)..) >1a8n-B #2 nts=12 0.63(2.31) [chain] DNA GGGCTTTTGGGC (..(....)..) **************************************************************************** Summary of structural features of 24 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 G ( A.DG1 0.019 anti,isolated-canonical,non-canonical,non-pair-contact,multiplet,internal-loop 2 G . A.DG2 0.015 syn,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,G-tetrad 3 G . A.DG3 0.022 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,internal-loop,G-tetrad 4 C ( A.DC4 0.011 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,internal-loop 5 T . A.DT5 0.019 anti,~C2'-endo,non-pair-contact,hairpin-loop 6 T . A.DT6 0.019 anti,~C3'-endo,non-stack,hairpin-loop 7 T . A.DT7 0.027 anti,non-stack,hairpin-loop,splayed-apart 8 T . A.DT8 0.018 anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 9 G ) A.DG9 0.022 anti,~C2'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,internal-loop,splayed-apart 10 G . A.DG10 0.010 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,G-tetrad 11 G . A.DG11 0.020 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,internal-loop,G-tetrad 12 C ) A.DC12 0.012 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,multiplet,internal-loop 13 G ( B.DG1 0.018 anti,isolated-canonical,non-canonical,non-pair-contact,multiplet,internal-loop 14 G . B.DG2 0.015 syn,non-canonical,non-pair-contact,helix,multiplet,internal-loop,G-tetrad 15 G . B.DG3 0.022 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,internal-loop,G-tetrad 16 C ( B.DC4 0.011 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,internal-loop 17 T . B.DT5 0.018 anti,~C2'-endo,non-pair-contact,hairpin-loop 18 T . B.DT6 0.018 anti,~C3'-endo,non-stack,hairpin-loop 19 T . B.DT7 0.026 anti,non-stack,hairpin-loop,splayed-apart 20 T . B.DT8 0.017 anti,~C2'-endo,non-pair-contact,hairpin-loop,splayed-apart 21 G ) B.DG9 0.022 anti,~C2'-endo,BI,isolated-canonical,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,internal-loop,splayed-apart 22 G . B.DG10 0.010 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,internal-loop,G-tetrad 23 G . B.DG11 0.021 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,internal-loop,G-tetrad 24 C ) B.DC12 0.012 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,multiplet,internal-loop **************************************************************************** List of 11 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-hairpins.pdb -- an ensemble of hairpin loops 5 dssr-iloops.pdb -- an ensemble of internal loops 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-splays.pdb -- an ensemble of splayed-apart units 11 dssr-stacks.pdb -- an ensemble of base stacks