**************************************************************************** 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=2org.pdb -o=2org.out File name: 2org.pdb no. of DNA/RNA chains: 2 [A=10,B=10] no. of nucleotides: 20 no. of atoms: 510 no. of waters: 106 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 BRU-u 1 A.BRU7 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG20 C-G WC 19-XIX cWW cW-W 2 A.DC2 B.DG19 C-G WC 19-XIX cWW cW-W 3 A.DG3 B.DC18 G-C WC 19-XIX cWW cW-W 4 A.DG4 B.DC17 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.DA16 T-A WC 20-XX cWW cW-W 6 A.DA6 B.DT15 A-T WC 20-XX cWW cW-W **************************************************************************** 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[1] bps=6 strand-1 5'-CCGGTA-3' bp-type |||||| strand-2 3'-GGCCAT-5' helix-form ...BB 1 A.DC1 B.DG20 C-G WC 19-XIX cWW cW-W 2 A.DC2 B.DG19 C-G WC 19-XIX cWW cW-W 3 A.DG3 B.DC18 G-C WC 19-XIX cWW cW-W 4 A.DG4 B.DC17 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.DA16 T-A WC 20-XX cWW cW-W 6 A.DA6 B.DT15 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 stem Note: a stem is defined as a helix consisting of only canonical WC/wobble pairs, with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=6 strand-1 5'-CCGGTA-3' bp-type |||||| strand-2 3'-GGCCAT-5' helix-form ...BB 1 A.DC1 B.DG20 C-G WC 19-XIX cWW cW-W 2 A.DC2 B.DG19 C-G WC 19-XIX cWW cW-W 3 A.DG3 B.DC18 G-C WC 19-XIX cWW cW-W 4 A.DG4 B.DC17 G-C WC 19-XIX cWW cW-W 5 A.DT5 B.DA16 T-A WC 20-XX cWW cW-W 6 A.DA6 B.DT15 A-T WC 20-XX cWW cW-W **************************************************************************** List of 2 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=4 uCGG A.BRU7,A.DC8,A.DG9,A.DG10 2 nts=4 CGAT B.DC12,B.DG13,B.DA14,B.DT15 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C B.DC11 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=4 uCGG A.BRU7,A.DC8,A.DG9,A.DG10 2 nts=4 CCGA B.DC11,B.DC12,B.DG13,B.DA14 **************************************************************************** List of 1 splayed-apart dinucleotide 1 A.DA6 A.BRU7 angle=120 distance=16.9 ratio=0.86 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 Au A.DA6,A.BRU7 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2org nts=20 [whole] CCGGTAuCGG&CCGATACCGG ((((((....&....)))))) >2org-A #1 nts=10 1.95(1.89) [chain] DNA CCGGTAuCGG ((((((.... >2org-B #2 nts=10 3.52(0.74) [chain] DNA CCGATACCGG ....)))))) **************************************************************************** Summary of structural features of 20 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 C ( A.DC1 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 2 C ( A.DC2 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 3 G ( A.DG3 0.009 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 4 G ( A.DG4 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 T ( A.DT5 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 6 A ( A.DA6 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 7 u . A.BRU7 0.003 modified,anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 8 C . A.DC8 0.007 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 9 G . A.DG9 0.008 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 10 G . A.DG10 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop 11 C . B.DC11 0.003 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop 12 C . B.DC12 0.003 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 13 G . B.DG13 0.013 anti,~C2'-endo,non-pair-contact,ss-non-loop 14 A . B.DA14 0.014 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 15 T ) B.DT15 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 16 A ) B.DA16 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ) B.DC17 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 C ) B.DC18 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 19 G ) B.DG19 0.008 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 20 G ) B.DG20 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 9 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 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