**************************************************************************** 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=4ofe.pdb -o=4ofe.out File name: 4ofe.pdb no. of DNA/RNA chains: 2 [C=12,D=12] no. of nucleotides: 24 no. of atoms: 1829 no. of waters: 133 no. of metals: 1 [Mg=1] **************************************************************************** List of 11 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DC1 D.DG12 C-G WC 19-XIX cWW cW-W 2 C.DC2 D.DG11 C-G WC 19-XIX cWW cW-W 3 C.DA3 D.DT10 A-T WC 20-XX cWW cW-W 4 C.DG4 D.DC9 G-C WC 19-XIX cWW cW-W 5 C.DC5 D.DG8 C-G WC 19-XIX cWW cW-W 6 C.DG6 D.DC7 G-C WC 19-XIX cWW cW-W 7 C.DG8 D.DC5 G-C WC 19-XIX cWW cW-W 8 C.DC9 D.DG4 C-G WC 19-XIX cWW cW-W 9 C.DA10 D.DT3 A-T WC 20-XX cWW cW-W 10 C.DG11 D.DC2 G-C WC 19-XIX cWW cW-W 11 C.DC12 D.DG1 C-G WC 19-XIX 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[2] bps=11 strand-1 5'-CCAGCGGCAGC-3' bp-type ||||||||||| strand-2 3'-GGTCGCCGTCG-5' helix-form B.BBBxBBBB 1 C.DC1 D.DG12 C-G WC 19-XIX cWW cW-W 2 C.DC2 D.DG11 C-G WC 19-XIX cWW cW-W 3 C.DA3 D.DT10 A-T WC 20-XX cWW cW-W 4 C.DG4 D.DC9 G-C WC 19-XIX cWW cW-W 5 C.DC5 D.DG8 C-G WC 19-XIX cWW cW-W 6 C.DG6 D.DC7 G-C WC 19-XIX cWW cW-W 7 C.DG8 D.DC5 G-C WC 19-XIX cWW cW-W 8 C.DC9 D.DG4 C-G WC 19-XIX cWW cW-W 9 C.DA10 D.DT3 A-T WC 20-XX cWW cW-W 10 C.DG11 D.DC2 G-C WC 19-XIX cWW cW-W 11 C.DC12 D.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems 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'-CCAGCG-3' bp-type |||||| strand-2 3'-GGTCGC-5' helix-form B.BBB 1 C.DC1 D.DG12 C-G WC 19-XIX cWW cW-W 2 C.DC2 D.DG11 C-G WC 19-XIX cWW cW-W 3 C.DA3 D.DT10 A-T WC 20-XX cWW cW-W 4 C.DG4 D.DC9 G-C WC 19-XIX cWW cW-W 5 C.DC5 D.DG8 C-G WC 19-XIX cWW cW-W 6 C.DG6 D.DC7 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=5 strand-1 5'-GCAGC-3' bp-type ||||| strand-2 3'-CGTCG-5' helix-form BBBB 1 C.DG8 D.DC5 G-C WC 19-XIX cWW cW-W 2 C.DC9 D.DG4 C-G WC 19-XIX cWW cW-W 3 C.DA10 D.DT3 A-T WC 20-XX cWW cW-W 4 C.DG11 D.DC2 G-C WC 19-XIX cWW cW-W 5 C.DC12 D.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 1 base stack 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 CGC D.DC5,D.DG6,D.DC7 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T C.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 1 internal loop 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [C.6 D.7 C.8 D.5] 6 5 nts=6 GTGCGC C.DG6,C.DT7,C.DG8,D.DC5,D.DG6,D.DC7 nts=1 T C.DT7 nts=1 G D.DG6 **************************************************************************** List of 2 splayed-apart dinucleotides 1 C.DG6 C.DT7 angle=130 distance=17.6 ratio=0.90 2 C.DT7 C.DG8 angle=144 distance=18.6 ratio=0.95 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=3 GTG C.DG6,C.DT7,C.DG8 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4ofe nts=24 [whole] CCAGCGTGCAGC&GCTGCGCGCTGG ((((((.(((((&))))).)))))) >4ofe-C #1 nts=12 3.37(1.34) [chain] DNA CCAGCGTGCAGC ((((((.((((( >4ofe-D #2 nts=12 2.95(1.12) [chain] DNA GCTGCGCGCTGG ))))).)))))) **************************************************************************** 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 C ( C.DC1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 C ( C.DC2 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 3 A ( C.DA3 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 G ( C.DG4 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 C ( C.DC5 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 G ( C.DG6 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,splayed-apart 7 T . C.DT7 0.007 turn,anti,non-stack,internal-loop,phosphate,splayed-apart 8 G ( C.DG8 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate,splayed-apart 9 C ( C.DC9 0.008 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 10 A ( C.DA10 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 11 G ( C.DG11 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 C ( C.DC12 0.004 anti,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 13 G ) D.DG1 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 14 C ) D.DC2 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 T ) D.DT3 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 16 G ) D.DG4 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 C ) D.DC5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 18 G . D.DG6 0.008 anti,~C2'-endo,non-pair-contact,internal-loop,phosphate 19 C ) D.DC7 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 20 G ) D.DG8 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 C ) D.DC9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 T ) D.DT10 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 G ) D.DG11 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 24 G ) D.DG12 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 10 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-iloops.pdb -- an ensemble of internal loops 5 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 6 dssr-2ndstrs.ct -- secondary structure in connectivity table format 7 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 8 dssr-torsions.txt -- backbone torsion angles and suite names 9 dssr-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks