**************************************************************************** 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=6ras.pdb -o=6ras.out File name: 6ras.pdb no. of DNA/RNA chains: 3 [B=21,C=10,D=12] no. of nucleotides: 43 no. of atoms: 8624 no. of waters: 196 no. of metals: 0 **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 AMP-a 1 D.AMP300 2 OMC-c 1 C.OMC30 **************************************************************************** List of 21 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DT1 D.DA42 T-A WC 20-XX cWW cW-W 2 B.DT2 D.DA41 T-A WC 20-XX cWW cW-W 3 B.DC3 D.DG40 C-G WC 19-XIX cWW cW-W 4 B.DC4 D.DG39 C-G WC 19-XIX cWW cW-W 5 B.DG5 D.DC38 G-C WC 19-XIX cWW cW-W 6 B.DA6 D.DT37 A-T WC 20-XX cWW cW-W 7 B.DC7 D.DA36 C-A -- -- cWW cW-W 8 B.DA8 D.DT35 A-T WC 20-XX cWW cW-W 9 B.DG9 D.DC34 G-C WC 19-XIX cWW cW-W 10 B.DT10 D.DA33 T-A WC 20-XX cWW cW-W 11 B.DG11 D.DC32 G-C WC 19-XIX cWW cW-W 12 B.DG12 C.DC31 G-C WC 19-XIX cWW cW-W 13 B.DG13 C.OMC30 G-c WC 19-XIX cWW cW-W 14 B.DG14 C.DC29 G-C WC 19-XIX cWW cW-W 15 B.DT15 C.DA28 T-A WC 20-XX cWW cW-W 16 B.DC16 C.DG27 C-G WC 19-XIX cWW cW-W 17 B.DG17 C.DC26 G-C WC 19-XIX cWW cW-W 18 B.DC18 C.DG25 C-G WC 19-XIX cWW cW-W 19 B.DA19 C.DT24 A-T WC 20-XX cWW cW-W 20 B.DA20 C.DT23 A-T WC 20-XX cWW cW-W 21 B.DT21 C.DA22 T-A 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[3] bps=21 strand-1 5'-TTCCGACAGTGGGGTCGCAAT-3' bp-type ||||||.|||||||||||||| strand-2 3'-AAGGCTATCACCcCAGCGTTA-5' helix-form BBBBBBBBB.x.BBBBBBBB 1 B.DT1 D.DA42 T-A WC 20-XX cWW cW-W 2 B.DT2 D.DA41 T-A WC 20-XX cWW cW-W 3 B.DC3 D.DG40 C-G WC 19-XIX cWW cW-W 4 B.DC4 D.DG39 C-G WC 19-XIX cWW cW-W 5 B.DG5 D.DC38 G-C WC 19-XIX cWW cW-W 6 B.DA6 D.DT37 A-T WC 20-XX cWW cW-W 7 B.DC7 D.DA36 C-A -- -- cWW cW-W 8 B.DA8 D.DT35 A-T WC 20-XX cWW cW-W 9 B.DG9 D.DC34 G-C WC 19-XIX cWW cW-W 10 B.DT10 D.DA33 T-A WC 20-XX cWW cW-W 11 B.DG11 D.DC32 G-C WC 19-XIX cWW cW-W 12 B.DG12 C.DC31 G-C WC 19-XIX cWW cW-W 13 B.DG13 C.OMC30 G-c WC 19-XIX cWW cW-W 14 B.DG14 C.DC29 G-C WC 19-XIX cWW cW-W 15 B.DT15 C.DA28 T-A WC 20-XX cWW cW-W 16 B.DC16 C.DG27 C-G WC 19-XIX cWW cW-W 17 B.DG17 C.DC26 G-C WC 19-XIX cWW cW-W 18 B.DC18 C.DG25 C-G WC 19-XIX cWW cW-W 19 B.DA19 C.DT24 A-T WC 20-XX cWW cW-W 20 B.DA20 C.DT23 A-T WC 20-XX cWW cW-W 21 B.DT21 C.DA22 T-A WC 20-XX cWW cW-W **************************************************************************** List of 3 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'-TTCCGA-3' bp-type |||||| strand-2 3'-AAGGCT-5' helix-form BBBBB 1 B.DT1 D.DA42 T-A WC 20-XX cWW cW-W 2 B.DT2 D.DA41 T-A WC 20-XX cWW cW-W 3 B.DC3 D.DG40 C-G WC 19-XIX cWW cW-W 4 B.DC4 D.DG39 C-G WC 19-XIX cWW cW-W 5 B.DG5 D.DC38 G-C WC 19-XIX cWW cW-W 6 B.DA6 D.DT37 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=4 strand-1 5'-AGTG-3' bp-type |||| strand-2 3'-TCAC-5' helix-form BB. 1 B.DA8 D.DT35 A-T WC 20-XX cWW cW-W 2 B.DG9 D.DC34 G-C WC 19-XIX cWW cW-W 3 B.DT10 D.DA33 T-A WC 20-XX cWW cW-W 4 B.DG11 D.DC32 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=10 strand-1 5'-GGGTCGCAAT-3' bp-type |||||||||| strand-2 3'-CcCAGCGTTA-5' helix-form .BBBBBBBB 1 B.DG12 C.DC31 G-C WC 19-XIX cWW cW-W 2 B.DG13 C.OMC30 G-c WC 19-XIX cWW cW-W 3 B.DG14 C.DC29 G-C WC 19-XIX cWW cW-W 4 B.DT15 C.DA28 T-A WC 20-XX cWW cW-W 5 B.DC16 C.DG27 C-G WC 19-XIX cWW cW-W 6 B.DG17 C.DC26 G-C WC 19-XIX cWW cW-W 7 B.DC18 C.DG25 C-G WC 19-XIX cWW cW-W 8 B.DA19 C.DT24 A-T WC 20-XX cWW cW-W 9 B.DA20 C.DT23 A-T WC 20-XX cWW cW-W 10 B.DT21 C.DA22 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#3] **************************************************************************** List of 5 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=2 GG B.DG11,B.DG12 2 nts=2 CC C.DC31,D.DC32 3 nts=2 Fa I.PHE249,D.AMP300 4 nts=3 ACA B.DA6,B.DC7,B.DA8 5 nts=3 TAT D.DT35,D.DA36,D.DT37 **************************************************************************** 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 [B.6 D.37 B.8 D.35] 6 4 nts=6 ACATAT B.DA6,B.DC7,B.DA8,D.DT35,D.DA36,D.DT37 nts=1 C B.DC7 nts=1 A D.DA36 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=1 a D.AMP300 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6ras nts=43 [whole] TTCCGACAGTGGGGTCGCAAT&ATTGCGACcC&CACTATCGGAA&a ((((((.((((((((((((((&))))))))))&)))).))))))&. >6ras-B #1 nts=21 3.19(0.45) [chain] DNA TTCCGACAGTGGGGTCGCAAT ((((((.(((((((((((((( >6ras-C #2 nts=10 3.31(0.36) [chain] DNA[9]/1 ATTGCGACcC )))))))))) >6ras-D #3 nts=12 0.76(2.27) [chain] DNA[11]/1* CACTATCGGAA&a )))).))))))&. **************************************************************************** Summary of structural features of 43 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 T ( B.DT1 0.007 anti,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 T ( B.DT2 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 C ( B.DC3 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 C ( B.DC4 0.007 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 5 G ( B.DG5 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 A ( B.DA6 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 7 C . B.DC7 0.010 anti,BI,non-canonical,non-pair-contact,helix,internal-loop 8 A ( B.DA8 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 9 G ( B.DG9 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 10 T ( B.DT10 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 11 G ( B.DG11 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 12 G ( B.DG12 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 13 G ( B.DG13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 14 G ( B.DG14 0.013 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 15 T ( B.DT15 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 16 C ( B.DC16 0.006 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 17 G ( B.DG17 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 18 C ( B.DC18 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 19 A ( B.DA19 0.011 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 A ( B.DA20 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 21 T ( B.DT21 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 22 A ) C.DA22 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 23 T ) C.DT23 0.010 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 T ) C.DT24 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ) C.DG25 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 26 C ) C.DC26 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 G ) C.DG27 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 28 A ) C.DA28 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 29 C ) C.DC29 0.012 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 30 c ) C.OMC30 0.046 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 31 C ) C.DC31 0.011 anti,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 32 C ) D.DC32 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 33 A ) D.DA33 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 34 C ) D.DC34 0.006 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 35 T ) D.DT35 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 36 A . D.DA36 0.010 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 37 T ) D.DT37 0.009 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 38 C ) D.DC38 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 39 G ) D.DG39 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 40 G ) D.DG40 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 41 A ) D.DA41 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 A ) D.DA42 0.007 break,anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 43 a . D.AMP300 0.060 modified,syn,ss-non-loop,phosphate **************************************************************************** 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-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-stacks.pdb -- an ensemble of base stacks