**************************************************************************** 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=5iwi.pdb -o=5iwi.out File name: 5iwi.pdb no. of DNA/RNA chains: 3 [E=20,F=8,G=11] no. of nucleotides: 39 no. of atoms: 12478 no. of waters: 949 no. of metals: 3 [Mn=3] **************************************************************************** List of 19 base pairs nt1 nt2 bp name Saenger LW DSSR 1 E.DG2 G.DC2019 G-C WC 19-XIX cWW cW-W 2 E.DC3 G.DG2018 C-G WC 19-XIX cWW cW-W 3 E.DC4 G.DG2017 C-G WC 19-XIX cWW cW-W 4 E.DG5 G.DC2016 G-C WC 19-XIX cWW cW-W 5 E.DT6 G.DA2015 T-A WC 20-XX cWW cW-W 6 E.DA7 G.DT2014 A-T WC 20-XX cWW cW-W 7 E.DG8 G.DC2013 G-C WC 19-XIX cWW cW-W 8 E.DG9 G.DC2012 G-C WC 19-XIX cWW cW-W 9 E.DT10 G.DA2011 T-A WC 20-XX cWW cW-W 10 E.DA11 G.DT2010 A-T WC 20-XX cWW cW-W 11 E.DC12 G.DG2009 C-G WC 19-XIX cWW cW-W 12 E.DA13 F.DT1008 A-T WC 20-XX cWW cW-W 13 E.DC14 F.DG1007 C-G WC 19-XIX cWW cW-W 14 E.DC15 F.DG1006 C-G WC 19-XIX cWW cW-W 15 E.DG16 F.DC1005 G-C WC 19-XIX cWW cW-W 16 E.DC17 F.DG1004 C-G WC 19-XIX cWW cW-W 17 E.DA18 F.DT1003 A-T WC 20-XX cWW cW-W 18 E.DC19 F.DG1002 C-G WC 19-XIX cWW cW-W 19 E.DA20 F.DT1001 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[2] bps=19 strand-1 5'-GCCGTAGGTACACCGCACA-3' bp-type ||||||||||||||||||| strand-2 3'-CGGCATCCATGTGGCGTGT-5' helix-form BB.B......x..B.BBB 1 E.DG2 G.DC2019 G-C WC 19-XIX cWW cW-W 2 E.DC3 G.DG2018 C-G WC 19-XIX cWW cW-W 3 E.DC4 G.DG2017 C-G WC 19-XIX cWW cW-W 4 E.DG5 G.DC2016 G-C WC 19-XIX cWW cW-W 5 E.DT6 G.DA2015 T-A WC 20-XX cWW cW-W 6 E.DA7 G.DT2014 A-T WC 20-XX cWW cW-W 7 E.DG8 G.DC2013 G-C WC 19-XIX cWW cW-W 8 E.DG9 G.DC2012 G-C WC 19-XIX cWW cW-W 9 E.DT10 G.DA2011 T-A WC 20-XX cWW cW-W 10 E.DA11 G.DT2010 A-T WC 20-XX cWW cW-W 11 E.DC12 G.DG2009 C-G WC 19-XIX cWW cW-W 12 E.DA13 F.DT1008 A-T WC 20-XX cWW cW-W 13 E.DC14 F.DG1007 C-G WC 19-XIX cWW cW-W 14 E.DC15 F.DG1006 C-G WC 19-XIX cWW cW-W 15 E.DG16 F.DC1005 G-C WC 19-XIX cWW cW-W 16 E.DC17 F.DG1004 C-G WC 19-XIX cWW cW-W 17 E.DA18 F.DT1003 A-T WC 20-XX cWW cW-W 18 E.DC19 F.DG1002 C-G WC 19-XIX cWW cW-W 19 E.DA20 F.DT1001 A-T WC 20-XX 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=11 strand-1 5'-GCCGTAGGTAC-3' bp-type ||||||||||| strand-2 3'-CGGCATCCATG-5' helix-form BB.B...... 1 E.DG2 G.DC2019 G-C WC 19-XIX cWW cW-W 2 E.DC3 G.DG2018 C-G WC 19-XIX cWW cW-W 3 E.DC4 G.DG2017 C-G WC 19-XIX cWW cW-W 4 E.DG5 G.DC2016 G-C WC 19-XIX cWW cW-W 5 E.DT6 G.DA2015 T-A WC 20-XX cWW cW-W 6 E.DA7 G.DT2014 A-T WC 20-XX cWW cW-W 7 E.DG8 G.DC2013 G-C WC 19-XIX cWW cW-W 8 E.DG9 G.DC2012 G-C WC 19-XIX cWW cW-W 9 E.DT10 G.DA2011 T-A WC 20-XX cWW cW-W 10 E.DA11 G.DT2010 A-T WC 20-XX cWW cW-W 11 E.DC12 G.DG2009 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=8 strand-1 5'-ACCGCACA-3' bp-type |||||||| strand-2 3'-TGGCGTGT-5' helix-form ..B.BBB 1 E.DA13 F.DT1008 A-T WC 20-XX cWW cW-W 2 E.DC14 F.DG1007 C-G WC 19-XIX cWW cW-W 3 E.DC15 F.DG1006 C-G WC 19-XIX cWW cW-W 4 E.DG16 F.DC1005 G-C WC 19-XIX cWW cW-W 5 E.DC17 F.DG1004 C-G WC 19-XIX cWW cW-W 6 E.DA18 F.DT1003 A-T WC 20-XX cWW cW-W 7 E.DC19 F.DG1002 C-G WC 19-XIX cWW cW-W 8 E.DA20 F.DT1001 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** 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=2 AG E.DA1,E.DG2 2 nts=2 AG E.DA13,G.DG2009 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T F.DT1001 **************************************************************************** List of 4 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other N10.A@E.6EJ101 E.DT10 3.40 2 other O9.A@E.6EJ101 E.DT10 2.62 3 sugar O4'.A@G.DG2009 F.DT1008 3.29 4 other F1.A@E.6EJ101 G.DT2010 2.98 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=1 A E.DA1 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5iwi nts=39 [whole] AGCCGTAGGTACACCGCACA&TGTGCGGT>ACCTACGGC .(((((((((((((((((((&))))))))&))))))))))) >5iwi-E #1 nts=20 2.93(1.40) [chain] DNA AGCCGTAGGTACACCGCACA .((((((((((((((((((( >5iwi-F #2 nts=8 3.07(1.09) [chain] DNA TGTGCGGT )))))))) >5iwi-G #3 nts=11 3.73(1.23) [chain] DNA GTACCTACGGC ))))))))))) **************************************************************************** Summary of structural features of 39 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 . E.DA1 0.004 syn,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 G ( E.DG2 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 3 C ( E.DC3 0.003 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 C ( E.DC4 0.004 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 5 G ( E.DG5 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 6 T ( E.DT6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 7 A ( E.DA7 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 8 G ( E.DG8 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 9 G ( E.DG9 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 10 T ( E.DT10 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-acceptor,phosphate 11 A ( E.DA11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 C ( E.DC12 0.002 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 13 A ( E.DA13 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 14 C ( E.DC14 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 15 C ( E.DC15 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 16 G ( E.DG16 0.004 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 17 C ( E.DC17 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 18 A ( E.DA18 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 19 C ( E.DC19 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 20 A ( E.DA20 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 21 T ) F.DT1001 0.002 anti,~C2'-endo,non-stack,canonical,helix-end,stem-end,coaxial-stack 22 G ) F.DG1002 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 T ) F.DT1003 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 24 G ) F.DG1004 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 25 C ) F.DC1005 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 26 G ) F.DG1006 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 27 G ) F.DG1007 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 28 T ) F.DT1008 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-acceptor,phosphate 29 G ) G.DG2009 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,cap-donor 30 T ) G.DT2010 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-acceptor,phosphate 31 A ) G.DA2011 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 C ) G.DC2012 0.007 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 33 C ) G.DC2013 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 T ) G.DT2014 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 35 A ) G.DA2015 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 36 C ) G.DC2016 0.005 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 37 G ) G.DG2017 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 38 G ) G.DG2018 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 39 C ) G.DC2019 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** 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-stacks.pdb -- an ensemble of base stacks 9 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions