**************************************************************************** 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=2e9r.pdb -o=2e9r.out File name: 2e9r.pdb no. of DNA/RNA chains: 2 [A=9,B=6] no. of nucleotides: 16 no. of atoms: 4033 no. of waters: 7 no. of metals: 1 [Mg=1] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 RTP-? 1 X.RTP3832 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G905 B.C920 G-C WC 19-XIX cWW cW-W 2 A.G906 B.C919 G-C WC 19-XIX cWW cW-W 3 A.G907 B.C918 G-C WC 19-XIX cWW cW-W 4 A.C908 B.G917 C-G WC 19-XIX cWW cW-W 5 A.C909 B.G916 C-G WC 19-XIX cWW cW-W 6 A.C910 B.G915 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[1] bps=6 strand-1 5'-GGGCCC-3' bp-type |||||| strand-2 3'-CCCGGG-5' helix-form .AAAA 1 A.G905 B.C920 G-C WC 19-XIX cWW cW-W 2 A.G906 B.C919 G-C WC 19-XIX cWW cW-W 3 A.G907 B.C918 G-C WC 19-XIX cWW cW-W 4 A.C908 B.G917 C-G WC 19-XIX cWW cW-W 5 A.C909 B.G916 C-G WC 19-XIX cWW cW-W 6 A.C910 B.G915 C-G WC 19-XIX 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'-GGGCCC-3' bp-type |||||| strand-2 3'-CCCGGG-5' helix-form .AAAA 1 A.G905 B.C920 G-C WC 19-XIX cWW cW-W 2 A.G906 B.C919 G-C WC 19-XIX cWW cW-W 3 A.G907 B.C918 G-C WC 19-XIX cWW cW-W 4 A.C908 B.G917 C-G WC 19-XIX cWW cW-W 5 A.C909 B.G916 C-G WC 19-XIX cWW cW-W 6 A.C910 B.G915 C-G WC 19-XIX cWW cW-W **************************************************************************** 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=2 UG A.U904,A.G905 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 CA A.C902,A.A903 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other N3@X.RTP3832 A.G905 2.99 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=3 CAU A.C902,A.A903,A.U904 2 nts=1 ? X.RTP3832 **************************************************************************** List of 1 splayed-apart dinucleotide 1 A.C902 A.A903 angle=127 distance=15.3 ratio=0.89 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 CA A.C902,A.A903 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2e9r nts=16 [whole] CAUGGGCCC&GGGCCC&? ...((((((&))))))&. >2e9r-A #1 nts=9 0.23(1.69) [chain] RNA CAUGGGCCC ...(((((( >2e9r-B #2 nts=6 2.64(0.10) [chain] RNA GGGCCC )))))) **************************************************************************** Summary of structural features of 16 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.C902 0.017 anti,~C3'-endo,non-stack,ss-non-loop,splayed-apart 2 A . A.A903 0.036 ~C3'-endo,BI,non-stack,ss-non-loop,splayed-apart 3 U . A.U904 0.017 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 4 G ( A.G905 0.021 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,cap-acceptor,phosphate 5 G ( A.G906 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 G ( A.G907 0.020 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 7 C ( A.C908 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 C ( A.C909 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 9 C ( A.C910 0.015 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 10 G ) B.G915 0.031 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 11 G ) B.G916 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ) B.G917 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 C ) B.C918 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 14 C ) B.C919 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 15 C ) B.C920 0.020 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 16 ? . X.RTP3832 --- modified,~C3'-endo,non-stack,ss-non-loop,cap-donor **************************************************************************** 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-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 10 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions