**************************************************************************** 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=2loa.pdb -o=2loa.out File name: 2loa.pdb no. of DNA/RNA chains: 1 [A=10] no. of nucleotides: 10 no. of atoms: 365 no. of waters: 0 no. of metals: 1 [Zn=1] **************************************************************************** List of 4 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG2 A.DC11 G-C WC 19-XIX cWW cW-W 2 A.DC3 A.DG10 C-G WC 19-XIX cWW cW-W 3 A.DC4 A.DG8 C-G WC 19-XIX cWW cW-W 4 A.DG5 A.DA7 G-A Sheared 11-XI tSH tm-M **************************************************************************** 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=4 strand-1 5'-GCCG-3' bp-type |||. strand-2 3'-CGGA-5' helix-form .x. 1 A.DG2 A.DC11 G-C WC 19-XIX cWW cW-W 2 A.DC3 A.DG10 C-G WC 19-XIX cWW cW-W 3 A.DC4 A.DG8 C-G WC 19-XIX cWW cW-W 4 A.DG5 A.DA7 G-A Sheared 11-XI tSH tm-M **************************************************************************** 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=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 A.DG2 A.DC11 G-C WC 19-XIX cWW cW-W 2 A.DC3 A.DG10 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- [#1] -1 A.DC4 A.DG8 C-G WC 19-XIX 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=2 GG A.DG8,A.DG10 2 nts=4 CCGC A.DC3,A.DC4,A.DG5,A.DC6 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 AT A.DA7,A.DT9 **************************************************************************** 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 hairpin loop 1 hairpin loop: nts=5; [3]; linked by [#-1] summary: [1] 3 [A.4 A.8] 1 nts=5 CGCAG A.DC4,A.DG5,A.DC6,A.DA7,A.DG8 nts=3 GCA A.DG5,A.DC6,A.DA7 **************************************************************************** List of 1 bulge 1 bulge: nts=5; [0,1]; linked by [#1,#-1] summary: [2] 0 1 [A.3 A.10 A.4 A.8] 2 1 nts=5 CCGTG A.DC3,A.DC4,A.DG8,A.DT9,A.DG10 nts=0 nts=1 T A.DT9 **************************************************************************** List of 2 splayed-apart dinucleotides 1 A.DG8 A.DT9 angle=98 distance=14.2 ratio=0.76 2 A.DT9 A.DG10 angle=93 distance=14.5 ratio=0.72 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=3 GTG A.DG8,A.DT9,A.DG10 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2loa nts=10 [whole] GCCGCAGTGC (((...).)) >2loa-A #1 nts=10 0.93(2.09) [chain] DNA GCCGCAGTGC (((...).)) **************************************************************************** Summary of structural features of 10 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 G ( A.DG2 0.036 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 2 C ( A.DC3 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,bulge 3 C ( A.DC4 0.011 anti,~C2'-endo,isolated-canonical,non-pair-contact,helix,hairpin-loop,bulge 4 G . A.DG5 0.036 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 5 C . A.DC6 0.011 anti,~C2'-endo,non-pair-contact,hairpin-loop 6 A . A.DA7 0.014 ~C2'-endo,BI,non-stack,non-canonical,helix-end,hairpin-loop 7 G ) A.DG8 0.036 anti,isolated-canonical,non-pair-contact,helix,hairpin-loop,bulge,splayed-apart 8 T . A.DT9 0.021 turn,anti,~C3'-endo,non-stack,bulge,splayed-apart 9 G ) A.DG10 0.036 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,bulge,splayed-apart 10 C ) A.DC11 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 11 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-hairpins.pdb -- an ensemble of hairpin loops 5 dssr-bulges.pdb -- an ensemble of bulges 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-splays.pdb -- an ensemble of splayed-apart units 11 dssr-stacks.pdb -- an ensemble of base stacks