**************************************************************************** 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=4e59.pdb -o=4e59.out File name: 4e59.pdb no. of DNA/RNA chains: 2 [A=7,B=7] no. of nucleotides: 14 no. of atoms: 316 no. of waters: 16 no. of metals: 0 **************************************************************************** List of 5 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 B.C5 G-C WC 19-XIX cWW cW-W 2 A.C2 B.G4 C-G WC 19-XIX cWW cW-W 3 A.C3 B.C3 C-C -- -- cWW cW-W 4 A.G4 B.C2 G-C WC 19-XIX cWW cW-W 5 A.C5 B.G1 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=5 strand-1 5'-GCCGC-3' bp-type ||.|| strand-2 3'-CGCCG-5' helix-form AAAA 1 A.G1 B.C5 G-C WC 19-XIX cWW cW-W 2 A.C2 B.G4 C-G WC 19-XIX cWW cW-W 3 A.C3 B.C3 C-C -- -- cWW cW-W 4 A.G4 B.C2 G-C WC 19-XIX cWW cW-W 5 A.C5 B.G1 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=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G1 B.C5 G-C WC 19-XIX cWW cW-W 2 A.C2 B.G4 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form A 1 A.G4 B.C2 G-C WC 19-XIX cWW cW-W 2 A.C5 B.G1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 4 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 CC B.C2,B.C3 2 nts=3 GCG A.G4,A.C3,B.G4 3 nts=3 CCG A.C5,A.C6,A.G7 4 nts=3 CCG B.C5,B.C6,B.G7 **************************************************************************** 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 [A.2 B.4 A.4 B.2] 2 2 nts=6 CCGCCG A.C2,A.C3,A.G4,B.C2,B.C3,B.G4 nts=1 C A.C3 nts=1 C B.C3 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=2 CG A.C6,A.G7 2 nts=2 CG B.C6,B.G7 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4e59 nts=14 [whole] GCCGCCG&GCCGCCG ((.((..&)).)).. >4e59-A #1 nts=7 2.48(0.09) [chain] RNA GCCGCCG ((.((.. >4e59-B #2 nts=7 2.60(0.11) [chain] RNA GCCGCCG )).)).. **************************************************************************** Summary of structural features of 14 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.G1 0.032 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 C ( A.C2 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 3 C . A.C3 0.019 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 4 G ( A.G4 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 5 C ( A.C5 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 6 C . A.C6 0.028 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 7 G . A.G7 0.038 anti,~C3'-endo,non-pair-contact,ss-non-loop 8 G ) B.G1 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 9 C ) B.C2 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 10 C . B.C3 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 11 G ) B.G4 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 12 C ) B.C5 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 13 C . B.C6 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 14 G . B.G7 0.023 anti,~C3'-endo,non-pair-contact,ss-non-loop **************************************************************************** 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