**************************************************************************** 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=4e58.pdb -o=4e58.out File name: 4e58.pdb no. of DNA/RNA chains: 3 [C=8,D=8,E=7] no. of nucleotides: 23 no. of atoms: 510 no. of waters: 14 no. of metals: 0 **************************************************************************** List of 1 type of 3 modified nucleotides nt count list 1 LCG-g 3 C.LCG4,E.LCG4,D.LCG4 **************************************************************************** List of 8 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.C3 D.G7 C-G WC 19-XIX cWW cW-W 2 C.LCG4 D.C6 g-C WC 19-XIX cWW cW-W 3 C.C5 D.C5 C-C -- -- cWW cW-W 4 C.C6 D.LCG4 C-g WC 19-XIX cWW cW-W 5 C.G7 D.C3 G-C WC 19-XIX cWW cW-W 6 E.G1 D.C2 G-C WC 19-XIX cWW cW-W 7 E.C2 D.G1 C-G WC 19-XIX cWW cW-W 8 D.G7 D.C8 G-C Platform -- cSS cm-m **************************************************************************** List of 1 multiplet 1 nts=3 CGC C.C3,D.G7,D.C8 **************************************************************************** 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=7 strand-1 5'-CgCCGGC-3' bp-type ||.|||| strand-2 3'-GCCgCCG-5' helix-form A...x. 1 C.C3 D.G7 C-G WC 19-XIX cWW cW-W 2 C.LCG4 D.C6 g-C WC 19-XIX cWW cW-W 3 C.C5 D.C5 C-C -- -- cWW cW-W 4 C.C6 D.LCG4 C-g WC 19-XIX cWW cW-W 5 C.G7 D.C3 G-C WC 19-XIX cWW cW-W 6 E.G1 D.C2 G-C WC 19-XIX cWW cW-W 7 E.C2 D.G1 C-G WC 19-XIX 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=2 strand-1 5'-Cg-3' bp-type || strand-2 3'-GC-5' helix-form A 1 C.C3 D.G7 C-G WC 19-XIX cWW cW-W 2 C.LCG4 D.C6 g-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=2 strand-1 5'-CG-3' bp-type || strand-2 3'-gC-5' helix-form . 1 C.C6 D.LCG4 C-g WC 19-XIX cWW cW-W 2 C.G7 D.C3 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=2 strand-1 5'-GC-3' bp-type || strand-2 3'-CG-5' helix-form . 1 E.G1 D.C2 G-C WC 19-XIX cWW cW-W 2 E.C2 D.G1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#3] **************************************************************************** List of 7 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 GC C.G1,C.C2 2 nts=2 GG C.G7,E.G1 3 nts=2 CC E.C2,E.C3 4 nts=2 CC D.C2,D.C3 5 nts=3 gCC C.LCG4,C.C5,C.C6 6 nts=3 gCC D.LCG4,D.C5,D.C6 7 nts=4 gCCG E.LCG4,E.C5,E.C6,E.G7 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 CC C.C8,D.C8 **************************************************************************** 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 [C.4 D.6 C.6 D.4] 2 2 nts=6 gCCgCC C.LCG4,C.C5,C.C6,D.LCG4,D.C5,D.C6 nts=1 C C.C5 nts=1 C D.C5 **************************************************************************** List of 4 non-loop single-stranded segments 1 nts=2 GC C.G1,C.C2 2 nts=1 C C.C8 3 nts=5 CgCCG E.C3,E.LCG4,E.C5,E.C6,E.G7 4 nts=1 C D.C8 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4e58 nts=23 [whole] GCCgCCGC&GCCgCCG&GCCgCCGC ..((.((.&((.....&)))).)). >4e58-C #1 nts=8 3.35(1.18) [chain] RNA GCCgCCGC ..((.((. >4e58-E #2 nts=7 2.64(0.12) [chain] RNA GCCgCCG ((..... >4e58-D #3 nts=8 2.05(1.27) [chain] RNA GCCgCCGC )))).)). **************************************************************************** Summary of structural features of 23 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 . C.G1 0.011 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 2 C . C.C2 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 3 C ( C.C3 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet 4 g ( C.LCG4 0.010 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 5 C . C.C5 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 6 C ( C.C6 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 7 G ( C.G7 0.025 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 8 C . C.C8 0.011 anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop 9 G ( E.G1 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 10 C ( E.C2 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 11 C . E.C3 0.022 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 12 g . E.LCG4 0.018 modified,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 13 C . E.C5 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 14 C . E.C6 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 15 G . E.G7 0.011 anti,~C3'-endo,non-pair-contact,ss-non-loop 16 G ) D.G1 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 17 C ) D.C2 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 18 C ) D.C3 0.022 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 19 g ) D.LCG4 0.027 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 20 C . D.C5 0.016 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 21 C ) D.C6 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 22 G ) D.G7 0.028 anti,~C2'-endo,BII,canonical,non-canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,multiplet 23 C . D.C8 0.018 anti,~C3'-endo,non-stack,non-canonical,multiplet,ss-non-loop **************************************************************************** List of 10 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-iloops.pdb -- an ensemble of internal loops 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-stacks.pdb -- an ensemble of base stacks