**************************************************************************** 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=4jcy.pdb -o=4jcy.out File name: 4jcy.pdb no. of DNA/RNA chains: 2 [C=21,D=21] no. of nucleotides: 42 no. of atoms: 2755 no. of waters: 402 no. of metals: 0 **************************************************************************** List of 21 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DA1 D.DT21 A-T WC 20-XX cWW cW-W 2 C.DA2 D.DT20 A-T WC 20-XX cWW cW-W 3 C.DA3 D.DT19 A-T WC 20-XX cWW cW-W 4 C.DC4 D.DG18 C-G WC 19-XIX cWW cW-W 5 C.DT5 D.DA17 T-A WC 20-XX cWW cW-W 6 C.DA6 D.DT16 A-T WC 20-XX cWW cW-W 7 C.DA7 D.DT15 A-T WC 20-XX cWW cW-W 8 C.DG8 D.DC14 G-C WC 19-XIX cWW cW-W 9 C.DA9 D.DT13 A-T WC 20-XX cWW cW-W 10 C.DA10 D.DT12 A-T WC 20-XX cWW cW-W 11 C.DA11 D.DT11 A-T WC 20-XX cWW cW-W 12 C.DA12 D.DT10 A-T WC 20-XX cWW cW-W 13 C.DT13 D.DA9 T-A WC 20-XX cWW cW-W 14 C.DC14 D.DG8 C-G WC 19-XIX cWW cW-W 15 C.DT15 D.DA7 T-A WC 20-XX cWW cW-W 16 C.DT16 D.DA6 T-A WC 20-XX cWW cW-W 17 C.DA17 D.DT5 A-T WC 20-XX cWW cW-W 18 C.DG18 D.DC4 G-C WC 19-XIX cWW cW-W 19 C.DC19 D.DG3 C-G WC 19-XIX cWW cW-W 20 C.DA20 D.DT2 A-T WC 20-XX cWW cW-W 21 C.DA21 D.DT1 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[1] bps=21 strand-1 5'-AAACTAAGAAAATCTTAGCAA-3' bp-type ||||||||||||||||||||| strand-2 3'-TTTGATTCTTTTAGAATCGTT-5' helix-form BB..BBBBBBBBBBBB..BB 1 C.DA1 D.DT21 A-T WC 20-XX cWW cW-W 2 C.DA2 D.DT20 A-T WC 20-XX cWW cW-W 3 C.DA3 D.DT19 A-T WC 20-XX cWW cW-W 4 C.DC4 D.DG18 C-G WC 19-XIX cWW cW-W 5 C.DT5 D.DA17 T-A WC 20-XX cWW cW-W 6 C.DA6 D.DT16 A-T WC 20-XX cWW cW-W 7 C.DA7 D.DT15 A-T WC 20-XX cWW cW-W 8 C.DG8 D.DC14 G-C WC 19-XIX cWW cW-W 9 C.DA9 D.DT13 A-T WC 20-XX cWW cW-W 10 C.DA10 D.DT12 A-T WC 20-XX cWW cW-W 11 C.DA11 D.DT11 A-T WC 20-XX cWW cW-W 12 C.DA12 D.DT10 A-T WC 20-XX cWW cW-W 13 C.DT13 D.DA9 T-A WC 20-XX cWW cW-W 14 C.DC14 D.DG8 C-G WC 19-XIX cWW cW-W 15 C.DT15 D.DA7 T-A WC 20-XX cWW cW-W 16 C.DT16 D.DA6 T-A WC 20-XX cWW cW-W 17 C.DA17 D.DT5 A-T WC 20-XX cWW cW-W 18 C.DG18 D.DC4 G-C WC 19-XIX cWW cW-W 19 C.DC19 D.DG3 C-G WC 19-XIX cWW cW-W 20 C.DA20 D.DT2 A-T WC 20-XX cWW cW-W 21 C.DA21 D.DT1 A-T WC 20-XX 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=21 strand-1 5'-AAACTAAGAAAATCTTAGCAA-3' bp-type ||||||||||||||||||||| strand-2 3'-TTTGATTCTTTTAGAATCGTT-5' helix-form BB..BBBBBBBBBBBB..BB 1 C.DA1 D.DT21 A-T WC 20-XX cWW cW-W 2 C.DA2 D.DT20 A-T WC 20-XX cWW cW-W 3 C.DA3 D.DT19 A-T WC 20-XX cWW cW-W 4 C.DC4 D.DG18 C-G WC 19-XIX cWW cW-W 5 C.DT5 D.DA17 T-A WC 20-XX cWW cW-W 6 C.DA6 D.DT16 A-T WC 20-XX cWW cW-W 7 C.DA7 D.DT15 A-T WC 20-XX cWW cW-W 8 C.DG8 D.DC14 G-C WC 19-XIX cWW cW-W 9 C.DA9 D.DT13 A-T WC 20-XX cWW cW-W 10 C.DA10 D.DT12 A-T WC 20-XX cWW cW-W 11 C.DA11 D.DT11 A-T WC 20-XX cWW cW-W 12 C.DA12 D.DT10 A-T WC 20-XX cWW cW-W 13 C.DT13 D.DA9 T-A WC 20-XX cWW cW-W 14 C.DC14 D.DG8 C-G WC 19-XIX cWW cW-W 15 C.DT15 D.DA7 T-A WC 20-XX cWW cW-W 16 C.DT16 D.DA6 T-A WC 20-XX cWW cW-W 17 C.DA17 D.DT5 A-T WC 20-XX cWW cW-W 18 C.DG18 D.DC4 G-C WC 19-XIX cWW cW-W 19 C.DC19 D.DG3 C-G WC 19-XIX cWW cW-W 20 C.DA20 D.DT2 A-T WC 20-XX cWW cW-W 21 C.DA21 D.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4jcy nts=42 [whole] AAACTAAGAAAATCTTAGCAA&TTGCTAAGATTTTCTTAGTTT (((((((((((((((((((((&))))))))))))))))))))) >4jcy-C #1 nts=21 3.00(0.71) [chain] DNA AAACTAAGAAAATCTTAGCAA ((((((((((((((((((((( >4jcy-D #2 nts=21 3.00(0.70) [chain] DNA TTGCTAAGATTTTCTTAGTTT ))))))))))))))))))))) **************************************************************************** Summary of structural features of 42 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 ( C.DA1 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 A ( C.DA2 0.003 anti,BI,canonical,non-pair-contact,helix,stem 3 A ( C.DA3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 C ( C.DC4 0.002 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 5 T ( C.DT5 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 A ( C.DA6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 A ( C.DA7 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 8 G ( C.DG8 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 A ( C.DA9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( C.DA10 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 A ( C.DA11 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 A ( C.DA12 0.003 anti,BI,canonical,non-pair-contact,helix,stem 13 T ( C.DT13 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 C ( C.DC14 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 15 T ( C.DT15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 16 T ( C.DT16 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 A ( C.DA17 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 G ( C.DG18 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 19 C ( C.DC19 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 A ( C.DA20 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 A ( C.DA21 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 22 T ) D.DT1 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 23 T ) D.DT2 0.004 anti,BI,canonical,non-pair-contact,helix,stem 24 G ) D.DG3 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 C ) D.DC4 0.002 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 26 T ) D.DT5 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 A ) D.DA6 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 A ) D.DA7 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 29 G ) D.DG8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 A ) D.DA9 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 T ) D.DT10 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 32 T ) D.DT11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 33 T ) D.DT12 0.002 anti,BI,canonical,non-pair-contact,helix,stem 34 T ) D.DT13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 35 C ) D.DC14 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 36 T ) D.DT15 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 37 T ) D.DT16 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 38 A ) D.DA17 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 39 G ) D.DG18 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 40 T ) D.DT19 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 41 T ) D.DT20 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 42 T ) D.DT21 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 7 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