**************************************************************************** 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=1t03.pdb -o=1t03.out File name: 1t03.pdb no. of DNA/RNA chains: 2 [P=20,T=23] no. of nucleotides: 43 no. of atoms: 12218 no. of waters: 0 no. of metals: 1 [Mg=1] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 MRG-g 1 P.MRG817 2 TFO-a 1 P.TFO822 **************************************************************************** List of 19 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DG707 P.DC821 G-C WC 19-XIX cWW cW-W 2 T.DG708 P.DC820 G-C WC 19-XIX cWW cW-W 3 T.DC709 P.DG819 C-G WC 19-XIX cWW cW-W 4 T.DG710 P.DC818 G-C WC 19-XIX cWW cW-W 5 T.DC711 P.MRG817 C-g WC 19-XIX cWW cW-W 6 T.DC712 P.DG816 C-G WC 19-XIX cWW cW-W 7 T.DC713 P.DG815 C-G WC 19-XIX cWW cW-W 8 T.DG714 P.DC814 G-C WC 19-XIX cWW cW-W 9 T.DA715 P.DT813 A-T WC 20-XX cWW cW-W 10 T.DA716 P.DT812 A-T WC 20-XX cWW cW-W 11 T.DC717 P.DG811 C-G WC 19-XIX cWW cW-W 12 T.DA718 P.DT810 A-T WC 20-XX cWW cW-W 13 T.DG719 P.DC809 G-C WC 19-XIX cWW cW-W 14 T.DG720 P.DC808 G-C WC 19-XIX cWW cW-W 15 T.DG721 P.DC807 G-C WC 19-XIX cWW cW-W 16 T.DA722 P.DT806 A-T WC 20-XX cWW cW-W 17 T.DC723 P.DG805 C-G WC 19-XIX cWW cW-W 18 T.DT724 P.DA804 T-A WC 20-XX cWW cW-W 19 T.DG725 P.DC803 G-C 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=19 strand-1 5'-GGCGCCCGAACAGGGACTG-3' bp-type ||||||||||||||||||| strand-2 3'-CCGCgGGCTTGTCCCTGAC-5' helix-form AA.A..BBB.BBBBBBBB 1 T.DG707 P.DC821 G-C WC 19-XIX cWW cW-W 2 T.DG708 P.DC820 G-C WC 19-XIX cWW cW-W 3 T.DC709 P.DG819 C-G WC 19-XIX cWW cW-W 4 T.DG710 P.DC818 G-C WC 19-XIX cWW cW-W 5 T.DC711 P.MRG817 C-g WC 19-XIX cWW cW-W 6 T.DC712 P.DG816 C-G WC 19-XIX cWW cW-W 7 T.DC713 P.DG815 C-G WC 19-XIX cWW cW-W 8 T.DG714 P.DC814 G-C WC 19-XIX cWW cW-W 9 T.DA715 P.DT813 A-T WC 20-XX cWW cW-W 10 T.DA716 P.DT812 A-T WC 20-XX cWW cW-W 11 T.DC717 P.DG811 C-G WC 19-XIX cWW cW-W 12 T.DA718 P.DT810 A-T WC 20-XX cWW cW-W 13 T.DG719 P.DC809 G-C WC 19-XIX cWW cW-W 14 T.DG720 P.DC808 G-C WC 19-XIX cWW cW-W 15 T.DG721 P.DC807 G-C WC 19-XIX cWW cW-W 16 T.DA722 P.DT806 A-T WC 20-XX cWW cW-W 17 T.DC723 P.DG805 C-G WC 19-XIX cWW cW-W 18 T.DT724 P.DA804 T-A WC 20-XX cWW cW-W 19 T.DG725 P.DC803 G-C 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=19 strand-1 5'-GGCGCCCGAACAGGGACTG-3' bp-type ||||||||||||||||||| strand-2 3'-CCGCgGGCTTGTCCCTGAC-5' helix-form AA.A..BBB.BBBBBBBB 1 T.DG707 P.DC821 G-C WC 19-XIX cWW cW-W 2 T.DG708 P.DC820 G-C WC 19-XIX cWW cW-W 3 T.DC709 P.DG819 C-G WC 19-XIX cWW cW-W 4 T.DG710 P.DC818 G-C WC 19-XIX cWW cW-W 5 T.DC711 P.MRG817 C-g WC 19-XIX cWW cW-W 6 T.DC712 P.DG816 C-G WC 19-XIX cWW cW-W 7 T.DC713 P.DG815 C-G WC 19-XIX cWW cW-W 8 T.DG714 P.DC814 G-C WC 19-XIX cWW cW-W 9 T.DA715 P.DT813 A-T WC 20-XX cWW cW-W 10 T.DA716 P.DT812 A-T WC 20-XX cWW cW-W 11 T.DC717 P.DG811 C-G WC 19-XIX cWW cW-W 12 T.DA718 P.DT810 A-T WC 20-XX cWW cW-W 13 T.DG719 P.DC809 G-C WC 19-XIX cWW cW-W 14 T.DG720 P.DC808 G-C WC 19-XIX cWW cW-W 15 T.DG721 P.DC807 G-C WC 19-XIX cWW cW-W 16 T.DA722 P.DT806 A-T WC 20-XX cWW cW-W 17 T.DC723 P.DG805 C-G WC 19-XIX cWW cW-W 18 T.DT724 P.DA804 T-A WC 20-XX cWW cW-W 19 T.DG725 P.DC803 G-C 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 GW T.DG703,A.TRP24 2 nts=2 AT T.DA705,T.DT706 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 Ca T.DC704,P.TFO822 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=4 GCAT T.DG703,T.DC704,T.DA705,T.DT706 2 nts=1 a P.TFO822 **************************************************************************** List of 2 splayed-apart dinucleotides 1 T.DC704 T.DA705 angle=90 distance=14.5 ratio=0.71 2 P.DC821 P.TFO822 angle=144 distance=18.3 ratio=0.95 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 CA T.DC704,T.DA705 2 nts=2 Ca P.DC821,P.TFO822 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1t03 nts=43 [whole] GCATGGCGCCCGAACAGGGACTG&CAGTCCCTGTTCGGgCGCCa ....(((((((((((((((((((&))))))))))))))))))). >1t03-T #1 nts=23 2.73(0.96) [chain] DNA GCATGGCGCCCGAACAGGGACTG ....((((((((((((((((((( >1t03-P #2 nts=20 3.36(1.29) [chain] DNA CAGTCCCTGTTCGGgCGCCa ))))))))))))))))))). **************************************************************************** Summary of structural features of 43 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 . T.DG703 0.008 anti,~C2'-endo,ss-non-loop 2 C . T.DC704 0.011 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 3 A . T.DA705 0.021 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 4 T . T.DT706 0.012 ~C2'-endo,BI,non-pair-contact,ss-non-loop 5 G ( T.DG707 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 6 G ( T.DG708 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 7 C ( T.DC709 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 G ( T.DG710 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 9 C ( T.DC711 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 10 C ( T.DC712 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 C ( T.DC713 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ( T.DG714 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 13 A ( T.DA715 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 A ( T.DA716 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 C ( T.DC717 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 A ( T.DA718 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 G ( T.DG719 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 G ( T.DG720 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 G ( T.DG721 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 A ( T.DA722 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 21 C ( T.DC723 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ( T.DT724 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 G ( T.DG725 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 24 C ) P.DC803 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 25 A ) P.DA804 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 G ) P.DG805 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 T ) P.DT806 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 C ) P.DC807 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 C ) P.DC808 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 C ) P.DC809 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 T ) P.DT810 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 32 G ) P.DG811 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 33 T ) P.DT812 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 34 T ) P.DT813 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 35 C ) P.DC814 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 36 G ) P.DG815 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 37 G ) P.DG816 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 38 g ) P.MRG817 0.007 modified,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 39 C ) P.DC818 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 40 G ) P.DG819 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 41 C ) P.DC820 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 42 C ) P.DC821 0.023 anti,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 43 a . P.TFO822 0.079 modified,anti,non-stack,ss-non-loop,splayed-apart **************************************************************************** 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-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