**************************************************************************** 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=5uhd.pdb -o=5uhd.out File name: 5uhd.pdb no. of DNA/RNA chains: 2 [G=14,H=23] no. of nucleotides: 37 no. of atoms: 26022 no. of waters: 0 no. of metals: 3 [Mg=1,Zn=2] **************************************************************************** List of 9 base pairs nt1 nt2 bp name Saenger LW DSSR 1 H.DT15 G.DA13 T-A WC 20-XX cWW cW-W 2 H.DC16 G.DG12 C-G WC 19-XIX cWW cW-W 3 H.DA17 G.DT11 A-T WC 20-XX cWW cW-W 4 H.DC18 G.DG10 C-G WC 19-XIX cWW cW-W 5 H.DG19 G.DC9 G-C WC 19-XIX cWW cW-W 6 H.DG20 G.DC8 G-C WC 19-XIX cWW cW-W 7 H.DA21 G.DT7 A-T WC 20-XX cWW cW-W 8 H.DT22 G.DA6 T-A WC 20-XX cWW cW-W 9 H.DG23 G.DC5 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=9 strand-1 5'-TCACGGATG-3' bp-type ||||||||| strand-2 3'-AGTGCCTAC-5' helix-form .B.BBB.. 1 H.DT15 G.DA13 T-A WC 20-XX cWW cW-W 2 H.DC16 G.DG12 C-G WC 19-XIX cWW cW-W 3 H.DA17 G.DT11 A-T WC 20-XX cWW cW-W 4 H.DC18 G.DG10 C-G WC 19-XIX cWW cW-W 5 H.DG19 G.DC9 G-C WC 19-XIX cWW cW-W 6 H.DG20 G.DC8 G-C WC 19-XIX cWW cW-W 7 H.DA21 G.DT7 A-T WC 20-XX cWW cW-W 8 H.DT22 G.DA6 T-A WC 20-XX cWW cW-W 9 H.DG23 G.DC5 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=9 strand-1 5'-TCACGGATG-3' bp-type ||||||||| strand-2 3'-AGTGCCTAC-5' helix-form .B.BBB.. 1 H.DT15 G.DA13 T-A WC 20-XX cWW cW-W 2 H.DC16 G.DG12 C-G WC 19-XIX cWW cW-W 3 H.DA17 G.DT11 A-T WC 20-XX cWW cW-W 4 H.DC18 G.DG10 C-G WC 19-XIX cWW cW-W 5 H.DG19 G.DC9 G-C WC 19-XIX cWW cW-W 6 H.DG20 G.DC8 G-C WC 19-XIX cWW cW-W 7 H.DA21 G.DT7 A-T WC 20-XX cWW cW-W 8 H.DT22 G.DA6 T-A WC 20-XX cWW cW-W 9 H.DG23 G.DC5 G-C WC 19-XIX cWW cW-W **************************************************************************** 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 EA C.GLU466,G.DA13 2 nts=2 YA F.TYR346,H.DA2 3 nts=2 WT F.TRP350,H.DT1 4 nts=2 CT H.DC12,H.DT13 5 nts=3 TAA H.DT3,H.DA4,H.DA5 6 nts=4 GGAG H.DG8,H.DG9,H.DA10,H.DG11 7 nts=5 GTCGA G.DG14,G.DT15,G.DC16,G.DG17,G.DA18 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 TGG H.DT6,H.DG7,H.DG14 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other OG1@F.THR348 H.DA5 3.36 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=14 TATAATGGGAGCTG H.DT1,H.DA2,H.DT3,H.DA4,H.DA5,H.DT6,H.DG7,H.DG8,H.DG9,H.DA10,H.DG11,H.DC12,H.DT13,H.DG14 2 nts=5 GTCGA G.DG14,G.DT15,G.DC16,G.DG17,G.DA18 **************************************************************************** List of 7 splayed-apart dinucleotides 1 H.DT1 H.DA2 angle=88 distance=13.4 ratio=0.70 2 H.DA2 H.DT3 angle=145 distance=18.8 ratio=0.95 3 H.DA5 H.DT6 angle=87 distance=13.7 ratio=0.69 4 H.DT6 H.DG7 angle=103 distance=15.9 ratio=0.78 5 H.DT13 H.DG14 angle=101 distance=16.6 ratio=0.77 6 H.DG14 H.DT15 angle=122 distance=17.1 ratio=0.87 7 G.DA13 G.DG14 angle=126 distance=16.8 ratio=0.89 ---------------------------------------------------------------- Summary of 4 splayed-apart units 1 nts=3 TAT H.DT1,H.DA2,H.DT3 2 nts=3 ATG H.DA5,H.DT6,H.DG7 3 nts=3 TGT H.DT13,H.DG14,H.DT15 4 nts=2 AG G.DA13,G.DG14 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5uhd nts=37 [whole] TATAATGGGAGCTGTCACGGATG&CATCCGTGAGTCGA ..............(((((((((&)))))))))..... >5uhd-H #1 nts=23 2.49(2.01) [chain] DNA TATAATGGGAGCTGTCACGGATG ..............((((((((( >5uhd-G #2 nts=14 3.56(0.99) [chain] DNA CATCCGTGAGTCGA )))))))))..... **************************************************************************** Summary of structural features of 37 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 T . H.DT1 0.005 syn,~C2'-endo,ss-non-loop,splayed-apart 2 A . H.DA2 0.004 anti,~C2'-endo,BII,ss-non-loop,splayed-apart 3 T . H.DT3 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 4 A . H.DA4 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 5 A . H.DA5 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-acceptor,phosphate,splayed-apart 6 T . H.DT6 0.002 anti,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 7 G . H.DG7 0.004 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 8 G . H.DG8 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 9 G . H.DG9 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate 10 A . H.DA10 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 11 G . H.DG11 0.004 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 12 C . H.DC12 0.005 anti,BI,non-pair-contact,ss-non-loop,phosphate 13 T . H.DT13 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 14 G . H.DG14 0.004 anti,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 15 T ( H.DT15 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 16 C ( H.DC16 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 17 A ( H.DA17 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 C ( H.DC18 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 G ( H.DG19 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 G ( H.DG20 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 21 A ( H.DA21 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 22 T ( H.DT22 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 G ( H.DG23 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 24 C ) G.DC5 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 25 A ) G.DA6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 T ) G.DT7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 C ) G.DC8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 28 C ) G.DC9 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 G ) G.DG10 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 T ) G.DT11 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 31 G ) G.DG12 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 32 A ) G.DA13 0.004 anti,~C3'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 33 G . G.DG14 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 34 T . G.DT15 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 35 C . G.DC16 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 36 G . G.DG17 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 37 A . G.DA18 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop **************************************************************************** List of 10 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 10 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions