**************************************************************************** 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=1feq.pdb -o=1feq.out File name: 1feq.pdb no. of DNA/RNA chains: 1 [A=17] no. of nucleotides: 17 no. of atoms: 554 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 T6A-a 1 A.T6A37 **************************************************************************** List of 6 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G27 A.C43 G-C WC 19-XIX cWW cW-W 2 A.C28 A.G42 C-G WC 19-XIX cWW cW-W 3 A.A29 A.U41 A-U WC 20-XX cWW cW-W 4 A.G30 A.C40 G-C WC 19-XIX cWW cW-W 5 A.A31 A.U39 A-U WC 20-XX cWW cW-W 6 A.C32 A.A38 C-A -- -- 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=6 strand-1 5'-GCAGAC-3' bp-type |||||. strand-2 3'-CGUCUA-5' helix-form ..... 1 A.G27 A.C43 G-C WC 19-XIX cWW cW-W 2 A.C28 A.G42 C-G WC 19-XIX cWW cW-W 3 A.A29 A.U41 A-U WC 20-XX cWW cW-W 4 A.G30 A.C40 G-C WC 19-XIX cWW cW-W 5 A.A31 A.U39 A-U WC 20-XX cWW cW-W 6 A.C32 A.A38 C-A -- -- 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=5 strand-1 5'-GCAGA-3' bp-type ||||| strand-2 3'-CGUCU-5' helix-form .... 1 A.G27 A.C43 G-C WC 19-XIX cWW cW-W 2 A.C28 A.G42 C-G WC 19-XIX cWW cW-W 3 A.A29 A.U41 A-U WC 20-XX cWW cW-W 4 A.G30 A.C40 G-C WC 19-XIX cWW cW-W 5 A.A31 A.U39 A-U WC 20-XX 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=3 ACU A.A31,A.C32,A.U33 2 nts=3 aAU A.T6A37,A.A38,A.U39 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 UUUC A.U34,A.U35,A.U36,A.C40 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.A38 A.T6A37 3.19 **************************************************************************** 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 hairpin loop 1 hairpin loop: nts=9; [7]; linked by [#1] summary: [1] 7 [A.31 A.39] 5 nts=9 ACUUUUaAU A.A31,A.C32,A.U33,A.U34,A.U35,A.U36,A.T6A37,A.A38,A.U39 nts=7 CUUUUaA A.C32,A.U33,A.U34,A.U35,A.U36,A.T6A37,A.A38 **************************************************************************** List of 2 splayed-apart dinucleotides 1 A.U34 A.U35 angle=172 distance=17.7 ratio=1.00 2 A.U36 A.T6A37 angle=103 distance=16.4 ratio=0.78 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 UU A.U34,A.U35 2 nts=2 Ua A.U36,A.T6A37 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1feq nts=17 [whole] GCAGACUUUUaAUCUGC (((((.......))))) >1feq-A #1 nts=17 0.40(2.26) [chain] RNA GCAGACUUUUaAUCUGC (((((.......))))) **************************************************************************** Summary of structural features of 17 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.G27 0.024 anti,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( A.C28 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 3 A ( A.A29 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( A.G30 0.024 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 5 A ( A.A31 0.019 anti,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 6 C . A.C32 0.028 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 7 U . A.U33 0.032 anti,~C2'-endo,non-pair-contact,hairpin-loop 8 U . A.U34 0.023 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,splayed-apart 9 U . A.U35 0.024 syn,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 10 U . A.U36 0.022 anti,~C2'-endo,non-stack,hairpin-loop,splayed-apart 11 a . A.T6A37 0.018 modified,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,splayed-apart 12 A . A.A38 0.040 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-donor 13 U ) A.U39 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop 14 C ) A.C40 0.013 anti,~C3'-endo,BI,non-stack,canonical,helix,stem 15 U ) A.U41 0.023 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 G ) A.G42 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 17 C ) A.C43 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 11 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-hairpins.pdb -- an ensemble of hairpin 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-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions