**************************************************************************** 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=2lqz.pdb -o=2lqz.out File name: 2lqz.pdb no. of DNA/RNA chains: 1 [A=27] no. of nucleotides: 27 no. of atoms: 859 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.G1 A.C27 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C26 G-C WC 19-XIX cWW cW-W 3 A.A3 A.U25 A-U WC 20-XX cWW cW-W 4 A.C4 A.G24 C-G WC 19-XIX cWW cW-W 5 A.U5 A.A9 U+A -- -- tSW tm+W 6 A.U5 A.A23 U-A WC 20-XX cWW cW-W 7 A.A9 A.G24 A-G -- -- cWS cW-m 8 A.U10 A.A21 U-A WC 20-XX cWW cW-W 9 A.U11 A.A20 U-A WC 20-XX cWW cW-W 10 A.G12 A.C19 G-C WC 19-XIX cWW cW-W 11 A.C13 A.G18 C-G WC 19-XIX cWW cW-W 12 A.U14 A.G17 U+G -- -- tSW tm+W **************************************************************************** List of 2 multiplets 1 nts=3 CAG A.C4,A.A9,A.G24 2 nts=3 UAA A.U5,A.A9,A.A23 **************************************************************************** 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[2] bps=10 strand-1 5'-GGACUUUGCU-3' bp-type |||||||||. strand-2 3'-CCUGAAACGG-5' helix-form A...x.AA. 1 A.G1 A.C27 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C26 G-C WC 19-XIX cWW cW-W 3 A.A3 A.U25 A-U WC 20-XX cWW cW-W 4 A.C4 A.G24 C-G WC 19-XIX cWW cW-W 5 A.U5 A.A23 U-A WC 20-XX cWW cW-W 6 A.U10 A.A21 U-A WC 20-XX cWW cW-W 7 A.U11 A.A20 U-A WC 20-XX cWW cW-W 8 A.G12 A.C19 G-C WC 19-XIX cWW cW-W 9 A.C13 A.G18 C-G WC 19-XIX cWW cW-W 10 A.U14 A.G17 U+G -- -- tSW tm+W **************************************************************************** List of 2 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=5 strand-1 5'-GGACU-3' bp-type ||||| strand-2 3'-CCUGA-5' helix-form A... 1 A.G1 A.C27 G-C WC 19-XIX cWW cW-W 2 A.G2 A.C26 G-C WC 19-XIX cWW cW-W 3 A.A3 A.U25 A-U WC 20-XX cWW cW-W 4 A.C4 A.G24 C-G WC 19-XIX cWW cW-W 5 A.U5 A.A23 U-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=4 strand-1 5'-UUGC-3' bp-type |||| strand-2 3'-AACG-5' helix-form .AA 1 A.U10 A.A21 U-A WC 20-XX cWW cW-W 2 A.U11 A.A20 U-A WC 20-XX cWW cW-W 3 A.G12 A.C19 G-C WC 19-XIX cWW cW-W 4 A.C13 A.G18 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 3 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 UU A.U5,A.U6 2 nts=2 GG A.G17,A.G18 3 nts=3 CUC A.C13,A.U14,A.C16 **************************************************************************** Nucleotides not involved in stacking interactions nts=6 CCAUUA A.C7,A.C8,A.A9,A.U10,A.U15,A.A22 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O2'@A.A9 A.U10 2.78 2 sugar O2'@A.U10 A.A22 2.70 **************************************************************************** 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=6; [4]; linked by [#2] summary: [1] 4 [A.13 A.18] 4 nts=6 CUUCGG A.C13,A.U14,A.U15,A.C16,A.G17,A.G18 nts=4 UUCG A.U14,A.U15,A.C16,A.G17 **************************************************************************** List of 1 internal loop 1 asymmetric internal loop: nts=9; [4,1]; linked by [#1,#2] summary: [2] 4 1 [A.5 A.23 A.10 A.21] 5 4 nts=9 UUCCAUAAA A.U5,A.U6,A.C7,A.C8,A.A9,A.U10,A.A21,A.A22,A.A23 nts=4 UCCA A.U6,A.C7,A.C8,A.A9 nts=1 A A.A22 **************************************************************************** List of 1 A-minor motif (types I, II, or X) 1 type=X A|U-A A.A9|A.U5,A.A23 WC +A.U5 H-bonds[1]: "N6(amino)-O2(carbonyl)[2.67]" -A.A23 H-bonds[0]: "" **************************************************************************** List of 3 splayed-apart dinucleotides 1 A.U6 A.C7 angle=153 distance=20.1 ratio=0.97 2 A.C7 A.C8 angle=141 distance=19.4 ratio=0.94 3 A.U14 A.U15 angle=106 distance=13.9 ratio=0.80 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 UCC A.U6,A.C7,A.C8 2 nts=2 UU A.U14,A.U15 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2lqz nts=27 [whole] GGACUUCCAUUGCUUCGGCAAAAGUCC (((((....((((....)))).))))) >2lqz-A #1 nts=27 0.06(2.86) [chain] RNA GGACUUCCAUUGCUUCGGCAAAAGUCC (((((....((((....)))).))))) **************************************************************************** Summary of structural features of 27 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.G1 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 G ( A.G2 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 A ( A.A3 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 C ( A.C4 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 5 U ( A.U5 0.004 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 6 U . A.U6 0.003 anti,~C2'-endo,non-pair-contact,internal-loop,splayed-apart 7 C . A.C7 0.001 turn,anti,~C3'-endo,non-stack,internal-loop,splayed-apart 8 C . A.C8 0.002 turn,anti,~C3'-endo,non-stack,non-pair-contact,internal-loop,splayed-apart 9 A . A.A9 0.002 anti,~C2'-endo,BII,non-stack,non-canonical,multiplet,internal-loop,A-minor,cap-donor 10 U ( A.U10 0.003 anti,~C3'-endo,non-stack,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,cap-donor,cap-acceptor 11 U ( A.U11 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 12 G ( A.G12 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 C ( A.C13 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 14 U . A.U14 0.003 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart 15 U . A.U15 0.003 turn,anti,~C2'-endo,non-stack,non-pair-contact,hairpin-loop,phosphate,splayed-apart 16 C . A.C16 0.003 turn,anti,~C2'-endo,non-pair-contact,hairpin-loop 17 G . A.G17 0.004 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 18 G ) A.G18 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 19 C ) A.C19 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 20 A ) A.A20 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 21 A ) A.A21 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 22 A . A.A22 0.004 turn,syn,~C3'-endo,non-stack,internal-loop,cap-acceptor 23 A ) A.A23 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,multiplet,internal-loop,A-minor 24 G ) A.G24 0.004 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,multiplet 25 U ) A.U25 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 C ) A.C26 0.001 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 C ) A.C27 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 14 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-hairpins.pdb -- an ensemble of hairpin loops 6 dssr-iloops.pdb -- an ensemble of internal loops 7 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 8 dssr-2ndstrs.ct -- secondary structure in connectivity table format 9 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 10 dssr-torsions.txt -- backbone torsion angles and suite names 11 dssr-splays.pdb -- an ensemble of splayed-apart units 12 dssr-Aminors.pdb -- an ensemble of A minor motifs (types I and II) 13 dssr-stacks.pdb -- an ensemble of base stacks 14 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions