**************************************************************************** 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=6pmj.pdb -o=6pmj.out File name: 6pmj.pdb no. of DNA/RNA chains: 3 [1=54,2=54,3=3] no. of nucleotides: 111 no. of atoms: 57995 no. of waters: 0 no. of metals: 3 [Mg=1,Zn=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 ATP-a 1 3.ATP1 **************************************************************************** List of 45 base pairs nt1 nt2 bp name Saenger LW DSSR 1 1.DA35 2.DT54 A-T WC 20-XX cWW cW-W 2 1.DG36 2.DC53 G-C WC 19-XIX cWW cW-W 3 1.DC37 2.DG52 C-G WC 19-XIX cWW cW-W 4 1.DA38 2.DT51 A-T WC 20-XX cWW cW-W 5 1.DA39 2.DT50 A-T WC 20-XX cWW cW-W 6 1.DT40 2.DA49 T-A WC 20-XX cWW cW-W 7 1.DA41 2.DT48 A-T WC 20-XX cWW cW-W 8 1.DA42 2.DT47 A-T WC 20-XX cWW cW-W 9 1.DA43 2.DT46 A-T WC 20-XX cWW cW-W 10 1.DG44 2.DC45 G-C WC 19-XIX cWW cW-W 11 1.DT45 2.DA44 T-A WC 20-XX cWW cW-W 12 1.DT46 2.DA43 T-A WC 20-XX cWW cW-W 13 1.DT47 2.DA42 T-A WC 20-XX cWW cW-W 14 1.DC48 2.DG41 C-G WC 19-XIX cWW cW-W 15 1.DT50 2.DA39 T-A ~Wobble -- cWW cW-W 16 1.DT51 2.DA38 T-A -- -- cWW cW-W 17 1.DC52 2.DG37 C-G ~Wobble -- cWW cW-W 18 1.DC53 2.DG36 C-G -- -- cWW cW-W 19 1.DC55 2.DG34 C-G WC 19-XIX cWW cW-W 20 1.DC56 2.DG33 C-G WC 19-XIX cWW cW-W 21 1.DT57 2.DA31 T-A -- -- cWH cW-M 22 1.DT57 2.DA32 T-A WC 20-XX cWW cW-W 23 1.DT58 2.DA31 T-A WC 20-XX cWW cW-W 24 1.DG59 2.DC30 G-C WC 19-XIX cWW cW-W 25 1.DC60 2.DG28 C-G -- -- cWW cW-W 26 1.DC60 2.DG29 C-G WC 19-XIX cWW cW-W 27 1.DC61 2.DG28 C-G WC 19-XIX cWW cW-W 28 1.DG62 2.DC27 G-C WC 19-XIX cWW cW-W 29 1.DT78 2.DA11 T-A WC 20-XX cWW cW-W 30 1.DG79 2.DC10 G-C WC 19-XIX cWW cW-W 31 1.DT80 2.DA8 T-A -- -- cWW cW-W 32 1.DT80 2.DA9 T-A WC 20-XX cWW cW-W 33 1.DT81 2.DA7 T-A -- -- cWW cW-W 34 1.DT81 2.DA8 T-A WC 20-XX cWW cW-W 35 1.DT82 2.DC6 T-C -- -- cWW cW-W 36 1.DT82 2.DA7 T-A WC 20-XX cWW cW-W 37 1.DG83 2.DC6 G-C WC 19-XIX cWW cW-W 38 1.DC84 2.DG5 C-G WC 19-XIX cWW cW-W 39 1.DG85 2.DC4 G-C WC 19-XIX cWW cW-W 40 1.DG86 2.DC3 G-C WC 19-XIX cWW cW-W 41 1.DC87 2.DG2 C-G WC 19-XIX cWW cW-W 42 1.DG88 2.DC1 G-C -- -- cWW cW-W 43 2.DG13 3.C3 G-C WC 19-XIX cWW cW-W 44 2.DT14 3.A2 T-A WC 20-XX cWW cW-W 45 2.DT15 3.ATP1 T-a WC 20-XX cWW cW-W **************************************************************************** List of 3 helices 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=26 strand-1 5'-AGCAATAAAGTTTCTTCCCCTTGCCG-3' bp-type |||||||||||||||.|.|||||||| strand-2 3'-TCGTTATTTCAAAGAAGGGGAACGGC-5' helix-form B...BBBBB....x...x....... 1 1.DA35 2.DT54 A-T WC 20-XX cWW cW-W 2 1.DG36 2.DC53 G-C WC 19-XIX cWW cW-W 3 1.DC37 2.DG52 C-G WC 19-XIX cWW cW-W 4 1.DA38 2.DT51 A-T WC 20-XX cWW cW-W 5 1.DA39 2.DT50 A-T WC 20-XX cWW cW-W 6 1.DT40 2.DA49 T-A WC 20-XX cWW cW-W 7 1.DA41 2.DT48 A-T WC 20-XX cWW cW-W 8 1.DA42 2.DT47 A-T WC 20-XX cWW cW-W 9 1.DA43 2.DT46 A-T WC 20-XX cWW cW-W 10 1.DG44 2.DC45 G-C WC 19-XIX cWW cW-W 11 1.DT45 2.DA44 T-A WC 20-XX cWW cW-W 12 1.DT46 2.DA43 T-A WC 20-XX cWW cW-W 13 1.DT47 2.DA42 T-A WC 20-XX cWW cW-W 14 1.DC48 2.DG41 C-G WC 19-XIX cWW cW-W 15 1.DT50 2.DA39 T-A WC 20-XX cWW cW-W 16 1.DT51 2.DA38 T-A -- -- cWW cW-W 17 1.DC52 2.DG37 C-G WC 19-XIX cWW cW-W 18 1.DC53 2.DG36 C-G -- -- cWW cW-W 19 1.DC55 2.DG34 C-G WC 19-XIX cWW cW-W 20 1.DC56 2.DG33 C-G WC 19-XIX cWW cW-W 21 1.DT57 2.DA32 T-A WC 20-XX cWW cW-W 22 1.DT58 2.DA31 T-A WC 20-XX cWW cW-W 23 1.DG59 2.DC30 G-C WC 19-XIX cWW cW-W 24 1.DC60 2.DG29 C-G WC 19-XIX cWW cW-W 25 1.DC61 2.DG28 C-G WC 19-XIX cWW cW-W 26 1.DG62 2.DC27 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=11 strand-1 5'-TGTTTGCGGCG-3' bp-type ||||||||||. strand-2 3'-ACAAACGCCGC-5' helix-form ...BBBBBB. 1 1.DT78 2.DA11 T-A WC 20-XX cWW cW-W 2 1.DG79 2.DC10 G-C WC 19-XIX cWW cW-W 3 1.DT80 2.DA9 T-A WC 20-XX cWW cW-W 4 1.DT81 2.DA8 T-A WC 20-XX cWW cW-W 5 1.DT82 2.DA7 T-A WC 20-XX cWW cW-W 6 1.DG83 2.DC6 G-C WC 19-XIX cWW cW-W 7 1.DC84 2.DG5 C-G WC 19-XIX cWW cW-W 8 1.DG85 2.DC4 G-C WC 19-XIX cWW cW-W 9 1.DG86 2.DC3 G-C WC 19-XIX cWW cW-W 10 1.DC87 2.DG2 C-G WC 19-XIX cWW cW-W 11 1.DG88 2.DC1 G-C -- -- cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=3 strand-1 5'-GTT-3' bp-type ||| strand-2 3'-CAa-5' helix-form .. 1 2.DG13 3.C3 G-C WC 19-XIX cWW cW-W 2 2.DT14 3.A2 T-A WC 20-XX cWW cW-W 3 2.DT15 3.ATP1 T-a WC 20-XX cWW cW-W **************************************************************************** List of 4 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=14 strand-1 5'-AGCAATAAAGTTTC-3' bp-type |||||||||||||| strand-2 3'-TCGTTATTTCAAAG-5' helix-form B...BBBBB.... 1 1.DA35 2.DT54 A-T WC 20-XX cWW cW-W 2 1.DG36 2.DC53 G-C WC 19-XIX cWW cW-W 3 1.DC37 2.DG52 C-G WC 19-XIX cWW cW-W 4 1.DA38 2.DT51 A-T WC 20-XX cWW cW-W 5 1.DA39 2.DT50 A-T WC 20-XX cWW cW-W 6 1.DT40 2.DA49 T-A WC 20-XX cWW cW-W 7 1.DA41 2.DT48 A-T WC 20-XX cWW cW-W 8 1.DA42 2.DT47 A-T WC 20-XX cWW cW-W 9 1.DA43 2.DT46 A-T WC 20-XX cWW cW-W 10 1.DG44 2.DC45 G-C WC 19-XIX cWW cW-W 11 1.DT45 2.DA44 T-A WC 20-XX cWW cW-W 12 1.DT46 2.DA43 T-A WC 20-XX cWW cW-W 13 1.DT47 2.DA42 T-A WC 20-XX cWW cW-W 14 1.DC48 2.DG41 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=8 strand-1 5'-CCTTGCCG-3' bp-type |||||||| strand-2 3'-GGAACGGC-5' helix-form ....... 1 1.DC55 2.DG34 C-G WC 19-XIX cWW cW-W 2 1.DC56 2.DG33 C-G WC 19-XIX cWW cW-W 3 1.DT57 2.DA32 T-A WC 20-XX cWW cW-W 4 1.DT58 2.DA31 T-A WC 20-XX cWW cW-W 5 1.DG59 2.DC30 G-C WC 19-XIX cWW cW-W 6 1.DC60 2.DG29 C-G WC 19-XIX cWW cW-W 7 1.DC61 2.DG28 C-G WC 19-XIX cWW cW-W 8 1.DG62 2.DC27 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=10 strand-1 5'-TGTTTGCGGC-3' bp-type |||||||||| strand-2 3'-ACAAACGCCG-5' helix-form ...BBBBBB 1 1.DT78 2.DA11 T-A WC 20-XX cWW cW-W 2 1.DG79 2.DC10 G-C WC 19-XIX cWW cW-W 3 1.DT80 2.DA9 T-A WC 20-XX cWW cW-W 4 1.DT81 2.DA8 T-A WC 20-XX cWW cW-W 5 1.DT82 2.DA7 T-A WC 20-XX cWW cW-W 6 1.DG83 2.DC6 G-C WC 19-XIX cWW cW-W 7 1.DC84 2.DG5 C-G WC 19-XIX cWW cW-W 8 1.DG85 2.DC4 G-C WC 19-XIX cWW cW-W 9 1.DG86 2.DC3 G-C WC 19-XIX cWW cW-W 10 1.DC87 2.DG2 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#3] bps=3 strand-1 5'-GTT-3' bp-type ||| strand-2 3'-CAa-5' helix-form .. 1 2.DG13 3.C3 G-C WC 19-XIX cWW cW-W 2 2.DT14 3.A2 T-A WC 20-XX cWW cW-W 3 2.DT15 3.ATP1 T-a WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 14 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.GLU541,2.DA11 2 nts=2 RA F.ARG25,1.DA69 3 nts=2 HG F.HIS26,1.DG68 4 nts=2 CG 1.DC87,1.DG88 5 nts=2 CG 2.DC1,2.DG2 6 nts=2 AG 2.DA12,2.DG13 7 nts=2 GC 2.DG21,2.DC22 8 nts=3 RAG C.ARG371,1.DA71,1.DG70 9 nts=4 WCAA C.TRP183,1.DC76,1.DA75,1.DA74 10 nts=4 TAAC 1.DT64,1.DA65,1.DA66,1.DC67 11 nts=5 RTTAT C.ARG470,2.DT23,2.DT24,2.DA25,2.DT26 12 nts=5 TGTAG 2.DT15,2.DG16,2.DT17,2.DA18,2.DG19 13 nts=8 CCTTCCTC 1.DC48,1.DC49,1.DT50,1.DT51,1.DC52,1.DC53,1.DT54,1.DC55 14 nts=8 GAGGAAGG 2.DG34,2.DA35,2.DG36,2.DG37,2.DA38,2.DA39,2.DG40,2.DG41 **************************************************************************** Nucleotides not involved in stacking interactions nts=6 GATCTA 1.DG62,1.DA63,1.DT72,1.DC73,1.DT77,2.DA20 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 phosphate O3'@1.DG62 1.DA63 2.75 **************************************************************************** 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 internal loop 1 symmetric internal loop: nts=16; [6,6]; linked by [#1,#2] summary: [2] 6 6 [1.48 2.41 1.55 2.34] 14 8 nts=16 CCTTCCTCGAGGAAGG 1.DC48,1.DC49,1.DT50,1.DT51,1.DC52,1.DC53,1.DT54,1.DC55,2.DG34,2.DA35,2.DG36,2.DG37,2.DA38,2.DA39,2.DG40,2.DG41 nts=6 CTTCCT 1.DC49,1.DT50,1.DT51,1.DC52,1.DC53,1.DT54 nts=6 AGGAAG 2.DA35,2.DG36,2.DG37,2.DA38,2.DA39,2.DG40 **************************************************************************** List of 5 non-loop single-stranded segments 1 nts=15 ATAACGAGATCAACT 1.DA63,1.DT64,1.DA65,1.DA66,1.DC67,1.DG68,1.DA69,1.DG70,1.DA71,1.DT72,1.DC73,1.DA74,1.DA75,1.DC76,1.DT77 2 nts=1 G 1.DG88 3 nts=1 C 2.DC1 4 nts=1 A 2.DA12 5 nts=11 GTAGAGCTTAT 2.DG16,2.DT17,2.DA18,2.DG19,2.DA20,2.DG21,2.DC22,2.DT23,2.DT24,2.DA25,2.DT26 **************************************************************************** List of 5 splayed-apart dinucleotides 1 1.DG62 1.DA63 angle=103 distance=11.8 ratio=0.79 2 1.DA63 1.DT64 angle=163 distance=17.5 ratio=0.99 3 1.DT77 1.DT78 angle=165 distance=18.8 ratio=0.99 4 2.DA11 2.DA12 angle=138 distance=18.9 ratio=0.93 5 2.DT26 2.DC27 angle=116 distance=18.0 ratio=0.85 ---------------------------------------------------------------- Summary of 4 splayed-apart units 1 nts=3 GAT 1.DG62,1.DA63,1.DT64 2 nts=2 TT 1.DT77,1.DT78 3 nts=2 AA 2.DA11,2.DA12 4 nts=2 TC 2.DT26,2.DC27 **************************************************************************** Special notes: o cross-paired segments in separate chains, be *careful* with .dbn **************************************************************************** This structure contains *1-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. o The DSSR-derived dbn may be problematic (see notes above). **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6pmj nts=111 [whole] AGCAATAAAGTTTCCTTCCTCCTTGCCGATAACGAGATCAACTTGTTTGCGGCG&CGCCGCAAACAAGTTGTAGAGCTTATCGGCAAGGAGGAAGGAAACTTTATTGCT&aAC ((((((((((((((......((((((((...............((((((((((.&.)))))))))).[[[...........))))))))......))))))))))))))&]]] >6pmj-1 #1 nts=54 2.17(1.97) [chain] DNA AGCAATAAAGTTTCCTTCCTCCTTGCCGATAACGAGATCAACTTGTTTGCGGCG ((((((((((((((......((((((((...............((((((((((. >6pmj-2 #2 nts=54 2.22(1.91) [chain] DNA CGCCGCAAACAAGTTGTAGAGCTTATCGGCAAGGAGGAAGGAAACTTTATTGCT .)))))))))).[[[...........))))))))......)))))))))))))) >6pmj-3 #3 nts=3 2.31(0.04) [chain] RNA aAC ]]] **************************************************************************** Summary of structural features of 111 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 ( 1.DA35 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 G ( 1.DG36 0.011 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 C ( 1.DC37 0.006 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 A ( 1.DA38 0.012 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 A ( 1.DA39 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 T ( 1.DT40 0.006 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 A ( 1.DA41 0.016 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 A ( 1.DA42 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 9 A ( 1.DA43 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 G ( 1.DG44 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 T ( 1.DT45 0.014 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 12 T ( 1.DT46 0.008 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 T ( 1.DT47 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 14 C ( 1.DC48 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 15 C . 1.DC49 0.009 anti,BI,non-pair-contact,internal-loop 16 T . 1.DT50 0.006 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 17 T . 1.DT51 0.011 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 18 C . 1.DC52 0.010 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 19 C . 1.DC53 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 20 T . 1.DT54 0.009 anti,BI,non-pair-contact,internal-loop 21 C ( 1.DC55 0.013 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 22 C ( 1.DC56 0.013 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 T ( 1.DT57 0.010 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 24 T ( 1.DT58 0.019 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ( 1.DG59 0.030 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 C ( 1.DC60 0.014 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 27 C ( 1.DC61 0.016 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 28 G ( 1.DG62 0.013 anti,~C2'-endo,non-stack,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,cap-donor,splayed-apart 29 A . 1.DA63 0.013 anti,non-stack,non-pair-contact,ss-non-loop,cap-acceptor,splayed-apart 30 T . 1.DT64 0.008 anti,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 31 A . 1.DA65 0.011 anti,BI,non-pair-contact,ss-non-loop,phosphate 32 A . 1.DA66 0.011 anti,BI,non-pair-contact,ss-non-loop 33 C . 1.DC67 0.010 anti,non-pair-contact,ss-non-loop 34 G . 1.DG68 0.011 anti,~C3'-endo,BI,ss-non-loop 35 A . 1.DA69 0.005 anti,~C2'-endo,BII,ss-non-loop 36 G . 1.DG70 0.006 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 37 A . 1.DA71 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop 38 T . 1.DT72 0.005 anti,~C3'-endo,non-stack,ss-non-loop 39 C . 1.DC73 0.007 anti,~C2'-endo,BI,non-stack,ss-non-loop,phosphate 40 A . 1.DA74 0.006 anti,non-pair-contact,ss-non-loop 41 A . 1.DA75 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop 42 C . 1.DC76 0.012 anti,~C3'-endo,non-pair-contact,ss-non-loop 43 T . 1.DT77 0.006 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 44 T ( 1.DT78 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 45 G ( 1.DG79 0.013 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 46 T ( 1.DT80 0.009 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 47 T ( 1.DT81 0.009 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 48 T ( 1.DT82 0.010 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem 49 G ( 1.DG83 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 50 C ( 1.DC84 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 51 G ( 1.DG85 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 52 G ( 1.DG86 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 53 C ( 1.DC87 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end 54 G . 1.DG88 0.009 anti,~C3'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 55 C . 2.DC1 0.010 anti,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 56 G ) 2.DG2 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end 57 C ) 2.DC3 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 58 C ) 2.DC4 0.016 anti,BI,canonical,non-pair-contact,helix,stem 59 G ) 2.DG5 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 60 C ) 2.DC6 0.008 anti,BI,canonical,non-canonical,non-pair-contact,helix,stem 61 A ) 2.DA7 0.009 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 62 A ) 2.DA8 0.011 anti,~C2'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 63 A ) 2.DA9 0.012 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 64 C ) 2.DC10 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 65 A ) 2.DA11 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 66 A . 2.DA12 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 67 G [ 2.DG13 0.009 pseudoknotted,anti,BI,canonical,non-pair-contact,helix-end,stem-end 68 T [ 2.DT14 0.006 pseudoknotted,anti,BI,canonical,non-pair-contact,helix,stem,phosphate 69 T [ 2.DT15 0.006 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 70 G . 2.DG16 0.012 anti,non-pair-contact,ss-non-loop 71 T . 2.DT17 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop 72 A . 2.DA18 0.011 anti,~C3'-endo,non-pair-contact,ss-non-loop 73 G . 2.DG19 0.018 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 74 A . 2.DA20 0.010 anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop 75 G . 2.DG21 0.012 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 76 C . 2.DC22 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop 77 T . 2.DT23 0.011 turn,anti,non-pair-contact,ss-non-loop 78 T . 2.DT24 0.007 anti,non-pair-contact,ss-non-loop 79 A . 2.DA25 0.022 anti,BI,non-pair-contact,ss-non-loop 80 T . 2.DT26 0.011 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 81 C ) 2.DC27 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate,splayed-apart 82 G ) 2.DG28 0.020 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 83 G ) 2.DG29 0.024 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 84 C ) 2.DC30 0.020 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 85 A ) 2.DA31 0.015 anti,~C2'-endo,canonical,non-canonical,non-pair-contact,helix,stem,coaxial-stack 86 A ) 2.DA32 0.019 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 87 G ) 2.DG33 0.021 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 88 G ) 2.DG34 0.009 anti,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 89 A . 2.DA35 0.008 anti,~C2'-endo,BI,non-pair-contact,internal-loop 90 G . 2.DG36 0.016 anti,non-canonical,non-pair-contact,helix,internal-loop 91 G . 2.DG37 0.029 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 92 A . 2.DA38 0.020 anti,BI,non-canonical,non-pair-contact,helix,internal-loop 93 A . 2.DA39 0.015 anti,BI,non-canonical,non-pair-contact,helix,internal-loop 94 G . 2.DG40 0.009 anti,BI,non-pair-contact,internal-loop 95 G ) 2.DG41 0.010 anti,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 96 A ) 2.DA42 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 97 A ) 2.DA43 0.017 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 98 A ) 2.DA44 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 99 C ) 2.DC45 0.010 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 100 T ) 2.DT46 0.014 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 101 T ) 2.DT47 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 102 T ) 2.DT48 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 103 A ) 2.DA49 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 104 T ) 2.DT50 0.009 anti,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 105 T ) 2.DT51 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 106 G ) 2.DG52 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 107 C ) 2.DC53 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 108 T ) 2.DT54 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 109 a ] 3.ATP1 0.064 modified,pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 110 A ] 3.A2 0.013 pseudoknotted,anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 111 C ] 3.C3 0.007 pseudoknotted,anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate **************************************************************************** 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-iloops.pdb -- an ensemble of internal 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