**************************************************************************** File name: 8qem.pdb no. of DNA/RNA chains: 2 [Y=63,Z=63] no. of nucleotides: 126 no. of atoms: 71054 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 63 base pairs nt1 nt2 bp name Saenger LW DSSR 1 Z.DG1 Y.DC63 G-C WC 19-XIX cWW cW-W 2 Z.DA2 Y.DT62 A-T WC 20-XX cWW cW-W 3 Z.DT3 Y.DA61 T-A WC 20-XX cWW cW-W 4 Z.DA4 Y.DT60 A-T WC 20-XX cWW cW-W 5 Z.DG5 Y.DC59 G-C WC 19-XIX cWW cW-W 6 Z.DA6 Y.DT58 A-T WC 20-XX cWW cW-W 7 Z.DA7 Y.DT57 A-T WC 20-XX cWW cW-W 8 Z.DT8 Y.DA56 T-A WC 20-XX cWW cW-W 9 Z.DT9 Y.DA55 T-A WC 20-XX cWW cW-W 10 Z.DA10 Y.DT54 A-T WC 20-XX cWW cW-W 11 Z.DT11 Y.DA53 T-A WC 20-XX cWW cW-W 12 Z.DT12 Y.DA52 T-A WC 20-XX cWW cW-W 13 Z.DG13 Y.DC51 G-C WC 19-XIX cWW cW-W 14 Z.DG14 Y.DC50 G-C -- -- cWW cW-W 15 Z.DT15 Y.DA49 T-A WC 20-XX cWW cW-W 16 Z.DA16 Y.DT48 A-T WC 20-XX cWW cW-W 17 Z.DC17 Y.DG47 C-G WC 19-XIX cWW cW-W 18 Z.DC18 Y.DG46 C-G -- -- cWW cW-W 19 Z.DG19 Y.DC45 G-C WC 19-XIX cWW cW-W 20 Z.DT20 Y.DA44 T-A WC 20-XX cWW cW-W 21 Z.DT21 Y.DA43 T-A WC 20-XX cWW cW-W 22 Z.DG22 Y.DC42 G-C WC 19-XIX cWW cW-W 23 Z.DT23 Y.DA41 T-A WC 20-XX cWW cW-W 24 Z.DC24 Y.DG40 C-G WC 19-XIX cWW cW-W 25 Z.DT25 Y.DA39 T-A WC 20-XX cWW cW-W 26 Z.DT26 Y.DA38 T-A WC 20-XX cWW cW-W 27 Z.DC27 Y.DG37 C-G WC 19-XIX cWW cW-W 28 Z.DT28 Y.DA36 T-A WC 20-XX cWW cW-W 29 Z.DA29 Y.DT35 A-T WC 20-XX cWW cW-W 30 Z.DA30 Y.DT34 A-T WC 20-XX cWW cW-W 31 Z.DT31 Y.DA33 T-A WC 20-XX cWW cW-W 32 Z.DC32 Y.DG32 C-G WC 19-XIX cWW cW-W 33 Z.DT33 Y.DA31 T-A WC 20-XX cWW cW-W 34 Z.DA34 Y.DT30 A-T WC 20-XX cWW cW-W 35 Z.DC35 Y.DG29 C-G WC 19-XIX cWW cW-W 36 Z.DT36 Y.DA28 T-A WC 20-XX cWW cW-W 37 Z.DC37 Y.DG27 C-G WC 19-XIX cWW cW-W 38 Z.DT38 Y.DA26 T-A WC 20-XX cWW cW-W 39 Z.DC39 Y.DG25 C-G WC 19-XIX cWW cW-W 40 Z.DA40 Y.DT24 A-T WC 20-XX cWW cW-W 41 Z.DG41 Y.DC23 G-C WC 19-XIX cWW cW-W 42 Z.DT42 Y.DA22 T-A WC 20-XX cWW cW-W 43 Z.DA43 Y.DT21 A-T WC 20-XX cWW cW-W 44 Z.DG44 Y.DC20 G-C WC 19-XIX cWW cW-W 45 Z.DT45 Y.DA19 T-A WC 20-XX cWW cW-W 46 Z.DA46 Y.DT18 A-T WC 20-XX cWW cW-W 47 Z.DG47 Y.DC17 G-C WC 19-XIX cWW cW-W 48 Z.DT48 Y.DA16 T-A WC 20-XX cWW cW-W 49 Z.DA49 Y.DT15 A-T WC 20-XX cWW cW-W 50 Z.DA50 Y.DT14 A-T WC 20-XX cWW cW-W 51 Z.DT51 Y.DA13 T-A WC 20-XX cWW cW-W 52 Z.DA52 Y.DT12 A-T WC 20-XX cWW cW-W 53 Z.DG53 Y.DC11 G-C WC 19-XIX cWW cW-W 54 Z.DT54 Y.DA10 T-A WC 20-XX cWW cW-W 55 Z.DA55 Y.DT9 A-T WC 20-XX cWW cW-W 56 Z.DG56 Y.DC8 G-C WC 19-XIX cWW cW-W 57 Z.DT57 Y.DA7 T-A WC 20-XX cWW cW-W 58 Z.DA58 Y.DT6 A-T WC 20-XX cWW cW-W 59 Z.DC59 Y.DG5 C-G WC 19-XIX cWW cW-W 60 Z.DA60 Y.DT4 A-T WC 20-XX cWW cW-W 61 Z.DT61 Y.DA3 T-A WC 20-XX cWW cW-W 62 Z.DA62 Y.DT2 A-T WC 20-XX cWW cW-W 63 Z.DA63 Y.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 helix Note: A helix is defined by base-stacking interactions, regardless of pair 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[3] bps=63 strand-1 5'-GATAGAATTATTGGTACCGTTGTCTTCTAATCTACTCTCAGTAGTAGTAATAGTAGTACATAA-3' bp-type |||||||||||||.|||.||||||||||||||||||||||||||||||||||||||||||||| strand-2 3'-CTATCTTAATAACCATGGCAACAGAAGATTAGATGAGAGTCATCATCATTATCATCATGTATT-5' helix-form BBBBBBBBB.BB..BB............BB..BB..BBB.BBB..BBBB.....BBB.BBBB 1 Z.DG1 Y.DC63 G-C WC 19-XIX cWW cW-W 2 Z.DA2 Y.DT62 A-T WC 20-XX cWW cW-W 3 Z.DT3 Y.DA61 T-A WC 20-XX cWW cW-W 4 Z.DA4 Y.DT60 A-T WC 20-XX cWW cW-W 5 Z.DG5 Y.DC59 G-C WC 19-XIX cWW cW-W 6 Z.DA6 Y.DT58 A-T WC 20-XX cWW cW-W 7 Z.DA7 Y.DT57 A-T WC 20-XX cWW cW-W 8 Z.DT8 Y.DA56 T-A WC 20-XX cWW cW-W 9 Z.DT9 Y.DA55 T-A WC 20-XX cWW cW-W 10 Z.DA10 Y.DT54 A-T WC 20-XX cWW cW-W 11 Z.DT11 Y.DA53 T-A WC 20-XX cWW cW-W 12 Z.DT12 Y.DA52 T-A WC 20-XX cWW cW-W 13 Z.DG13 Y.DC51 G-C WC 19-XIX cWW cW-W 14 Z.DG14 Y.DC50 G-C -- -- cWW cW-W 15 Z.DT15 Y.DA49 T-A WC 20-XX cWW cW-W 16 Z.DA16 Y.DT48 A-T WC 20-XX cWW cW-W 17 Z.DC17 Y.DG47 C-G WC 19-XIX cWW cW-W 18 Z.DC18 Y.DG46 C-G -- -- cWW cW-W 19 Z.DG19 Y.DC45 G-C WC 19-XIX cWW cW-W 20 Z.DT20 Y.DA44 T-A WC 20-XX cWW cW-W 21 Z.DT21 Y.DA43 T-A WC 20-XX cWW cW-W 22 Z.DG22 Y.DC42 G-C WC 19-XIX cWW cW-W 23 Z.DT23 Y.DA41 T-A WC 20-XX cWW cW-W 24 Z.DC24 Y.DG40 C-G WC 19-XIX cWW cW-W 25 Z.DT25 Y.DA39 T-A WC 20-XX cWW cW-W 26 Z.DT26 Y.DA38 T-A WC 20-XX cWW cW-W 27 Z.DC27 Y.DG37 C-G WC 19-XIX cWW cW-W 28 Z.DT28 Y.DA36 T-A WC 20-XX cWW cW-W 29 Z.DA29 Y.DT35 A-T WC 20-XX cWW cW-W 30 Z.DA30 Y.DT34 A-T WC 20-XX cWW cW-W 31 Z.DT31 Y.DA33 T-A WC 20-XX cWW cW-W 32 Z.DC32 Y.DG32 C-G WC 19-XIX cWW cW-W 33 Z.DT33 Y.DA31 T-A WC 20-XX cWW cW-W 34 Z.DA34 Y.DT30 A-T WC 20-XX cWW cW-W 35 Z.DC35 Y.DG29 C-G WC 19-XIX cWW cW-W 36 Z.DT36 Y.DA28 T-A WC 20-XX cWW cW-W 37 Z.DC37 Y.DG27 C-G WC 19-XIX cWW cW-W 38 Z.DT38 Y.DA26 T-A WC 20-XX cWW cW-W 39 Z.DC39 Y.DG25 C-G WC 19-XIX cWW cW-W 40 Z.DA40 Y.DT24 A-T WC 20-XX cWW cW-W 41 Z.DG41 Y.DC23 G-C WC 19-XIX cWW cW-W 42 Z.DT42 Y.DA22 T-A WC 20-XX cWW cW-W 43 Z.DA43 Y.DT21 A-T WC 20-XX cWW cW-W 44 Z.DG44 Y.DC20 G-C WC 19-XIX cWW cW-W 45 Z.DT45 Y.DA19 T-A WC 20-XX cWW cW-W 46 Z.DA46 Y.DT18 A-T WC 20-XX cWW cW-W 47 Z.DG47 Y.DC17 G-C WC 19-XIX cWW cW-W 48 Z.DT48 Y.DA16 T-A WC 20-XX cWW cW-W 49 Z.DA49 Y.DT15 A-T WC 20-XX cWW cW-W 50 Z.DA50 Y.DT14 A-T WC 20-XX cWW cW-W 51 Z.DT51 Y.DA13 T-A WC 20-XX cWW cW-W 52 Z.DA52 Y.DT12 A-T WC 20-XX cWW cW-W 53 Z.DG53 Y.DC11 G-C WC 19-XIX cWW cW-W 54 Z.DT54 Y.DA10 T-A WC 20-XX cWW cW-W 55 Z.DA55 Y.DT9 A-T WC 20-XX cWW cW-W 56 Z.DG56 Y.DC8 G-C WC 19-XIX cWW cW-W 57 Z.DT57 Y.DA7 T-A WC 20-XX cWW cW-W 58 Z.DA58 Y.DT6 A-T WC 20-XX cWW cW-W 59 Z.DC59 Y.DG5 C-G WC 19-XIX cWW cW-W 60 Z.DA60 Y.DT4 A-T WC 20-XX cWW cW-W 61 Z.DT61 Y.DA3 T-A WC 20-XX cWW cW-W 62 Z.DA62 Y.DT2 A-T WC 20-XX cWW cW-W 63 Z.DA63 Y.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 3 stems Note: A stem is defined as a helix consisting strictly of 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=13 strand-1 5'-GATAGAATTATTG-3' bp-type ||||||||||||| strand-2 3'-CTATCTTAATAAC-5' helix-form BBBBBBBBB.BB 1 Z.DG1 Y.DC63 G-C WC 19-XIX cWW cW-W 2 Z.DA2 Y.DT62 A-T WC 20-XX cWW cW-W 3 Z.DT3 Y.DA61 T-A WC 20-XX cWW cW-W 4 Z.DA4 Y.DT60 A-T WC 20-XX cWW cW-W 5 Z.DG5 Y.DC59 G-C WC 19-XIX cWW cW-W 6 Z.DA6 Y.DT58 A-T WC 20-XX cWW cW-W 7 Z.DA7 Y.DT57 A-T WC 20-XX cWW cW-W 8 Z.DT8 Y.DA56 T-A WC 20-XX cWW cW-W 9 Z.DT9 Y.DA55 T-A WC 20-XX cWW cW-W 10 Z.DA10 Y.DT54 A-T WC 20-XX cWW cW-W 11 Z.DT11 Y.DA53 T-A WC 20-XX cWW cW-W 12 Z.DT12 Y.DA52 T-A WC 20-XX cWW cW-W 13 Z.DG13 Y.DC51 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=3 strand-1 5'-TAC-3' bp-type ||| strand-2 3'-ATG-5' helix-form BB 1 Z.DT15 Y.DA49 T-A WC 20-XX cWW cW-W 2 Z.DA16 Y.DT48 A-T WC 20-XX cWW cW-W 3 Z.DC17 Y.DG47 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=45 strand-1 5'-GTTGTCTTCTAATCTACTCTCAGTAGTAGTAATAGTAGTACATAA-3' bp-type ||||||||||||||||||||||||||||||||||||||||||||| strand-2 3'-CAACAGAAGATTAGATGAGAGTCATCATCATTATCATCATGTATT-5' helix-form ..........BB..BB..BBB.BBB..BBBB.....BBB.BBBB 1 Z.DG19 Y.DC45 G-C WC 19-XIX cWW cW-W 2 Z.DT20 Y.DA44 T-A WC 20-XX cWW cW-W 3 Z.DT21 Y.DA43 T-A WC 20-XX cWW cW-W 4 Z.DG22 Y.DC42 G-C WC 19-XIX cWW cW-W 5 Z.DT23 Y.DA41 T-A WC 20-XX cWW cW-W 6 Z.DC24 Y.DG40 C-G WC 19-XIX cWW cW-W 7 Z.DT25 Y.DA39 T-A WC 20-XX cWW cW-W 8 Z.DT26 Y.DA38 T-A WC 20-XX cWW cW-W 9 Z.DC27 Y.DG37 C-G WC 19-XIX cWW cW-W 10 Z.DT28 Y.DA36 T-A WC 20-XX cWW cW-W 11 Z.DA29 Y.DT35 A-T WC 20-XX cWW cW-W 12 Z.DA30 Y.DT34 A-T WC 20-XX cWW cW-W 13 Z.DT31 Y.DA33 T-A WC 20-XX cWW cW-W 14 Z.DC32 Y.DG32 C-G WC 19-XIX cWW cW-W 15 Z.DT33 Y.DA31 T-A WC 20-XX cWW cW-W 16 Z.DA34 Y.DT30 A-T WC 20-XX cWW cW-W 17 Z.DC35 Y.DG29 C-G WC 19-XIX cWW cW-W 18 Z.DT36 Y.DA28 T-A WC 20-XX cWW cW-W 19 Z.DC37 Y.DG27 C-G WC 19-XIX cWW cW-W 20 Z.DT38 Y.DA26 T-A WC 20-XX cWW cW-W 21 Z.DC39 Y.DG25 C-G WC 19-XIX cWW cW-W 22 Z.DA40 Y.DT24 A-T WC 20-XX cWW cW-W 23 Z.DG41 Y.DC23 G-C WC 19-XIX cWW cW-W 24 Z.DT42 Y.DA22 T-A WC 20-XX cWW cW-W 25 Z.DA43 Y.DT21 A-T WC 20-XX cWW cW-W 26 Z.DG44 Y.DC20 G-C WC 19-XIX cWW cW-W 27 Z.DT45 Y.DA19 T-A WC 20-XX cWW cW-W 28 Z.DA46 Y.DT18 A-T WC 20-XX cWW cW-W 29 Z.DG47 Y.DC17 G-C WC 19-XIX cWW cW-W 30 Z.DT48 Y.DA16 T-A WC 20-XX cWW cW-W 31 Z.DA49 Y.DT15 A-T WC 20-XX cWW cW-W 32 Z.DA50 Y.DT14 A-T WC 20-XX cWW cW-W 33 Z.DT51 Y.DA13 T-A WC 20-XX cWW cW-W 34 Z.DA52 Y.DT12 A-T WC 20-XX cWW cW-W 35 Z.DG53 Y.DC11 G-C WC 19-XIX cWW cW-W 36 Z.DT54 Y.DA10 T-A WC 20-XX cWW cW-W 37 Z.DA55 Y.DT9 A-T WC 20-XX cWW cW-W 38 Z.DG56 Y.DC8 G-C WC 19-XIX cWW cW-W 39 Z.DT57 Y.DA7 T-A WC 20-XX cWW cW-W 40 Z.DA58 Y.DT6 A-T WC 20-XX cWW cW-W 41 Z.DC59 Y.DG5 C-G WC 19-XIX cWW cW-W 42 Z.DA60 Y.DT4 A-T WC 20-XX cWW cW-W 43 Z.DT61 Y.DA3 T-A WC 20-XX cWW cW-W 44 Z.DA62 Y.DT2 A-T WC 20-XX cWW cW-W 45 Z.DA63 Y.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#3] **************************************************************************** List of 4 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 CC Z.DC17,Z.DC18 2 nts=3 GGT Z.DG13,Z.DG14,Z.DT15 3 nts=3 GGG Z.DG19,Y.DG46,Y.DG47 4 nts=3 ACC Y.DA49,Y.DC50,Y.DC51 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 2 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [Z.13 Y.51 Z.15 Y.49] 13 3 nts=6 GGTACC Z.DG13,Z.DG14,Z.DT15,Y.DA49,Y.DC50,Y.DC51 nts=1 G Z.DG14 nts=1 C Y.DC50 2 symmetric internal loop: nts=6; [1,1]; linked by [#2,#3] summary: [2] 1 1 [Z.17 Y.47 Z.19 Y.45] 3 45 nts=6 CCGCGG Z.DC17,Z.DC18,Z.DG19,Y.DC45,Y.DG46,Y.DG47 nts=1 C Z.DC18 nts=1 G Y.DG46 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >8qem nts=126 [whole] GATAGAATTATTGGTACCGTTGTCTTCTAATCTACTCTCAGTAGTAGTAATAGTAGTACATAA&TTATGTACTACTATTACTACTACTGAGAGTAGATTAGAAGACAACGGTACCAATAATTCTATC (((((((((((((.(((.(((((((((((((((((((((((((((((((((((((((((((((&))))))))))))))))))))))))))))))))))))))))))))).))).))))))))))))) >8qem-Z #1 nts=63 3.35(0.48) [chain] DNA GATAGAATTATTGGTACCGTTGTCTTCTAATCTACTCTCAGTAGTAGTAATAGTAGTACATAA (((((((((((((.(((.((((((((((((((((((((((((((((((((((((((((((((( >8qem-Y #2 nts=63 3.35(0.56) [chain] DNA TTATGTACTACTATTACTACTACTGAGAGTAGATTAGAAGACAACGGTACCAATAATTCTATC ))))))))))))))))))))))))))))))))))))))))))))).))).))))))))))))) **************************************************************************** Summary of structural features of 126 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 ( Z.DG1 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 A ( Z.DA2 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 T ( Z.DT3 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 4 A ( Z.DA4 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 5 G ( Z.DG5 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 A ( Z.DA6 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 7 A ( Z.DA7 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 T ( Z.DT8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 T ( Z.DT9 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 10 A ( Z.DA10 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 T ( Z.DT11 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 T ( Z.DT12 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 13 G ( Z.DG13 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 14 G . Z.DG14 0.010 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 15 T ( Z.DT15 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 16 A ( Z.DA16 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 C ( Z.DC17 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 18 C . Z.DC18 0.020 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 19 G ( Z.DG19 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 20 T ( Z.DT20 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 T ( Z.DT21 0.026 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 G ( Z.DG22 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 T ( Z.DT23 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 C ( Z.DC24 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 T ( Z.DT25 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 T ( Z.DT26 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 C ( Z.DC27 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 28 T ( Z.DT28 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 A ( Z.DA29 0.009 anti,canonical,non-pair-contact,helix,stem,coaxial-stack 30 A ( Z.DA30 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 T ( Z.DT31 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 32 C ( Z.DC32 0.033 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 33 T ( Z.DT33 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 A ( Z.DA34 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 35 C ( Z.DC35 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 36 T ( Z.DT36 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 37 C ( Z.DC37 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 38 T ( Z.DT38 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 39 C ( Z.DC39 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 40 A ( Z.DA40 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 41 G ( Z.DG41 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 T ( Z.DT42 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 A ( Z.DA43 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 44 G ( Z.DG44 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 45 T ( Z.DT45 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 46 A ( Z.DA46 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 47 G ( Z.DG47 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 48 T ( Z.DT48 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 49 A ( Z.DA49 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 50 A ( Z.DA50 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 51 T ( Z.DT51 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 52 A ( Z.DA52 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 53 G ( Z.DG53 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 54 T ( Z.DT54 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 55 A ( Z.DA55 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 56 G ( Z.DG56 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 57 T ( Z.DT57 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 58 A ( Z.DA58 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 59 C ( Z.DC59 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 60 A ( Z.DA60 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 61 T ( Z.DT61 0.023 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 62 A ( Z.DA62 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 63 A ( Z.DA63 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 64 T ) Y.DT1 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 65 T ) Y.DT2 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 66 A ) Y.DA3 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 67 T ) Y.DT4 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 68 G ) Y.DG5 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 69 T ) Y.DT6 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 70 A ) Y.DA7 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 71 C ) Y.DC8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 72 T ) Y.DT9 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 73 A ) Y.DA10 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 74 C ) Y.DC11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 75 T ) Y.DT12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 76 A ) Y.DA13 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 77 T ) Y.DT14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 78 T ) Y.DT15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 79 A ) Y.DA16 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 80 C ) Y.DC17 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 81 T ) Y.DT18 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 82 A ) Y.DA19 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 83 C ) Y.DC20 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 84 T ) Y.DT21 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 85 A ) Y.DA22 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 86 C ) Y.DC23 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 87 T ) Y.DT24 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 88 G ) Y.DG25 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 89 A ) Y.DA26 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 90 G ) Y.DG27 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 91 A ) Y.DA28 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 92 G ) Y.DG29 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 93 T ) Y.DT30 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 94 A ) Y.DA31 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 95 G ) Y.DG32 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 96 A ) Y.DA33 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 97 T ) Y.DT34 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 98 T ) Y.DT35 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 99 A ) Y.DA36 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 100 G ) Y.DG37 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 101 A ) Y.DA38 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 102 A ) Y.DA39 0.016 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 103 G ) Y.DG40 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 104 A ) Y.DA41 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 105 C ) Y.DC42 0.019 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 106 A ) Y.DA43 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 107 A ) Y.DA44 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 108 C ) Y.DC45 0.014 anti,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 109 G . Y.DG46 0.010 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 110 G ) Y.DG47 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 111 T ) Y.DT48 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 112 A ) Y.DA49 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 113 C . Y.DC50 0.020 anti,~C2'-endo,non-canonical,non-pair-contact,helix,internal-loop 114 C ) Y.DC51 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 115 A ) Y.DA52 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 116 A ) Y.DA53 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 117 T ) Y.DT54 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 118 A ) Y.DA55 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 119 A ) Y.DA56 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 120 T ) Y.DT57 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 121 T ) Y.DT58 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 122 C ) Y.DC59 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 123 T ) Y.DT60 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 124 A ) Y.DA61 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 125 T ) Y.DT62 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 126 C ) Y.DC63 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 13 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-stacks.pdb -- an ensemble of base stacks 10 dssr-rotmat.txt -- position vector and rotation matrix 11 dssr-viewV.pdb -- vertical view of the principal moment of inertia 12 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 13 dssr-viewT.pdb -- top view of the principal moment of inertia