ID code: '2AGN' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 2 2 P C A 3 3 P C A 4 4 P G A 5 5 P A A 6 6 P G A 7 7 P U A 8 8 P A A 9 9 P G A 10 10 P U A 11 11 P G A 12 12 P U A 13 13 P U A 14 14 P G A 15 15 P G A 16 16 P G A 17 17 P U A 18 18 P C A 19 19 P G A 20 20 P C A 21 21 P G A 22 22 P A A 23 23 P A A 24 24 P A A 25 25 P G A 26 26 P G A 27 27 P C A 28 28 P C A 29 30 P G B 2 31 P C B 3 32 P G B 4 33 P C B 5 34 P U B 6 35 P C B 7 36 P A B 8 37 P A B 9 38 P U B 10 39 P G B 11 40 P C B 12 41 P U B 13 42 P C B 14 43 P G B 19 44 P A B 20 45 P G B 21 46 P A B 22 47 P C B 23 48 P G B 24 49 P A B 25 50 P C B 26 51 P C B 27 52 P G B 28 53 P C B 29 54 P C B 30 56 P G C 2 57 P C C 3 58 P U C 4 59 P G C 5 60 P U C 6 61 P G C 7 62 P A C 8 63 P G C 9 64 P G C 10 65 P A C 11 66 P A C 12 67 P C C 13 68 P U C 14 69 P A C 15 70 P C C 16 71 P U C 17 72 P G C 18 73 P U C 19 74 P C C 20 75 P U C 21 76 P U C 22 77 P C C 23 78 P A C 24 79 P C C 25 80 P G C 26 81 P C C 27 82 P A C 28 83 P G C 29 84 P A C 30 85 P A C 31 86 P A C 32 87 P G C 33 88 P C C 34 89 P G C 35 90 P U C 36 91 P C C 37 92 P U C 38 93 P A C 39 94 P G C 40 95 P C C 41 96 P C C 42 97 P A C 43 98 P U C 44 99 P G C 45 100 P G C 46 101 P C C 47 102 P G C 48 103 P U C 49 104 P U C 50 105 P A C 51 106 P G C 52 107 P U C 53 108 P A C 54 109 P U C 55 110 P G C 56 111 P A C 57 112 P G C 58 113 P U C 59 114 P G C 60 115 P U C 61 116 P C C 62 117 P G C 63 118 P U C 64 119 P G C 65 120 P C C 66 121 P A C 67 122 P G C 68 123 P C C 69 124 P C C 70 125 P U C 71 126 P C C 72 127 P C C 73 128 P A C 74 129 P G C 75 130 P C C 76 131 P C C 77 133 P C D 2 134 P C D 3 135 P C D 4 136 P G D 5 137 P G D 6 138 P G D 7 139 P G D 8 140 P C D 9 141 P C D 10 142 P C D 11 143 P G D 12 144 P G D 13 145 P G D 14 146 P G D 15 148 P G E 2 149 P C E 3 150 P G E 4 151 P G E 5 152 P A E 6 153 P A E 7 154 P C E 8 155 P C E 9 156 P G E 10 157 P A E 17 158 P C E 18 159 P A E 19 160 P C E 20 161 P C E 21 162 P G E 22 163 P G E 23 164 P A E 24 165 P A E 25 166 P U E 26 167 P C E 27 168 P C E 28 169 P G E 33 170 P G E 34 171 P A E 35 172 P U E 36 173 P U E 37 174 P U E 38 175 P G E 39 176 P G E 40 177 P G E 41 178 P C E 42 179 P G E 43 180 P G E 45 181 P C E 46 182 P C E 47 183 P C E 48 184 P C E 49 185 P C E 50 186 P G E 51 187 P C E 52 ---------------------------------------------------------------------------------