ID code: '2ASB' 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' --------------------------------------------------------------------------------- 9 C1' G B 1 beta 4 10 7 32 C1' A B 2 beta 27 33 30 54 C1' A B 3 beta 49 55 52 76 C1' C B 4 beta 71 77 74 96 C1' U B 5 beta 91 97 94 116 C1' C B 6 beta 111 117 114 136 C1' A B 7 beta 131 137 134 158 C1' A B 8 beta 153 159 156 180 C1' U B 9 beta 175 181 178 200 C1' A B 10 beta 195 201 198 222 C1' G B 11 beta 217 223 220 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 1 OK 9 5 8 30 C2' A B 2 OK 32 28 31 52 C2' A B 3 OK 54 50 53 74 C2' C B 4 OK 76 72 75 94 C2' U B 5 OK 96 92 95 114 C2' C B 6 OK 116 112 115 134 C2' A B 7 OK 136 132 135 156 C2' A B 8 OK 158 154 157 178 C2' U B 9 OK 180 176 179 198 C2' A B 10 OK 200 196 199 220 C2' G B 11 OK 222 218 221 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 1 OK 3 6 7 28 C3' A B 2 OK 26 29 30 50 C3' A B 3 OK 48 51 52 72 C3' C B 4 OK 70 73 74 92 C3' U B 5 OK 90 93 94 112 C3' C B 6 OK 110 113 114 132 C3' A B 7 OK 130 133 134 154 C3' A B 8 OK 152 155 156 176 C3' U B 9 OK 174 177 178 196 C3' A B 10 OK 194 197 198 218 C3' G B 11 OK 216 219 220 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 1 OK 5 2 4 26 C4' A B 2 OK 28 25 27 48 C4' A B 3 OK 50 47 49 70 C4' C B 4 OK 72 69 71 90 C4' U B 5 OK 92 89 91 110 C4' C B 6 OK 112 109 111 130 C4' A B 7 OK 132 129 131 152 C4' A B 8 OK 154 151 153 174 C4' U B 9 OK 176 173 175 194 C4' A B 10 OK 196 193 195 216 C4' G B 11 OK 218 215 217 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 1 1 3 25 C5' A B 2 24 26 47 C5' A B 3 46 48 69 C5' C B 4 68 70 89 C5' U B 5 88 90 109 C5' C B 6 108 110 129 C5' A B 7 128 130 151 C5' A B 8 150 152 173 C5' U B 9 172 174 193 C5' A B 10 192 194 215 C5' G B 11 214 216 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P A B 2 distorted distorted 6 22 23 24 43 P A B 3 distorted distorted 29 44 45 46 65 P C B 4 distorted distorted 51 66 67 68 85 P U B 5 distorted distorted 73 86 87 88 105 P C B 6 distorted distorted 93 106 107 108 125 P A B 7 distorted distorted 113 126 127 128 147 P A B 8 distorted distorted 133 148 149 150 169 P U B 9 distorted distorted 155 170 171 172 189 P A B 10 distorted distorted 177 190 191 192 211 P G B 11 distorted distorted 197 212 213 214 ---------------------------------------------------------------------------------