ID code: '2V6W' 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 A 1 beta 4 10 7 32 C1' G A 2 beta 27 33 30 55 C1' A A 3 beta 50 56 53 77 C1' G A 4 beta 72 78 75 100 C1' A A 5 beta 95 101 98 122 C1' G A 6 beta 117 123 120 145 C1' A A 7 beta 140 146 143 165 C1' U B 66 beta 160 166 163 185 C1' C B 67 beta 180 186 183 205 C1' U B 68 beta 200 206 203 225 C1' C B 69 beta 220 226 223 245 C1' U B 70 beta 240 246 243 265 C1' C B 71 beta 260 266 263 285 C1' C B 72 beta 280 286 283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' G A 2 OK 32 28 31 53 C2' A A 3 OK 55 51 54 75 C2' G A 4 OK 77 73 76 98 C2' A A 5 OK 100 96 99 120 C2' G A 6 OK 122 118 121 143 C2' A A 7 OK 145 141 144 163 C2' U B 66 OK 165 161 164 183 C2' C B 67 OK 185 181 184 203 C2' U B 68 OK 205 201 204 223 C2' C B 69 OK 225 221 224 243 C2' U B 70 OK 245 241 244 263 C2' C B 71 OK 265 261 264 283 C2' C B 72 OK 285 281 284 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' A A 3 OK 49 52 53 73 C3' G A 4 OK 71 74 75 96 C3' A A 5 OK 94 97 98 118 C3' G A 6 OK 116 119 120 141 C3' A A 7 OK 139 142 143 161 C3' U B 66 OK 159 162 163 181 C3' C B 67 OK 179 182 183 201 C3' U B 68 OK 199 202 203 221 C3' C B 69 OK 219 222 223 241 C3' U B 70 OK 239 242 243 261 C3' C B 71 OK 259 262 263 281 C3' C B 72 OK 279 282 283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' A A 3 OK 51 48 50 71 C4' G A 4 OK 73 70 72 94 C4' A A 5 OK 96 93 95 116 C4' G A 6 OK 118 115 117 139 C4' A A 7 OK 141 138 140 159 C4' U B 66 OK 161 158 160 179 C4' C B 67 OK 181 178 180 199 C4' U B 68 OK 201 198 200 219 C4' C B 69 OK 221 218 220 239 C4' U B 70 OK 241 238 240 259 C4' C B 71 OK 261 258 260 279 C4' C B 72 OK 281 278 280 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' A A 3 47 49 70 C5' G A 4 69 71 93 C5' A A 5 92 94 115 C5' G A 6 114 116 138 C5' A A 7 137 139 158 C5' U B 66 157 159 178 C5' C B 67 177 179 198 C5' U B 68 197 199 218 C5' C B 69 217 219 238 C5' U B 70 237 239 258 C5' C B 71 257 259 278 C5' C B 72 277 279 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P A A 3 distorted distorted 29 45 46 47 66 P G A 4 distorted distorted 52 67 68 69 89 P A A 5 distorted distorted 74 90 91 92 111 P G A 6 distorted distorted 97 112 113 114 134 P A A 7 distorted distorted 119 135 136 137 174 P C B 67 distorted distorted 162 175 176 177 194 P U B 68 distorted distorted 182 195 196 197 214 P C B 69 distorted distorted 202 215 216 217 234 P U B 70 distorted distorted 222 235 236 237 254 P C B 71 distorted distorted 242 255 256 257 274 P C B 72 distorted distorted 262 275 276 277 ---------------------------------------------------------------------------------