ID code: '485D' 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' --------------------------------------------------------------------------------- 12 C1' G A 2 beta 7 13 10 35 C1' U A 3 beta 30 36 33 55 C1' G A 4 beta 50 56 53 78 C1' A A 5 beta 73 79 76 100 C1' U A 6 beta 95 101 98 120 C1' C A 7 beta 115 121 118 140 C1' G A 8 beta 135 141 138 162 C1' C A 9 beta 158 163 161 183 C1' G B 11 beta 178 184 181 206 C1' U B 12 beta 201 207 204 226 C1' G B 13 beta 221 227 224 249 C1' A B 14 beta 244 250 247 271 C1' U B 15 beta 266 272 269 291 C1' C B 16 beta 286 292 289 311 C1' G B 17 beta 306 312 309 333 C1' C B 18 beta 329 334 332 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 2 OK 12 8 11 33 C2' U A 3 OK 35 31 34 53 C2' G A 4 OK 55 51 54 76 C2' A A 5 OK 78 74 77 98 C2' U A 6 OK 100 96 99 118 C2' C A 7 OK 120 116 119 138 C2' G A 8 OK 140 136 139 161 C2' C A 9 162 159 181 C2' G B 11 OK 183 179 182 204 C2' U B 12 OK 206 202 205 224 C2' G B 13 OK 226 222 225 247 C2' A B 14 OK 249 245 248 269 C2' U B 15 OK 271 267 270 289 C2' C B 16 OK 291 287 290 309 C2' G B 17 OK 311 307 310 332 C2' C B 18 333 330 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 2 OK 6 9 10 31 C3' U A 3 OK 29 32 33 51 C3' G A 4 OK 49 52 53 74 C3' A A 5 OK 72 75 76 96 C3' U A 6 OK 94 97 98 116 C3' C A 7 OK 114 117 118 136 C3' G A 8 OK 134 137 138 159 C3' C A 9 OK 157 160 161 179 C3' G B 11 OK 177 180 181 202 C3' U B 12 OK 200 203 204 222 C3' G B 13 OK 220 223 224 245 C3' A B 14 OK 243 246 247 267 C3' U B 15 OK 265 268 269 287 C3' C B 16 OK 285 288 289 307 C3' G B 17 OK 305 308 309 330 C3' C B 18 OK 328 331 332 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 2 OK 8 5 7 29 C4' U A 3 OK 31 28 30 49 C4' G A 4 OK 51 48 50 72 C4' A A 5 OK 74 71 73 94 C4' U A 6 OK 96 93 95 114 C4' C A 7 OK 116 113 115 134 C4' G A 8 OK 136 133 135 157 C4' C A 9 OK 159 156 158 177 C4' G B 11 OK 179 176 178 200 C4' U B 12 OK 202 199 201 220 C4' G B 13 OK 222 219 221 243 C4' A B 14 OK 245 242 244 265 C4' U B 15 OK 267 264 266 285 C4' C B 16 OK 287 284 286 305 C4' G B 17 OK 307 304 306 328 C4' C B 18 OK 330 327 329 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 2 4 6 28 C5' U A 3 27 29 48 C5' G A 4 47 49 71 C5' A A 5 70 72 93 C5' U A 6 92 94 113 C5' C A 7 112 114 133 C5' G A 8 132 134 156 C5' C A 9 155 157 176 C5' G B 11 175 177 199 C5' U B 12 198 200 219 C5' G B 13 218 220 242 C5' A B 14 241 243 264 C5' U B 15 263 265 284 C5' C B 16 283 285 304 C5' G B 17 303 305 327 C5' C B 18 326 328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 2 distorted distorted 2 3 4 24 P U A 3 distorted distorted 9 25 26 27 44 P G A 4 distorted distorted 32 45 46 47 67 P A A 5 distorted distorted 52 68 69 70 89 P U A 6 distorted distorted 75 90 91 92 109 P C A 7 distorted distorted 97 110 111 112 129 P G A 8 distorted distorted 117 130 131 132 152 P C A 9 distorted distorted 137 153 154 155 172 P G B 11 distorted distorted 173 174 175 195 P U B 12 distorted distorted 180 196 197 198 215 P G B 13 distorted distorted 203 216 217 218 238 P A B 14 distorted distorted 223 239 240 241 260 P U B 15 distorted distorted 246 261 262 263 280 P C B 16 distorted distorted 268 281 282 283 300 P G B 17 distorted distorted 288 301 302 303 323 P C B 18 distorted distorted 308 324 325 326 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