ID code: '4JAB' 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' U A 2 beta 27 33 30 52 C1' G A 3 beta 47 53 50 75 C1' U A 4 beta 70 76 73 95 C1' A A 5 beta 90 96 93 117 C1' U A 6 beta 112 118 115 137 C1' A A 7 beta 132 138 135 159 C1' C A 8 beta 154 160 157 177 C1' G B 9 beta 172 178 175 200 C1' U B 10 beta 195 201 198 220 C1' G B 11 beta 215 221 218 243 C1' U B 12 beta 238 244 241 263 C1' A B 13 beta 258 264 261 285 C1' U B 14 beta 280 286 283 305 C1' A B 15 beta 300 306 303 327 C1' C B 16 beta 322 328 325 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 2 OK 32 28 31 50 C2' G A 3 OK 52 48 51 73 C2' U A 4 OK 75 71 74 93 C2' A A 5 OK 95 91 94 115 C2' U A 6 OK 117 113 116 135 C2' A A 7 OK 137 133 136 157 C2' C A 8 OK 159 155 158 175 C2' G B 9 OK 177 173 176 198 C2' U B 10 OK 200 196 199 218 C2' G B 11 OK 220 216 219 241 C2' U B 12 OK 243 239 242 261 C2' A B 13 OK 263 259 262 283 C2' U B 14 OK 285 281 284 303 C2' A B 15 OK 305 301 304 325 C2' C B 16 OK 327 323 326 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' U A 2 OK 26 29 30 48 C3' G A 3 OK 46 49 50 71 C3' U A 4 OK 69 72 73 91 C3' A A 5 OK 89 92 93 113 C3' U A 6 OK 111 114 115 133 C3' A A 7 OK 131 134 135 155 C3' C A 8 OK 153 156 157 173 C3' G B 9 OK 171 174 175 196 C3' U B 10 OK 194 197 198 216 C3' G B 11 OK 214 217 218 239 C3' U B 12 OK 237 240 241 259 C3' A B 13 OK 257 260 261 281 C3' U B 14 OK 279 282 283 301 C3' A B 15 OK 299 302 303 323 C3' C B 16 OK 321 324 325 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' U A 2 OK 28 25 27 46 C4' G A 3 OK 48 45 47 69 C4' U A 4 OK 71 68 70 89 C4' A A 5 OK 91 88 90 111 C4' U A 6 OK 113 110 112 131 C4' A A 7 OK 133 130 132 153 C4' C A 8 OK 155 152 154 171 C4' G B 9 OK 173 170 172 194 C4' U B 10 OK 196 193 195 214 C4' G B 11 OK 216 213 215 237 C4' U B 12 OK 239 236 238 257 C4' A B 13 OK 259 256 258 279 C4' U B 14 OK 281 278 280 299 C4' A B 15 OK 301 298 300 321 C4' C B 16 OK 323 320 322 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' U A 2 24 26 45 C5' G A 3 44 46 68 C5' U A 4 67 69 88 C5' A A 5 87 89 110 C5' U A 6 109 111 130 C5' A A 7 129 131 152 C5' C A 8 151 153 170 C5' G B 9 169 171 193 C5' U B 10 192 194 213 C5' G B 11 212 214 236 C5' U B 12 235 237 256 C5' A B 13 255 257 278 C5' U B 14 277 279 298 C5' A B 15 297 299 320 C5' C B 16 319 321 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P U A 2 distorted distorted 6 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P U A 4 distorted distorted 49 65 66 67 84 P A A 5 distorted distorted 72 85 86 87 106 P U A 6 distorted distorted 92 107 108 109 126 P A A 7 distorted distorted 114 127 128 129 148 P C A 8 distorted distorted 134 149 150 151 189 P U B 10 distorted distorted 174 190 191 192 209 P G B 11 distorted distorted 197 210 211 212 232 P U B 12 distorted distorted 217 233 234 235 252 P A B 13 distorted distorted 240 253 254 255 274 P U B 14 distorted distorted 260 275 276 277 294 P A B 15 distorted distorted 282 295 296 297 316 P C B 16 distorted distorted 302 317 318 319 ---------------------------------------------------------------------------------