ID code: '1AFX' 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 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' U A 5 alpha beta 137 157 143 140 172 C1' G A 6 alpha beta 167 190 173 170 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' A A 8 alpha beta 234 256 240 237 272 C1' C A 9 alpha beta 267 287 273 270 303 C1' A A 10 alpha beta 298 320 304 301 336 C1' C A 11 alpha beta 331 351 337 334 367 C1' C A 12 alpha beta 362 383 368 365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' U A 5 OK OK 142 138 155 141 170 C2' G A 6 OK OK 172 168 188 171 204 C2' A A 7 OK OK 206 202 221 205 237 C2' A A 8 OK OK 239 235 254 238 270 C2' C A 9 OK OK 272 268 285 271 301 C2' A A 10 OK OK 303 299 318 302 334 C2' C A 11 OK OK 336 332 349 335 365 C2' C A 12 OK OK 367 363 381 366 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' U A 5 OK OK 136 154 139 140 168 C3' G A 6 OK OK 166 187 169 170 202 C3' A A 7 OK OK 200 220 203 204 235 C3' A A 8 OK OK 233 253 236 237 268 C3' C A 9 OK OK 266 284 269 270 299 C3' A A 10 OK OK 297 317 300 301 332 C3' C A 11 OK OK 330 348 333 334 363 C3' C A 12 OK OK 361 379 364 365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' U A 5 OK OK 138 153 135 137 166 C4' G A 6 OK OK 168 186 165 167 200 C4' A A 7 OK OK 202 219 199 201 233 C4' A A 8 OK OK 235 252 232 234 266 C4' C A 9 OK OK 268 283 265 267 297 C4' A A 10 OK OK 299 316 296 298 330 C4' C A 11 OK OK 332 347 329 331 361 C4' C A 12 OK OK 363 378 360 362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' U A 5 OK OK 134 151 152 136 165 C5' G A 6 OK OK 164 184 185 166 199 C5' A A 7 OK OK 198 217 218 200 232 C5' A A 8 OK OK 231 250 251 233 265 C5' C A 9 OK OK 264 281 282 266 296 C5' A A 10 OK OK 295 314 315 297 329 C5' C A 11 OK OK 328 345 346 330 360 C5' C A 12 OK OK 359 376 377 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P U A 5 distorted distorted 105 132 133 134 161 P G A 6 distorted distorted 139 162 163 164 195 P A A 7 distorted distorted 169 196 197 198 228 P A A 8 distorted distorted 203 229 230 231 261 P C A 9 distorted distorted 236 262 263 264 292 P A A 10 distorted distorted 269 293 294 295 325 P C A 11 distorted distorted 300 326 327 328 356 P C A 12 distorted distorted 333 357 358 359 ---------------------------------------------------------------------------------