ID code: '2Y95' 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' C A 3 alpha beta 73 93 79 76 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' C A 5 alpha beta 138 158 144 141 174 C1' A A 6 alpha beta 169 191 175 172 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' C A 8 alpha beta 232 252 238 235 268 C1' G A 9 alpha beta 263 286 269 266 302 C1' G A 10 alpha beta 297 320 303 300 336 C1' C A 11 alpha beta 331 351 337 334 367 C1' G A 12 alpha beta 362 385 368 365 401 C1' C A 13 alpha beta 396 416 402 399 432 C1' C A 14 alpha beta 427 448 433 430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' G A 4 OK OK 109 105 125 108 141 C2' C A 5 OK OK 143 139 156 142 172 C2' A A 6 OK OK 174 170 189 173 205 C2' U A 7 OK OK 207 203 220 206 235 C2' C A 8 OK OK 237 233 250 236 266 C2' G A 9 OK OK 268 264 284 267 300 C2' G A 10 OK OK 302 298 318 301 334 C2' C A 11 OK OK 336 332 349 335 365 C2' G A 12 OK OK 367 363 383 366 399 C2' C A 13 OK OK 401 397 414 400 430 C2' C A 14 OK OK 432 428 446 431 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' G A 4 OK OK 103 124 106 107 139 C3' C A 5 OK OK 137 155 140 141 170 C3' A A 6 OK OK 168 188 171 172 203 C3' U A 7 OK OK 201 219 204 205 233 C3' C A 8 OK OK 231 249 234 235 264 C3' G A 9 OK OK 262 283 265 266 298 C3' G A 10 OK OK 296 317 299 300 332 C3' C A 11 OK OK 330 348 333 334 363 C3' G A 12 OK OK 361 382 364 365 397 C3' C A 13 OK OK 395 413 398 399 428 C3' C A 14 OK OK 426 444 429 430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' G A 4 OK OK 105 123 102 104 137 C4' C A 5 OK OK 139 154 136 138 168 C4' A A 6 OK OK 170 187 167 169 201 C4' U A 7 OK OK 203 218 200 202 231 C4' C A 8 OK OK 233 248 230 232 262 C4' G A 9 OK OK 264 282 261 263 296 C4' G A 10 OK OK 298 316 295 297 330 C4' C A 11 OK OK 332 347 329 331 361 C4' G A 12 OK OK 363 381 360 362 395 C4' C A 13 OK OK 397 412 394 396 426 C4' C A 14 OK OK 428 443 425 427 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' G A 4 OK OK 101 121 122 103 136 C5' C A 5 OK OK 135 152 153 137 167 C5' A A 6 OK OK 166 185 186 168 200 C5' U A 7 OK OK 199 216 217 201 230 C5' C A 8 OK OK 229 246 247 231 261 C5' G A 9 OK OK 260 280 281 262 295 C5' G A 10 OK OK 294 314 315 296 329 C5' C A 11 OK OK 328 345 346 330 360 C5' G A 12 OK OK 359 379 380 361 394 C5' C A 13 OK OK 393 410 411 395 425 C5' C A 14 OK OK 424 441 442 426 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 75 99 100 101 132 P C A 5 distorted distorted 106 133 134 135 163 P A A 6 distorted distorted 140 164 165 166 196 P U A 7 distorted distorted 171 197 198 199 226 P C A 8 distorted distorted 204 227 228 229 257 P G A 9 distorted distorted 234 258 259 260 291 P G A 10 distorted distorted 265 292 293 294 325 P C A 11 distorted distorted 299 326 327 328 356 P G A 12 distorted distorted 333 357 358 359 390 P C A 13 distorted distorted 364 391 392 393 421 P C A 14 distorted distorted 398 422 423 424 ---------------------------------------------------------------------------------