ID code: '1XWU' 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' C A 1 alpha beta 4 24 10 7 41 C1' G A 2 alpha beta 36 59 42 39 75 C1' A A 3 alpha beta 70 92 76 73 108 C1' A A 4 alpha beta 103 125 109 106 141 C1' A A 5 alpha beta 136 158 142 139 174 C1' C A 6 alpha beta 169 189 175 172 205 C1' A A 7 alpha beta 200 222 206 203 238 C1' U A 8 alpha beta 233 253 239 236 268 C1' A A 9 alpha beta 263 285 269 266 301 C1' G A 10 alpha beta 296 319 302 299 335 C1' A A 11 alpha beta 330 352 336 333 368 C1' U A 12 alpha beta 363 383 369 366 398 C1' U A 13 alpha beta 393 413 399 396 428 C1' C A 14 alpha beta 423 443 429 426 459 C1' G A 15 alpha beta 454 477 460 457 493 C1' A A 16 alpha beta 488 511 494 491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK OK 9 5 22 8 39 C2' G A 2 OK OK 41 37 57 40 73 C2' A A 3 OK OK 75 71 90 74 106 C2' A A 4 OK OK 108 104 123 107 139 C2' A A 5 OK OK 141 137 156 140 172 C2' C A 6 OK OK 174 170 187 173 203 C2' A A 7 OK OK 205 201 220 204 236 C2' U A 8 OK OK 238 234 251 237 266 C2' A A 9 OK OK 268 264 283 267 299 C2' G A 10 OK OK 301 297 317 300 333 C2' A A 11 OK OK 335 331 350 334 366 C2' U A 12 OK OK 368 364 381 367 396 C2' U A 13 OK OK 398 394 411 397 426 C2' C A 14 OK OK 428 424 441 427 457 C2' G A 15 OK OK 459 455 475 458 491 C2' A A 16 OK OK 493 489 509 492 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' G A 2 OK OK 35 56 38 39 71 C3' A A 3 OK OK 69 89 72 73 104 C3' A A 4 OK OK 102 122 105 106 137 C3' A A 5 OK OK 135 155 138 139 170 C3' C A 6 OK OK 168 186 171 172 201 C3' A A 7 OK OK 199 219 202 203 234 C3' U A 8 OK OK 232 250 235 236 264 C3' A A 9 OK OK 262 282 265 266 297 C3' G A 10 OK OK 295 316 298 299 331 C3' A A 11 OK OK 329 349 332 333 364 C3' U A 12 OK OK 362 380 365 366 394 C3' U A 13 OK OK 392 410 395 396 424 C3' C A 14 OK OK 422 440 425 426 455 C3' G A 15 OK OK 453 474 456 457 489 C3' A A 16 OK OK 487 507 490 491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' G A 2 OK OK 37 55 34 36 69 C4' A A 3 OK OK 71 88 68 70 102 C4' A A 4 OK OK 104 121 101 103 135 C4' A A 5 OK OK 137 154 134 136 168 C4' C A 6 OK OK 170 185 167 169 199 C4' A A 7 OK OK 201 218 198 200 232 C4' U A 8 OK OK 234 249 231 233 262 C4' A A 9 OK OK 264 281 261 263 295 C4' G A 10 OK OK 297 315 294 296 329 C4' A A 11 OK OK 331 348 328 330 362 C4' U A 12 OK OK 364 379 361 363 392 C4' U A 13 OK OK 394 409 391 393 422 C4' C A 14 OK OK 424 439 421 423 453 C4' G A 15 OK OK 455 473 452 454 487 C4' A A 16 OK OK 489 506 486 488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 34 C5' G A 2 OK OK 33 53 54 35 68 C5' A A 3 OK OK 67 86 87 69 101 C5' A A 4 OK OK 100 119 120 102 134 C5' A A 5 OK OK 133 152 153 135 167 C5' C A 6 OK OK 166 183 184 168 198 C5' A A 7 OK OK 197 216 217 199 231 C5' U A 8 OK OK 230 247 248 232 261 C5' A A 9 OK OK 260 279 280 262 294 C5' G A 10 OK OK 293 313 314 295 328 C5' A A 11 OK OK 327 346 347 329 361 C5' U A 12 OK OK 360 377 378 362 391 C5' U A 13 OK OK 390 407 408 392 421 C5' C A 14 OK OK 420 437 438 422 452 C5' G A 15 OK OK 451 471 472 453 486 C5' A A 16 OK OK 485 504 505 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P G A 2 distorted distorted 6 31 32 33 64 P A A 3 distorted distorted 38 65 66 67 97 P A A 4 distorted distorted 72 98 99 100 130 P A A 5 distorted distorted 105 131 132 133 163 P C A 6 distorted distorted 138 164 165 166 194 P A A 7 distorted distorted 171 195 196 197 227 P U A 8 distorted distorted 202 228 229 230 257 P A A 9 distorted distorted 235 258 259 260 290 P G A 10 distorted distorted 265 291 292 293 324 P A A 11 distorted distorted 298 325 326 327 357 P U A 12 distorted distorted 332 358 359 360 387 P U A 13 distorted distorted 365 388 389 390 417 P C A 14 distorted distorted 395 418 419 420 448 P G A 15 distorted distorted 425 449 450 451 482 P A A 16 distorted distorted 456 483 484 485 ---------------------------------------------------------------------------------