ID code: '1C2Q' 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' --------------------------------------------------------------------------------- 8 C1' DA A 1 alpha beta 4 25 9 7 41 C1' DT A 2 alpha beta 37 57 42 40 73 C1' DG A 3 alpha beta 69 91 74 72 106 C1' DG A 4 alpha beta 102 124 107 105 139 C1' T3P A 5 beta alpha 135 155 140 138 171 C1' DG A 6 alpha beta 167 189 172 170 204 C1' DC A 7 alpha beta 200 219 205 203 234 C1' DT A 8 alpha beta 230 250 235 233 266 C1' DC A 9 alpha beta 262 282 267 265 296 C1' G B 10 alpha beta 291 314 297 294 331 C1' A B 11 alpha beta 326 348 332 329 364 C1' G B 12 alpha beta 359 382 365 362 398 C1' C B 13 alpha beta 393 413 399 396 429 C1' A B 14 alpha beta 424 446 430 427 462 C1' C B 15 alpha beta 457 477 463 460 493 C1' C B 16 alpha beta 488 508 494 491 524 C1' A B 17 alpha beta 519 541 525 522 557 C1' U B 18 alpha beta 552 573 558 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DA A 1 OK OK 8 5 23 24 40 C2' DT A 2 OK OK 41 38 55 56 72 C2' DG A 3 OK OK 73 70 89 90 105 C2' DG A 4 OK OK 106 103 122 123 138 C2' T3P A 5 OK OK 139 136 153 154 170 C2' DG A 6 OK OK 171 168 187 188 203 C2' DC A 7 OK OK 204 201 217 218 233 C2' DT A 8 OK OK 234 231 248 249 265 C2' DC A 9 OK OK 266 263 280 281 294 C2' G B 10 OK OK 296 292 312 295 329 C2' A B 11 OK OK 331 327 346 330 362 C2' G B 12 OK OK 364 360 380 363 396 C2' C B 13 OK OK 398 394 411 397 427 C2' A B 14 OK OK 429 425 444 428 460 C2' C B 15 OK OK 462 458 475 461 491 C2' C B 16 OK OK 493 489 506 492 522 C2' A B 17 OK OK 524 520 539 523 555 C2' U B 18 OK OK 557 553 571 556 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DA A 1 OK OK 3 22 6 7 38 C3' DT A 2 OK OK 36 54 39 40 70 C3' DG A 3 OK OK 68 88 71 72 103 C3' DG A 4 OK OK 101 121 104 105 136 C3' T3P A 5 OK OK 134 152 137 138 168 C3' DG A 6 OK OK 166 186 169 170 201 C3' DC A 7 OK OK 199 216 202 203 231 C3' DT A 8 OK OK 229 247 232 233 263 C3' DC A 9 OK OK 261 278 264 265 292 C3' G B 10 OK OK 290 311 293 294 327 C3' A B 11 OK OK 325 345 328 329 360 C3' G B 12 OK OK 358 379 361 362 394 C3' C B 13 OK OK 392 410 395 396 425 C3' A B 14 OK OK 423 443 426 427 458 C3' C B 15 OK OK 456 474 459 460 489 C3' C B 16 OK OK 487 505 490 491 520 C3' A B 17 OK OK 518 538 521 522 553 C3' U B 18 OK OK 551 569 554 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DA A 1 OK OK 5 21 2 4 36 C4' DT A 2 OK OK 38 53 35 37 68 C4' DG A 3 OK OK 70 87 67 69 101 C4' DG A 4 OK OK 103 120 100 102 134 C4' T3P A 5 OK OK 136 151 133 135 166 C4' DG A 6 OK OK 168 185 165 167 199 C4' DC A 7 OK OK 201 215 198 200 229 C4' DT A 8 OK OK 231 246 228 230 261 C4' DC A 9 OK OK 263 277 260 262 290 C4' G B 10 OK OK 292 310 289 291 325 C4' A B 11 OK OK 327 344 324 326 358 C4' G B 12 OK OK 360 378 357 359 392 C4' C B 13 OK OK 394 409 391 393 423 C4' A B 14 OK OK 425 442 422 424 456 C4' C B 15 OK OK 458 473 455 457 487 C4' C B 16 OK OK 489 504 486 488 518 C4' A B 17 OK OK 520 537 517 519 551 C4' U B 18 OK OK 553 568 550 552 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DA A 1 OK OK 1 19 20 3 35 C5' DT A 2 OK OK 34 51 52 36 67 C5' DG A 3 OK OK 66 85 86 68 100 C5' DG A 4 OK OK 99 118 119 101 133 C5' T3P A 5 OK OK 132 149 150 134 165 C5' DG A 6 OK OK 164 183 184 166 198 C5' DC A 7 OK OK 197 213 214 199 228 C5' DT A 8 OK OK 227 244 245 229 260 C5' DC A 9 OK OK 259 275 276 261 289 C5' G B 10 OK OK 288 308 309 290 324 C5' A B 11 OK OK 323 342 343 325 357 C5' G B 12 OK OK 356 376 377 358 391 C5' C B 13 OK OK 390 407 408 392 422 C5' A B 14 OK OK 421 440 441 423 455 C5' C B 15 OK OK 454 471 472 456 486 C5' C B 16 OK OK 485 502 503 487 517 C5' A B 17 OK OK 516 535 536 518 550 C5' U B 18 OK OK 549 566 567 551 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 31 P DT A 2 distorted distorted 6 32 33 34 63 P DG A 3 distorted distorted 39 64 65 66 96 P DG A 4 distorted distorted 71 97 98 99 129 P T3P A 5 OK OK 137 130 131 161 P DG A 6 distorted distorted 162 163 164 194 P DC A 7 distorted distorted 169 195 196 197 224 P DT A 8 distorted distorted 202 225 226 227 256 P DC A 9 distorted distorted 232 257 258 259 320 P A B 11 distorted distorted 293 321 322 323 353 P G B 12 distorted distorted 328 354 355 356 387 P C B 13 distorted distorted 361 388 389 390 418 P A B 14 distorted distorted 395 419 420 421 451 P C B 15 distorted distorted 426 452 453 454 482 P C B 16 distorted distorted 459 483 484 485 513 P A B 17 distorted distorted 490 514 515 516 546 P U B 18 distorted distorted 521 547 548 549 ---------------------------------------------------------------------------------