ID code: '1MV2' 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' A A 4 alpha beta 104 126 110 107 140 C1' P5P A 5 alpha beta 146 155 139 141 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' C A 7 alpha beta 202 222 208 205 238 C1' C A 8 alpha beta 233 253 239 236 269 C1' U A 9 alpha beta 264 285 270 267 298 C1' G B 1 alpha beta 293 316 299 296 333 C1' G B 2 alpha beta 328 351 334 331 367 C1' C B 3 alpha beta 362 382 368 365 398 C1' A B 4 alpha beta 393 415 399 396 429 C1' P5P B 5 alpha beta 435 444 428 430 462 C1' G B 6 alpha beta 457 480 463 460 496 C1' C B 7 alpha beta 491 511 497 494 527 C1' C B 8 alpha beta 522 542 528 525 558 C1' U B 9 alpha beta 553 574 559 556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 4 OK OK 109 105 124 108 141 C2' P5P A 5 OK OK 140 143 156 142 171 C2' G A 6 OK OK 173 169 189 172 205 C2' C A 7 OK OK 207 203 220 206 236 C2' C A 8 OK OK 238 234 251 237 267 C2' U A 9 OK OK 269 265 283 268 296 C2' G B 1 OK OK 298 294 314 297 331 C2' G B 2 OK OK 333 329 349 332 365 C2' C B 3 OK OK 367 363 380 366 396 C2' A B 4 OK OK 398 394 413 397 430 C2' P5P B 5 OK OK 429 432 445 431 460 C2' G B 6 OK OK 462 458 478 461 494 C2' C B 7 OK OK 496 492 509 495 525 C2' C B 8 OK OK 527 523 540 526 556 C2' U B 9 OK OK 558 554 572 557 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 103 123 106 107 143 C3' P5P A 5 OK OK 145 158 144 141 169 C3' G A 6 OK OK 167 188 170 171 203 C3' C A 7 OK OK 201 219 204 205 234 C3' C A 8 OK OK 232 250 235 236 265 C3' U A 9 OK OK 263 281 266 267 294 C3' G B 1 OK OK 292 313 295 296 329 C3' G B 2 OK OK 327 348 330 331 363 C3' C B 3 OK OK 361 379 364 365 394 C3' A B 4 OK OK 392 412 395 396 432 C3' P5P B 5 OK OK 434 447 433 430 458 C3' G B 6 OK OK 456 477 459 460 492 C3' C B 7 OK OK 490 508 493 494 523 C3' C B 8 OK OK 521 539 524 525 554 C3' U B 9 OK OK 552 570 555 556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 105 122 102 104 145 C4' P5P A 5 OK OK 143 159 147 146 167 C4' G A 6 OK OK 169 187 166 168 201 C4' C A 7 OK OK 203 218 200 202 232 C4' C A 8 OK OK 234 249 231 233 263 C4' U A 9 OK OK 265 280 262 264 292 C4' G B 1 OK OK 294 312 291 293 327 C4' G B 2 OK OK 329 347 326 328 361 C4' C B 3 OK OK 363 378 360 362 392 C4' A B 4 OK OK 394 411 391 393 434 C4' P5P B 5 OK OK 432 448 436 435 456 C4' G B 6 OK OK 458 476 455 457 490 C4' C B 7 OK OK 492 507 489 491 521 C4' C B 8 OK OK 523 538 520 522 552 C4' U B 9 OK OK 554 569 551 553 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 101 120 121 103 147 C5' P5P A 5 OK OK 148 160 161 145 166 C5' G A 6 OK OK 165 185 186 167 200 C5' C A 7 OK OK 199 216 217 201 231 C5' C A 8 OK OK 230 247 248 232 262 C5' U A 9 OK OK 261 278 279 263 291 C5' G B 1 OK OK 290 310 311 292 326 C5' G B 2 OK OK 325 345 346 327 360 C5' C B 3 OK OK 359 376 377 361 391 C5' A B 4 OK OK 390 409 410 392 436 C5' P5P B 5 OK OK 437 449 450 434 455 C5' G B 6 OK OK 454 474 475 456 489 C5' C B 7 OK OK 488 505 506 490 520 C5' C B 8 OK OK 519 536 537 521 551 C5' U B 9 OK OK 550 567 568 552 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 4 distorted distorted 75 99 100 101 149 P P5P A 5 distorted distorted 106 150 151 148 162 P G A 6 distorted distorted 144 163 164 165 196 P C A 7 distorted distorted 170 197 198 199 227 P C A 8 distorted distorted 204 228 229 230 258 P U A 9 distorted distorted 235 259 260 261 322 P G B 2 distorted distorted 295 323 324 325 356 P C B 3 distorted distorted 330 357 358 359 387 P A B 4 distorted distorted 364 388 389 390 438 P P5P B 5 distorted distorted 395 439 440 437 451 P G B 6 distorted distorted 433 452 453 454 485 P C B 7 distorted distorted 459 486 487 488 516 P C B 8 distorted distorted 493 517 518 519 547 P U B 9 distorted distorted 524 548 549 550 ---------------------------------------------------------------------------------