ID code: '2FY1' 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 B 109 alpha beta 4 27 10 7 44 C1' G B 110 alpha beta 39 62 45 42 78 C1' A B 111 alpha beta 73 95 79 76 111 C1' C B 112 alpha beta 106 126 112 109 142 C1' U B 113 alpha beta 137 157 143 140 172 C1' G B 114 alpha beta 167 190 173 170 206 C1' U B 115 alpha beta 201 221 207 204 236 C1' C B 116 alpha beta 231 251 237 234 267 C1' C B 117 alpha beta 262 282 268 265 298 C1' A B 118 alpha beta 293 315 299 296 331 C1' C B 119 alpha beta 326 346 332 329 362 C1' A B 120 alpha beta 357 379 363 360 395 C1' A B 121 alpha beta 390 412 396 393 428 C1' G B 122 alpha beta 423 446 429 426 462 C1' A B 123 alpha beta 457 479 463 460 495 C1' C B 124 alpha beta 490 510 496 493 526 C1' A B 125 alpha beta 521 543 527 524 559 C1' G B 126 alpha beta 554 577 560 557 593 C1' U B 127 alpha beta 588 608 594 591 623 C1' C B 128 alpha beta 618 638 624 621 654 C1' C B 129 alpha beta 649 670 655 652 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 109 OK OK 9 5 25 8 42 C2' G B 110 OK OK 44 40 60 43 76 C2' A B 111 OK OK 78 74 93 77 109 C2' C B 112 OK OK 111 107 124 110 140 C2' U B 113 OK OK 142 138 155 141 170 C2' G B 114 OK OK 172 168 188 171 204 C2' U B 115 OK OK 206 202 219 205 234 C2' C B 116 OK OK 236 232 249 235 265 C2' C B 117 OK OK 267 263 280 266 296 C2' A B 118 OK OK 298 294 313 297 329 C2' C B 119 OK OK 331 327 344 330 360 C2' A B 120 OK OK 362 358 377 361 393 C2' A B 121 OK OK 395 391 410 394 426 C2' G B 122 OK OK 428 424 444 427 460 C2' A B 123 OK OK 462 458 477 461 493 C2' C B 124 OK OK 495 491 508 494 524 C2' A B 125 OK OK 526 522 541 525 557 C2' G B 126 OK OK 559 555 575 558 591 C2' U B 127 OK OK 593 589 606 592 621 C2' C B 128 OK OK 623 619 636 622 652 C2' C B 129 OK OK 654 650 668 653 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 109 OK OK 3 24 6 7 40 C3' G B 110 OK OK 38 59 41 42 74 C3' A B 111 OK OK 72 92 75 76 107 C3' C B 112 OK OK 105 123 108 109 138 C3' U B 113 OK OK 136 154 139 140 168 C3' G B 114 OK OK 166 187 169 170 202 C3' U B 115 OK OK 200 218 203 204 232 C3' C B 116 OK OK 230 248 233 234 263 C3' C B 117 OK OK 261 279 264 265 294 C3' A B 118 OK OK 292 312 295 296 327 C3' C B 119 OK OK 325 343 328 329 358 C3' A B 120 OK OK 356 376 359 360 391 C3' A B 121 OK OK 389 409 392 393 424 C3' G B 122 OK OK 422 443 425 426 458 C3' A B 123 OK OK 456 476 459 460 491 C3' C B 124 OK OK 489 507 492 493 522 C3' A B 125 OK OK 520 540 523 524 555 C3' G B 126 OK OK 553 574 556 557 589 C3' U B 127 OK OK 587 605 590 591 619 C3' C B 128 OK OK 617 635 620 621 650 C3' C B 129 OK OK 648 666 651 652 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 109 OK OK 5 23 2 4 38 C4' G B 110 OK OK 40 58 37 39 72 C4' A B 111 OK OK 74 91 71 73 105 C4' C B 112 OK OK 107 122 104 106 136 C4' U B 113 OK OK 138 153 135 137 166 C4' G B 114 OK OK 168 186 165 167 200 C4' U B 115 OK OK 202 217 199 201 230 C4' C B 116 OK OK 232 247 229 231 261 C4' C B 117 OK OK 263 278 260 262 292 C4' A B 118 OK OK 294 311 291 293 325 C4' C B 119 OK OK 327 342 324 326 356 C4' A B 120 OK OK 358 375 355 357 389 C4' A B 121 OK OK 391 408 388 390 422 C4' G B 122 OK OK 424 442 421 423 456 C4' A B 123 OK OK 458 475 455 457 489 C4' C B 124 OK OK 491 506 488 490 520 C4' A B 125 OK OK 522 539 519 521 553 C4' G B 126 OK OK 555 573 552 554 587 C4' U B 127 OK OK 589 604 586 588 617 C4' C B 128 OK OK 619 634 616 618 648 C4' C B 129 OK OK 650 665 647 649 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 109 OK OK 1 21 22 3 37 C5' G B 110 OK OK 36 56 57 38 71 C5' A B 111 OK OK 70 89 90 72 104 C5' C B 112 OK OK 103 120 121 105 135 C5' U B 113 OK OK 134 151 152 136 165 C5' G B 114 OK OK 164 184 185 166 199 C5' U B 115 OK OK 198 215 216 200 229 C5' C B 116 OK OK 228 245 246 230 260 C5' C B 117 OK OK 259 276 277 261 291 C5' A B 118 OK OK 290 309 310 292 324 C5' C B 119 OK OK 323 340 341 325 355 C5' A B 120 OK OK 354 373 374 356 388 C5' A B 121 OK OK 387 406 407 389 421 C5' G B 122 OK OK 420 440 441 422 455 C5' A B 123 OK OK 454 473 474 456 488 C5' C B 124 OK OK 487 504 505 489 519 C5' A B 125 OK OK 518 537 538 520 552 C5' G B 126 OK OK 551 571 572 553 586 C5' U B 127 OK OK 585 602 603 587 616 C5' C B 128 OK OK 615 632 633 617 647 C5' C B 129 OK OK 646 663 664 648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G B 110 distorted distorted 6 34 35 36 67 P A B 111 distorted distorted 41 68 69 70 100 P C B 112 distorted distorted 75 101 102 103 131 P U B 113 distorted distorted 108 132 133 134 161 P G B 114 distorted distorted 139 162 163 164 195 P U B 115 distorted distorted 169 196 197 198 225 P C B 116 distorted distorted 203 226 227 228 256 P C B 117 distorted distorted 233 257 258 259 287 P A B 118 distorted distorted 264 288 289 290 320 P C B 119 distorted distorted 295 321 322 323 351 P A B 120 distorted distorted 328 352 353 354 384 P A B 121 distorted distorted 359 385 386 387 417 P G B 122 distorted distorted 392 418 419 420 451 P A B 123 distorted distorted 425 452 453 454 484 P C B 124 distorted distorted 459 485 486 487 515 P A B 125 distorted distorted 492 516 517 518 548 P G B 126 distorted distorted 523 549 550 551 582 P U B 127 distorted distorted 556 583 584 585 612 P C B 128 distorted distorted 590 613 614 615 643 P C B 129 distorted distorted 620 644 645 646 ---------------------------------------------------------------------------------