ID code: '1CX5' 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' DC A 1 alpha beta 4 23 9 7 39 C1' DG A 2 alpha beta 35 57 40 38 72 C1' DC A 3 alpha beta 68 87 73 71 102 C1' DG A 4 alpha beta 98 120 103 101 135 C1' DT A 5 alpha beta 131 151 136 134 166 C1' DT A 6 alpha beta 163 182 167 165 195 C1' MMT A 7 alpha beta 194 216 199 196 235 C1' DT A 8 alpha beta 231 251 236 234 267 C1' DG A 9 alpha beta 263 285 268 266 300 C1' DC A 10 alpha beta 296 315 301 299 330 C1' DG A 11 alpha beta 326 348 331 329 363 C1' DC A 12 alpha beta 359 379 364 362 393 C1' G B 101 alpha beta 388 411 394 391 428 C1' C B 102 alpha beta 423 443 429 426 459 C1' G B 103 alpha beta 454 477 460 457 493 C1' C B 104 alpha beta 488 508 494 491 524 C1' A B 105 alpha beta 519 541 525 522 557 C1' A B 106 alpha beta 552 574 558 555 590 C1' A B 107 alpha beta 585 607 591 588 623 C1' A B 108 alpha beta 618 640 624 621 656 C1' C B 109 alpha beta 651 671 657 654 687 C1' G B 110 alpha beta 682 705 688 685 721 C1' C B 111 alpha beta 716 736 722 719 752 C1' G B 112 alpha beta 747 771 753 750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DC A 1 OK OK 8 5 21 22 38 C2' DG A 2 OK OK 39 36 55 56 71 C2' DC A 3 OK OK 72 69 85 86 101 C2' DG A 4 OK OK 102 99 118 119 134 C2' DT A 5 OK OK 135 132 149 150 165 C2' DT A 6 OK OK 166 164 180 181 196 C2' MMT A 7 distorted OK 195 197 217 218 234 C2' DT A 8 OK OK 235 232 249 250 266 C2' DG A 9 OK OK 267 264 283 284 299 C2' DC A 10 OK OK 300 297 313 314 329 C2' DG A 11 OK OK 330 327 346 347 362 C2' DC A 12 OK OK 363 360 377 378 391 C2' G B 101 OK OK 393 389 409 392 426 C2' C B 102 OK OK 428 424 441 427 457 C2' G B 103 OK OK 459 455 475 458 491 C2' C B 104 OK OK 493 489 506 492 522 C2' A B 105 OK OK 524 520 539 523 555 C2' A B 106 OK OK 557 553 572 556 588 C2' A B 107 OK OK 590 586 605 589 621 C2' A B 108 OK OK 623 619 638 622 654 C2' C B 109 OK OK 656 652 669 655 685 C2' G B 110 OK OK 687 683 703 686 719 C2' C B 111 OK OK 721 717 734 720 750 C2' G B 112 OK OK 752 748 769 751 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC A 1 OK OK 3 20 6 7 36 C3' DG A 2 OK OK 34 54 37 38 69 C3' DC A 3 OK OK 67 84 70 71 99 C3' DG A 4 OK OK 97 117 100 101 132 C3' DT A 5 OK OK 130 148 133 134 164 C3' DT A 6 OK 162 179 165 197 C3' MMT A 7 OK OK 193 219 198 196 232 C3' DT A 8 OK OK 230 248 233 234 264 C3' DG A 9 OK OK 262 282 265 266 297 C3' DC A 10 OK OK 295 312 298 299 327 C3' DG A 11 OK OK 325 345 328 329 360 C3' DC A 12 OK OK 358 375 361 362 389 C3' G B 101 OK OK 387 408 390 391 424 C3' C B 102 OK OK 422 440 425 426 455 C3' G B 103 OK OK 453 474 456 457 489 C3' C B 104 OK OK 487 505 490 491 520 C3' A B 105 OK OK 518 538 521 522 553 C3' A B 106 OK OK 551 571 554 555 586 C3' A B 107 OK OK 584 604 587 588 619 C3' A B 108 OK OK 617 637 620 621 652 C3' C B 109 OK OK 650 668 653 654 683 C3' G B 110 OK OK 681 702 684 685 717 C3' C B 111 OK OK 715 733 718 719 748 C3' G B 112 OK OK 746 767 749 750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC A 1 OK OK 5 19 2 4 34 C4' DG A 2 OK OK 36 53 33 35 67 C4' DC A 3 OK OK 69 83 66 68 97 C4' DG A 4 OK OK 99 116 96 98 130 C4' DT A 5 OK OK 132 147 129 131 162 C4' DT A 6 OK OK 164 178 161 163 193 C4' MMT A 7 OK OK 197 215 192 194 230 C4' DT A 8 OK OK 232 247 229 231 262 C4' DG A 9 OK OK 264 281 261 263 295 C4' DC A 10 OK OK 297 311 294 296 325 C4' DG A 11 OK OK 327 344 324 326 358 C4' DC A 12 OK OK 360 374 357 359 387 C4' G B 101 OK OK 389 407 386 388 422 C4' C B 102 OK OK 424 439 421 423 453 C4' G B 103 OK OK 455 473 452 454 487 C4' C B 104 OK OK 489 504 486 488 518 C4' A B 105 OK OK 520 537 517 519 551 C4' A B 106 OK OK 553 570 550 552 584 C4' A B 107 OK OK 586 603 583 585 617 C4' A B 108 OK OK 619 636 616 618 650 C4' C B 109 OK OK 652 667 649 651 681 C4' G B 110 OK OK 683 701 680 682 715 C4' C B 111 OK OK 717 732 714 716 746 C4' G B 112 OK OK 748 766 745 747 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC A 1 OK OK 1 17 18 3 33 C5' DG A 2 OK OK 32 51 52 34 66 C5' DC A 3 OK OK 65 81 82 67 96 C5' DG A 4 OK OK 95 114 115 97 129 C5' DT A 5 OK OK 128 145 146 130 161 C5' DT A 6 OK OK 160 176 177 162 192 C5' MMT A 7 OK OK 191 213 214 193 229 C5' DT A 8 OK OK 228 245 246 230 261 C5' DG A 9 OK OK 260 279 280 262 294 C5' DC A 10 OK OK 293 309 310 295 324 C5' DG A 11 OK OK 323 342 343 325 357 C5' DC A 12 OK OK 356 372 373 358 386 C5' G B 101 OK OK 385 405 406 387 421 C5' C B 102 OK OK 420 437 438 422 452 C5' G B 103 OK OK 451 471 472 453 486 C5' C B 104 OK OK 485 502 503 487 517 C5' A B 105 OK OK 516 535 536 518 550 C5' A B 106 OK OK 549 568 569 551 583 C5' A B 107 OK OK 582 601 602 584 616 C5' A B 108 OK OK 615 634 635 617 649 C5' C B 109 OK OK 648 665 666 650 680 C5' G B 110 OK OK 679 699 700 681 714 C5' C B 111 OK OK 713 730 731 715 745 C5' G B 112 OK OK 744 764 765 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P DG A 2 distorted distorted 6 30 31 32 62 P DC A 3 distorted distorted 37 63 64 65 92 P DG A 4 distorted distorted 70 93 94 95 125 P DT A 5 distorted distorted 100 126 127 128 157 P DT A 6 distorted distorted 133 158 159 160 225 P DT A 8 distorted distorted 198 226 227 228 257 P DG A 9 distorted distorted 233 258 259 260 290 P DC A 10 distorted distorted 265 291 292 293 320 P DG A 11 distorted distorted 298 321 322 323 353 P DC A 12 distorted distorted 328 354 355 356 417 P C B 102 distorted distorted 390 418 419 420 448 P G B 103 distorted distorted 425 449 450 451 482 P C B 104 distorted distorted 456 483 484 485 513 P A B 105 distorted distorted 490 514 515 516 546 P A B 106 distorted distorted 521 547 548 549 579 P A B 107 distorted distorted 554 580 581 582 612 P A B 108 distorted distorted 587 613 614 615 645 P C B 109 distorted distorted 620 646 647 648 676 P G B 110 distorted distorted 653 677 678 679 710 P C B 111 distorted distorted 684 711 712 713 741 P G B 112 distorted distorted 718 742 743 744 ---------------------------------------------------------------------------------