ID code: '1MY9' 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' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' G A 5 alpha beta 140 163 146 143 179 C1' U A 6 alpha beta 174 194 180 177 209 C1' U A 7 alpha beta 204 224 210 207 239 C1' U A 8 alpha beta 234 254 240 237 269 C1' U A 9 alpha beta 264 284 270 267 299 C1' G A 10 alpha beta 294 317 300 297 333 C1' G A 11 alpha beta 328 351 334 331 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' G A 14 alpha beta 429 453 435 432 467 C1' G B 15 alpha beta 462 485 468 465 502 C1' G B 16 alpha beta 497 520 503 500 536 C1' A B 17 alpha beta 531 553 537 534 569 C1' G B 18 alpha beta 564 587 570 567 603 C1' G B 19 alpha beta 598 621 604 601 637 C1' U B 20 alpha beta 632 652 638 635 667 C1' U B 21 alpha beta 662 682 668 665 697 C1' U B 22 alpha beta 692 712 698 695 727 C1' U B 23 alpha beta 722 742 728 725 757 C1' G B 24 alpha beta 752 775 758 755 791 C1' G B 25 alpha beta 786 809 792 789 825 C1' A B 26 alpha beta 820 842 826 823 858 C1' G B 27 alpha beta 853 876 859 856 892 C1' G B 28 alpha beta 887 911 893 890 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' G A 5 OK OK 145 141 161 144 177 C2' U A 6 OK OK 179 175 192 178 207 C2' U A 7 OK OK 209 205 222 208 237 C2' U A 8 OK OK 239 235 252 238 267 C2' U A 9 OK OK 269 265 282 268 297 C2' G A 10 OK OK 299 295 315 298 331 C2' G A 11 OK OK 333 329 349 332 365 C2' A A 12 OK OK 367 363 382 366 398 C2' G A 13 OK OK 400 396 416 399 432 C2' G A 14 OK OK 434 430 451 433 465 C2' G B 15 OK OK 467 463 483 466 500 C2' G B 16 OK OK 502 498 518 501 534 C2' A B 17 OK OK 536 532 551 535 567 C2' G B 18 OK OK 569 565 585 568 601 C2' G B 19 OK OK 603 599 619 602 635 C2' U B 20 OK OK 637 633 650 636 665 C2' U B 21 OK OK 667 663 680 666 695 C2' U B 22 OK OK 697 693 710 696 725 C2' U B 23 OK OK 727 723 740 726 755 C2' G B 24 OK OK 757 753 773 756 789 C2' G B 25 OK OK 791 787 807 790 823 C2' A B 26 OK OK 825 821 840 824 856 C2' G B 27 OK OK 858 854 874 857 890 C2' G B 28 OK OK 892 888 909 891 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' G A 5 OK OK 139 160 142 143 175 C3' U A 6 OK OK 173 191 176 177 205 C3' U A 7 OK OK 203 221 206 207 235 C3' U A 8 OK OK 233 251 236 237 265 C3' U A 9 OK OK 263 281 266 267 295 C3' G A 10 OK OK 293 314 296 297 329 C3' G A 11 OK OK 327 348 330 331 363 C3' A A 12 OK OK 361 381 364 365 396 C3' G A 13 OK OK 394 415 397 398 430 C3' G A 14 OK OK 428 449 431 432 463 C3' G B 15 OK OK 461 482 464 465 498 C3' G B 16 OK OK 496 517 499 500 532 C3' A B 17 OK OK 530 550 533 534 565 C3' G B 18 OK OK 563 584 566 567 599 C3' G B 19 OK OK 597 618 600 601 633 C3' U B 20 OK OK 631 649 634 635 663 C3' U B 21 OK OK 661 679 664 665 693 C3' U B 22 OK OK 691 709 694 695 723 C3' U B 23 OK OK 721 739 724 725 753 C3' G B 24 OK OK 751 772 754 755 787 C3' G B 25 OK OK 785 806 788 789 821 C3' A B 26 OK OK 819 839 822 823 854 C3' G B 27 OK OK 852 873 855 856 888 C3' G B 28 OK OK 886 907 889 890 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' G A 5 OK OK 141 159 138 140 173 C4' U A 6 OK OK 175 190 172 174 203 C4' U A 7 OK OK 205 220 202 204 233 C4' U A 8 OK OK 235 250 232 234 263 C4' U A 9 OK OK 265 280 262 264 293 C4' G A 10 OK OK 295 313 292 294 327 C4' G A 11 OK OK 329 347 326 328 361 C4' A A 12 OK OK 363 380 360 362 394 C4' G A 13 OK OK 396 414 393 395 428 C4' G A 14 OK OK 430 448 427 429 461 C4' G B 15 OK OK 463 481 460 462 496 C4' G B 16 OK OK 498 516 495 497 530 C4' A B 17 OK OK 532 549 529 531 563 C4' G B 18 OK OK 565 583 562 564 597 C4' G B 19 OK OK 599 617 596 598 631 C4' U B 20 OK OK 633 648 630 632 661 C4' U B 21 OK OK 663 678 660 662 691 C4' U B 22 OK OK 693 708 690 692 721 C4' U B 23 OK OK 723 738 720 722 751 C4' G B 24 OK OK 753 771 750 752 785 C4' G B 25 OK OK 787 805 784 786 819 C4' A B 26 OK OK 821 838 818 820 852 C4' G B 27 OK OK 854 872 851 853 886 C4' G B 28 OK OK 888 906 885 887 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' G A 5 OK OK 137 157 158 139 172 C5' U A 6 OK OK 171 188 189 173 202 C5' U A 7 OK OK 201 218 219 203 232 C5' U A 8 OK OK 231 248 249 233 262 C5' U A 9 OK OK 261 278 279 263 292 C5' G A 10 OK OK 291 311 312 293 326 C5' G A 11 OK OK 325 345 346 327 360 C5' A A 12 OK OK 359 378 379 361 393 C5' G A 13 OK OK 392 412 413 394 427 C5' G A 14 OK OK 426 446 447 428 460 C5' G B 15 OK OK 459 479 480 461 495 C5' G B 16 OK OK 494 514 515 496 529 C5' A B 17 OK OK 528 547 548 530 562 C5' G B 18 OK OK 561 581 582 563 596 C5' G B 19 OK OK 595 615 616 597 630 C5' U B 20 OK OK 629 646 647 631 660 C5' U B 21 OK OK 659 676 677 661 690 C5' U B 22 OK OK 689 706 707 691 720 C5' U B 23 OK OK 719 736 737 721 750 C5' G B 24 OK OK 749 769 770 751 784 C5' G B 25 OK OK 783 803 804 785 818 C5' A B 26 OK OK 817 836 837 819 851 C5' G B 27 OK OK 850 870 871 852 885 C5' G B 28 OK OK 884 904 905 886 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P G A 5 distorted distorted 108 135 136 137 168 P U A 6 distorted distorted 142 169 170 171 198 P U A 7 distorted distorted 176 199 200 201 228 P U A 8 distorted distorted 206 229 230 231 258 P U A 9 distorted distorted 236 259 260 261 288 P G A 10 distorted distorted 266 289 290 291 322 P G A 11 distorted distorted 296 323 324 325 356 P A A 12 distorted distorted 330 357 358 359 389 P G A 13 distorted distorted 364 390 391 392 423 P G A 14 distorted distorted 397 424 425 426 491 P G B 16 distorted distorted 464 492 493 494 525 P A B 17 distorted distorted 499 526 527 528 558 P G B 18 distorted distorted 533 559 560 561 592 P G B 19 distorted distorted 566 593 594 595 626 P U B 20 distorted distorted 600 627 628 629 656 P U B 21 distorted distorted 634 657 658 659 686 P U B 22 distorted distorted 664 687 688 689 716 P U B 23 distorted distorted 694 717 718 719 746 P G B 24 distorted distorted 724 747 748 749 780 P G B 25 distorted distorted 754 781 782 783 814 P A B 26 distorted distorted 788 815 816 817 847 P G B 27 distorted distorted 822 848 849 850 881 P G B 28 distorted distorted 855 882 883 884 ---------------------------------------------------------------------------------