ID code: '1I1T' 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' G A 1 beta 4 9 7 34 C1' G A 2 beta 30 35 33 59 C1' G A 3 beta 55 60 58 84 C1' G A 4 beta 80 85 83 109 C1' G A 5 beta 105 110 108 134 C1' G A 6 beta 130 135 133 159 C1' G A 7 beta 155 160 158 184 C1' G A 8 beta 180 185 183 209 C1' G A 9 beta 205 210 208 234 C1' G A 10 beta 230 235 233 259 C1' G A 11 beta 255 260 258 284 C1' G A 12 beta 280 285 283 309 C1' G A 13 beta 305 310 308 334 C1' G A 14 beta 330 335 333 359 C1' G A 15 beta 355 360 358 384 C1' G A 16 beta 380 385 383 409 C1' G A 17 beta 405 410 408 434 C1' G A 18 beta 430 435 433 458 C1' C B 19 beta 454 459 457 480 C1' C B 20 beta 476 481 479 501 C1' C B 21 beta 497 502 500 522 C1' C B 22 beta 518 523 521 543 C1' C B 23 beta 539 544 542 564 C1' C B 24 beta 560 565 563 585 C1' C B 25 beta 581 586 584 606 C1' C B 26 beta 602 607 605 627 C1' C B 27 beta 623 628 626 648 C1' C B 28 beta 644 649 647 669 C1' C B 29 beta 665 670 668 690 C1' C B 30 beta 686 691 689 711 C1' C B 31 beta 707 712 710 732 C1' C B 32 beta 728 733 731 753 C1' C B 33 beta 749 754 752 774 C1' C B 34 beta 770 775 773 795 C1' C B 35 beta 791 796 794 816 C1' C B 36 beta 812 817 815 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 33 C2' G A 2 34 31 58 C2' G A 3 59 56 83 C2' G A 4 84 81 108 C2' G A 5 109 106 133 C2' G A 6 134 131 158 C2' G A 7 159 156 183 C2' G A 8 184 181 208 C2' G A 9 209 206 233 C2' G A 10 234 231 258 C2' G A 11 259 256 283 C2' G A 12 284 281 308 C2' G A 13 309 306 333 C2' G A 14 334 331 358 C2' G A 15 359 356 383 C2' G A 16 384 381 408 C2' G A 17 409 406 433 C2' G A 18 434 431 457 C2' C B 19 458 455 479 C2' C B 20 480 477 500 C2' C B 21 501 498 521 C2' C B 22 522 519 542 C2' C B 23 543 540 563 C2' C B 24 564 561 584 C2' C B 25 585 582 605 C2' C B 26 606 603 626 C2' C B 27 627 624 647 C2' C B 28 648 645 668 C2' C B 29 669 666 689 C2' C B 30 690 687 710 C2' C B 31 711 708 731 C2' C B 32 732 729 752 C2' C B 33 753 750 773 C2' C B 34 774 771 794 C2' C B 35 795 792 815 C2' C B 36 816 813 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 31 C3' G A 2 OK 29 32 33 56 C3' G A 3 OK 54 57 58 81 C3' G A 4 OK 79 82 83 106 C3' G A 5 OK 104 107 108 131 C3' G A 6 OK 129 132 133 156 C3' G A 7 OK 154 157 158 181 C3' G A 8 OK 179 182 183 206 C3' G A 9 OK 204 207 208 231 C3' G A 10 OK 229 232 233 256 C3' G A 11 OK 254 257 258 281 C3' G A 12 OK 279 282 283 306 C3' G A 13 OK 304 307 308 331 C3' G A 14 OK 329 332 333 356 C3' G A 15 OK 354 357 358 381 C3' G A 16 OK 379 382 383 406 C3' G A 17 OK 404 407 408 431 C3' G A 18 OK 429 432 433 455 C3' C B 19 OK 453 456 457 477 C3' C B 20 OK 475 478 479 498 C3' C B 21 OK 496 499 500 519 C3' C B 22 OK 517 520 521 540 C3' C B 23 OK 538 541 542 561 C3' C B 24 OK 559 562 563 582 C3' C B 25 OK 580 583 584 603 C3' C B 26 OK 601 604 605 624 C3' C B 27 OK 622 625 626 645 C3' C B 28 OK 643 646 647 666 C3' C B 29 OK 664 667 668 687 C3' C B 30 OK 685 688 689 708 C3' C B 31 OK 706 709 710 729 C3' C B 32 OK 727 730 731 750 C3' C B 33 OK 748 751 752 771 C3' C B 34 OK 769 772 773 792 C3' C B 35 OK 790 793 794 813 C3' C B 36 OK 811 814 815 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 29 C4' G A 2 OK 31 28 30 54 C4' G A 3 OK 56 53 55 79 C4' G A 4 OK 81 78 80 104 C4' G A 5 OK 106 103 105 129 C4' G A 6 OK 131 128 130 154 C4' G A 7 OK 156 153 155 179 C4' G A 8 OK 181 178 180 204 C4' G A 9 OK 206 203 205 229 C4' G A 10 OK 231 228 230 254 C4' G A 11 OK 256 253 255 279 C4' G A 12 OK 281 278 280 304 C4' G A 13 OK 306 303 305 329 C4' G A 14 OK 331 328 330 354 C4' G A 15 OK 356 353 355 379 C4' G A 16 OK 381 378 380 404 C4' G A 17 OK 406 403 405 429 C4' G A 18 OK 431 428 430 453 C4' C B 19 OK 455 452 454 475 C4' C B 20 OK 477 474 476 496 C4' C B 21 OK 498 495 497 517 C4' C B 22 OK 519 516 518 538 C4' C B 23 OK 540 537 539 559 C4' C B 24 OK 561 558 560 580 C4' C B 25 OK 582 579 581 601 C4' C B 26 OK 603 600 602 622 C4' C B 27 OK 624 621 623 643 C4' C B 28 OK 645 642 644 664 C4' C B 29 OK 666 663 665 685 C4' C B 30 OK 687 684 686 706 C4' C B 31 OK 708 705 707 727 C4' C B 32 OK 729 726 728 748 C4' C B 33 OK 750 747 749 769 C4' C B 34 OK 771 768 770 790 C4' C B 35 OK 792 789 791 811 C4' C B 36 OK 813 810 812 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 28 C5' G A 2 27 29 53 C5' G A 3 52 54 78 C5' G A 4 77 79 103 C5' G A 5 102 104 128 C5' G A 6 127 129 153 C5' G A 7 152 154 178 C5' G A 8 177 179 203 C5' G A 9 202 204 228 C5' G A 10 227 229 253 C5' G A 11 252 254 278 C5' G A 12 277 279 303 C5' G A 13 302 304 328 C5' G A 14 327 329 353 C5' G A 15 352 354 378 C5' G A 16 377 379 403 C5' G A 17 402 404 428 C5' G A 18 427 429 452 C5' C B 19 451 453 474 C5' C B 20 473 475 495 C5' C B 21 494 496 516 C5' C B 22 515 517 537 C5' C B 23 536 538 558 C5' C B 24 557 559 579 C5' C B 25 578 580 600 C5' C B 26 599 601 621 C5' C B 27 620 622 642 C5' C B 28 641 643 663 C5' C B 29 662 664 684 C5' C B 30 683 685 705 C5' C B 31 704 706 726 C5' C B 32 725 727 747 C5' C B 33 746 748 768 C5' C B 34 767 769 789 C5' C B 35 788 790 810 C5' C B 36 809 811 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 24 P G A 2 distorted distorted 6 25 26 27 49 P G A 3 distorted distorted 32 50 51 52 74 P G A 4 distorted distorted 57 75 76 77 99 P G A 5 distorted distorted 82 100 101 102 124 P G A 6 distorted distorted 107 125 126 127 149 P G A 7 distorted distorted 132 150 151 152 174 P G A 8 distorted distorted 157 175 176 177 199 P G A 9 distorted distorted 182 200 201 202 224 P G A 10 distorted distorted 207 225 226 227 249 P G A 11 distorted distorted 232 250 251 252 274 P G A 12 distorted distorted 257 275 276 277 299 P G A 13 distorted distorted 282 300 301 302 324 P G A 14 distorted distorted 307 325 326 327 349 P G A 15 distorted distorted 332 350 351 352 374 P G A 16 distorted distorted 357 375 376 377 399 P G A 17 distorted distorted 382 400 401 402 424 P G A 18 distorted distorted 407 425 426 427 470 P C B 20 distorted distorted 456 471 472 473 491 P C B 21 distorted distorted 478 492 493 494 512 P C B 22 distorted distorted 499 513 514 515 533 P C B 23 distorted distorted 520 534 535 536 554 P C B 24 distorted distorted 541 555 556 557 575 P C B 25 distorted distorted 562 576 577 578 596 P C B 26 distorted distorted 583 597 598 599 617 P C B 27 distorted distorted 604 618 619 620 638 P C B 28 distorted distorted 625 639 640 641 659 P C B 29 distorted distorted 646 660 661 662 680 P C B 30 distorted distorted 667 681 682 683 701 P C B 31 distorted distorted 688 702 703 704 722 P C B 32 distorted distorted 709 723 724 725 743 P C B 33 distorted distorted 730 744 745 746 764 P C B 34 distorted distorted 751 765 766 767 785 P C B 35 distorted distorted 772 786 787 788 806 P C B 36 distorted distorted 793 807 808 809 ---------------------------------------------------------------------------------