ID code: '1Y99' 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' C A 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' U A 3 beta 44 50 47 69 C1' G A 4 beta 64 70 67 92 C1' C A 5 beta 87 93 90 112 C1' U A 6 beta 107 113 110 268 C1' G A 10 beta 263 269 266 291 C1' U A 11 beta 286 292 289 311 C1' G A 12 beta 306 312 309 334 C1' C A 13 beta 329 335 332 354 C1' A A 14 beta 349 355 352 376 C1' C A 15 beta 371 377 374 396 C1' A A 16 beta 391 397 394 418 C1' C A 17 beta 413 419 416 438 C1' A A 18 beta 433 439 436 460 C1' G A 19 beta 455 461 458 483 C1' C A 20 beta 478 484 481 503 C1' A A 21 beta 498 504 501 525 C1' A A 22 beta 520 526 523 547 C1' G A 23 beta 542 548 545 568 C1' C B 1 beta 563 569 566 588 C1' U B 2 beta 583 589 586 608 C1' U B 3 beta 603 609 606 628 C1' G B 4 beta 623 629 626 651 C1' C B 5 beta 646 652 649 671 C1' U B 6 beta 666 672 669 691 C1' G B 7 beta 686 692 689 714 C1' A B 8 beta 709 715 712 736 C1' G B 9 beta 731 737 734 759 C1' G B 10 beta 754 760 757 782 C1' U B 11 beta 777 783 780 802 C1' G B 12 beta 797 803 800 825 C1' C B 13 beta 820 826 823 845 C1' A B 14 beta 840 846 843 867 C1' C B 15 beta 862 868 865 887 C1' A B 16 beta 882 888 885 909 C1' C B 17 beta 904 910 907 929 C1' A B 18 beta 924 930 927 951 C1' G B 19 beta 946 952 949 974 C1' C B 20 beta 969 975 972 994 C1' A B 21 beta 989 995 992 1016 C1' A B 22 beta 1011 1017 1014 1038 C1' G B 23 beta 1033 1039 1036 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' U A 3 OK 49 45 48 67 C2' G A 4 OK 69 65 68 90 C2' C A 5 OK 92 88 91 110 C2' U A 6 OK 112 108 111 266 C2' G A 10 OK 268 264 267 289 C2' U A 11 OK 291 287 290 309 C2' G A 12 OK 311 307 310 332 C2' C A 13 OK 334 330 333 352 C2' A A 14 OK 354 350 353 374 C2' C A 15 OK 376 372 375 394 C2' A A 16 OK 396 392 395 416 C2' C A 17 OK 418 414 417 436 C2' A A 18 OK 438 434 437 458 C2' G A 19 OK 460 456 459 481 C2' C A 20 OK 483 479 482 501 C2' A A 21 OK 503 499 502 523 C2' A A 22 OK 525 521 524 545 C2' G A 23 OK 547 543 546 566 C2' C B 1 OK 568 564 567 586 C2' U B 2 OK 588 584 587 606 C2' U B 3 OK 608 604 607 626 C2' G B 4 OK 628 624 627 649 C2' C B 5 OK 651 647 650 669 C2' U B 6 OK 671 667 670 689 C2' G B 7 OK 691 687 690 712 C2' A B 8 OK 714 710 713 734 C2' G B 9 OK 736 732 735 757 C2' G B 10 OK 759 755 758 780 C2' U B 11 OK 782 778 781 800 C2' G B 12 OK 802 798 801 823 C2' C B 13 OK 825 821 824 843 C2' A B 14 OK 845 841 844 865 C2' C B 15 OK 867 863 866 885 C2' A B 16 OK 887 883 886 907 C2' C B 17 OK 909 905 908 927 C2' A B 18 OK 929 925 928 949 C2' G B 19 OK 951 947 950 972 C2' C B 20 OK 974 970 973 992 C2' A B 21 OK 994 990 993 1014 C2' A B 22 OK 1016 1012 1015 1036 C2' G B 23 OK 1038 1034 1037 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' U A 3 OK 43 46 47 65 C3' G A 4 OK 63 66 67 88 C3' C A 5 OK 86 89 90 108 C3' U A 6 OK 106 109 110 264 C3' G A 10 OK 262 265 266 287 C3' U A 11 OK 285 288 289 307 C3' G A 12 OK 305 308 309 330 C3' C A 13 OK 328 331 332 350 C3' A A 14 OK 348 351 352 372 C3' C A 15 OK 370 373 374 392 C3' A A 16 OK 390 393 394 414 C3' C A 17 OK 412 415 416 434 C3' A A 18 OK 432 435 436 456 C3' G A 19 OK 454 457 458 479 C3' C A 20 OK 477 480 481 499 C3' A A 21 OK 497 500 501 521 C3' A A 22 OK 519 522 523 543 C3' G A 23 OK 541 544 545 564 C3' C B 1 OK 562 565 566 584 C3' U B 2 OK 582 585 586 604 C3' U B 3 OK 602 605 606 624 C3' G B 4 OK 622 625 626 647 C3' C B 5 OK 645 648 649 667 C3' U B 6 OK 665 668 669 687 C3' G B 7 OK 685 688 689 710 C3' A B 8 OK 708 711 712 732 C3' G B 9 OK 730 733 734 755 C3' G B 10 OK 753 756 757 778 C3' U B 11 OK 776 779 780 798 C3' G B 12 OK 796 799 800 821 C3' C B 13 OK 819 822 823 841 C3' A B 14 OK 839 842 843 863 C3' C B 15 OK 861 864 865 883 C3' A B 16 OK 881 884 885 905 C3' C B 17 OK 903 906 907 925 C3' A B 18 OK 923 926 927 947 C3' G B 19 OK 945 948 949 970 C3' C B 20 OK 968 971 972 990 C3' A B 21 OK 988 991 992 1012 C3' A B 22 OK 1010 1013 1014 1034 C3' G B 23 OK 1032 1035 1036 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' U A 3 OK 45 42 44 63 C4' G A 4 OK 65 62 64 86 C4' C A 5 OK 88 85 87 106 C4' U A 6 OK 108 105 107 262 C4' G A 10 OK 264 261 263 285 C4' U A 11 OK 287 284 286 305 C4' G A 12 OK 307 304 306 328 C4' C A 13 OK 330 327 329 348 C4' A A 14 OK 350 347 349 370 C4' C A 15 OK 372 369 371 390 C4' A A 16 OK 392 389 391 412 C4' C A 17 OK 414 411 413 432 C4' A A 18 OK 434 431 433 454 C4' G A 19 OK 456 453 455 477 C4' C A 20 OK 479 476 478 497 C4' A A 21 OK 499 496 498 519 C4' A A 22 OK 521 518 520 541 C4' G A 23 OK 543 540 542 562 C4' C B 1 OK 564 561 563 582 C4' U B 2 OK 584 581 583 602 C4' U B 3 OK 604 601 603 622 C4' G B 4 OK 624 621 623 645 C4' C B 5 OK 647 644 646 665 C4' U B 6 OK 667 664 666 685 C4' G B 7 OK 687 684 686 708 C4' A B 8 OK 710 707 709 730 C4' G B 9 OK 732 729 731 753 C4' G B 10 OK 755 752 754 776 C4' U B 11 OK 778 775 777 796 C4' G B 12 OK 798 795 797 819 C4' C B 13 OK 821 818 820 839 C4' A B 14 OK 841 838 840 861 C4' C B 15 OK 863 860 862 881 C4' A B 16 OK 883 880 882 903 C4' C B 17 OK 905 902 904 923 C4' A B 18 OK 925 922 924 945 C4' G B 19 OK 947 944 946 968 C4' C B 20 OK 970 967 969 988 C4' A B 21 OK 990 987 989 1010 C4' A B 22 OK 1012 1009 1011 1032 C4' G B 23 OK 1034 1031 1033 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' U A 2 21 23 42 C5' U A 3 41 43 62 C5' G A 4 61 63 85 C5' C A 5 84 86 105 C5' U A 6 104 106 261 C5' G A 10 260 262 284 C5' U A 11 283 285 304 C5' G A 12 303 305 327 C5' C A 13 326 328 347 C5' A A 14 346 348 369 C5' C A 15 368 370 389 C5' A A 16 388 390 411 C5' C A 17 410 412 431 C5' A A 18 430 432 453 C5' G A 19 452 454 476 C5' C A 20 475 477 496 C5' A A 21 495 497 518 C5' A A 22 517 519 540 C5' G A 23 539 541 561 C5' C B 1 560 562 581 C5' U B 2 580 582 601 C5' U B 3 600 602 621 C5' G B 4 620 622 644 C5' C B 5 643 645 664 C5' U B 6 663 665 684 C5' G B 7 683 685 707 C5' A B 8 706 708 729 C5' G B 9 728 730 752 C5' G B 10 751 753 775 C5' U B 11 774 776 795 C5' G B 12 794 796 818 C5' C B 13 817 819 838 C5' A B 14 837 839 860 C5' C B 15 859 861 880 C5' A B 16 879 881 902 C5' C B 17 901 903 922 C5' A B 18 921 923 944 C5' G B 19 943 945 967 C5' C B 20 966 968 987 C5' A B 21 986 988 1009 C5' A B 22 1008 1010 1031 C5' G B 23 1030 1032 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P U A 3 distorted distorted 26 39 40 41 58 P G A 4 distorted distorted 46 59 60 61 81 P C A 5 distorted distorted 66 82 83 84 101 P U A 6 distorted distorted 89 102 103 104 121 P G A 7 109 122 P G A 7 167 P A A 8 168 P A A 8 211 P G A 9 212 P G A 9 257 P G A 10 OK OK 258 259 260 280 P U A 11 distorted distorted 265 281 282 283 300 P G A 12 distorted distorted 288 301 302 303 323 P C A 13 distorted distorted 308 324 325 326 343 P A A 14 distorted distorted 331 344 345 346 365 P C A 15 distorted distorted 351 366 367 368 385 P A A 16 distorted distorted 373 386 387 388 407 P C A 17 distorted distorted 393 408 409 410 427 P A A 18 distorted distorted 415 428 429 430 449 P G A 19 distorted distorted 435 450 451 452 472 P C A 20 distorted distorted 457 473 474 475 492 P A A 21 distorted distorted 480 493 494 495 514 P A A 22 distorted distorted 500 515 516 517 536 P G A 23 distorted distorted 522 537 538 539 577 P U B 2 distorted distorted 565 578 579 580 597 P U B 3 distorted distorted 585 598 599 600 617 P G B 4 distorted distorted 605 618 619 620 640 P C B 5 distorted distorted 625 641 642 643 660 P U B 6 distorted distorted 648 661 662 663 680 P G B 7 distorted distorted 668 681 682 683 703 P A B 8 distorted distorted 688 704 705 706 725 P G B 9 distorted distorted 711 726 727 728 748 P G B 10 distorted distorted 733 749 750 751 771 P U B 11 distorted distorted 756 772 773 774 791 P G B 12 distorted distorted 779 792 793 794 814 P C B 13 distorted distorted 799 815 816 817 834 P A B 14 distorted distorted 822 835 836 837 856 P C B 15 distorted distorted 842 857 858 859 876 P A B 16 distorted distorted 864 877 878 879 898 P C B 17 distorted distorted 884 899 900 901 918 P A B 18 distorted distorted 906 919 920 921 940 P G B 19 distorted distorted 926 941 942 943 963 P C B 20 distorted distorted 948 964 965 966 983 P A B 21 distorted distorted 971 984 985 986 1005 P A B 22 distorted distorted 991 1006 1007 1008 1027 P G B 23 distorted distorted 1013 1028 1029 1030 ---------------------------------------------------------------------------------