ID code: '1NYB' 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' --------------------------------------------------------------------------------- 389 C1' G B 1 alpha beta 384 407 390 387 423 C1' G B 2 alpha beta 418 441 424 421 457 C1' U B 3 alpha beta 452 472 458 455 487 C1' U B 4 alpha beta 482 502 488 485 517 C1' C B 5 alpha beta 512 532 518 515 548 C1' A B 6 alpha beta 543 565 549 546 581 C1' C B 7 alpha beta 576 596 582 579 612 C1' C B 8 alpha beta 607 627 613 610 643 C1' U B 9 alpha beta 638 658 644 641 673 C1' C B 10 alpha beta 668 688 674 671 704 C1' U B 11 alpha beta 699 719 705 702 734 C1' A B 12 alpha beta 729 751 735 732 767 C1' A B 13 alpha beta 762 784 768 765 800 C1' C B 14 alpha beta 795 815 801 798 831 C1' C B 15 alpha beta 826 846 832 829 862 C1' G B 16 alpha beta 857 880 863 860 896 C1' G B 17 alpha beta 891 914 897 894 930 C1' G B 18 alpha beta 925 948 931 928 964 C1' U B 19 alpha beta 959 979 965 962 994 C1' G B 20 alpha beta 989 1012 995 992 1028 C1' A B 21 alpha beta 1023 1045 1029 1026 1061 C1' G B 22 alpha beta 1056 1079 1062 1059 1095 C1' C B 23 alpha beta 1090 1110 1096 1093 1126 C1' C B 24 alpha beta 1121 1141 1127 1124 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 387 C2' G B 1 OK OK 389 385 405 388 421 C2' G B 2 OK OK 423 419 439 422 455 C2' U B 3 OK OK 457 453 470 456 485 C2' U B 4 OK OK 487 483 500 486 515 C2' C B 5 OK OK 517 513 530 516 546 C2' A B 6 OK OK 548 544 563 547 579 C2' C B 7 OK OK 581 577 594 580 610 C2' C B 8 OK OK 612 608 625 611 641 C2' U B 9 OK OK 643 639 656 642 671 C2' C B 10 OK OK 673 669 686 672 702 C2' U B 11 OK OK 704 700 717 703 732 C2' A B 12 OK OK 734 730 749 733 765 C2' A B 13 OK OK 767 763 782 766 798 C2' C B 14 OK OK 800 796 813 799 829 C2' C B 15 OK OK 831 827 844 830 860 C2' G B 16 OK OK 862 858 878 861 894 C2' G B 17 OK OK 896 892 912 895 928 C2' G B 18 OK OK 930 926 946 929 962 C2' U B 19 OK OK 964 960 977 963 992 C2' G B 20 OK OK 994 990 1010 993 1026 C2' A B 21 OK OK 1028 1024 1043 1027 1059 C2' G B 22 OK OK 1061 1057 1077 1060 1093 C2' C B 23 OK OK 1095 1091 1108 1094 1124 C2' C B 24 OK OK 1126 1122 1139 1125 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 385 C3' G B 1 distorted distorted 383 404 386 387 419 C3' G B 2 OK OK 417 438 420 421 453 C3' U B 3 OK OK 451 469 454 455 483 C3' U B 4 OK OK 481 499 484 485 513 C3' C B 5 OK OK 511 529 514 515 544 C3' A B 6 OK OK 542 562 545 546 577 C3' C B 7 OK OK 575 593 578 579 608 C3' C B 8 OK OK 606 624 609 610 639 C3' U B 9 OK OK 637 655 640 641 669 C3' C B 10 OK OK 667 685 670 671 700 C3' U B 11 OK OK 698 716 701 702 730 C3' A B 12 OK OK 728 748 731 732 763 C3' A B 13 OK OK 761 781 764 765 796 C3' C B 14 OK OK 794 812 797 798 827 C3' C B 15 OK OK 825 843 828 829 858 C3' G B 16 OK OK 856 877 859 860 892 C3' G B 17 OK OK 890 911 893 894 926 C3' G B 18 OK OK 924 945 927 928 960 C3' U B 19 OK OK 958 976 961 962 990 C3' G B 20 OK OK 988 1009 991 992 1024 C3' A B 21 OK OK 1022 1042 1025 1026 1057 C3' G B 22 OK OK 1055 1076 1058 1059 1091 C3' C B 23 OK OK 1089 1107 1092 1093 1122 C3' C B 24 OK OK 1120 1138 1123 1124 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 383 C4' G B 1 distorted distorted 385 403 382 384 417 C4' G B 2 OK OK 419 437 416 418 451 C4' U B 3 OK OK 453 468 450 452 481 C4' U B 4 OK OK 483 498 480 482 511 C4' C B 5 OK OK 513 528 510 512 542 C4' A B 6 OK OK 544 561 541 543 575 C4' C B 7 OK OK 577 592 574 576 606 C4' C B 8 OK OK 608 623 605 607 637 C4' U B 9 OK OK 639 654 636 638 667 C4' C B 10 OK OK 669 684 666 668 698 C4' U B 11 OK OK 700 715 697 699 728 C4' A B 12 OK OK 730 747 727 729 761 C4' A B 13 OK OK 763 780 760 762 794 C4' C B 14 OK OK 796 811 793 795 825 C4' C B 15 OK OK 827 842 824 826 856 C4' G B 16 OK OK 858 876 855 857 890 C4' G B 17 OK OK 892 910 889 891 924 C4' G B 18 OK OK 926 944 923 925 958 C4' U B 19 OK OK 960 975 957 959 988 C4' G B 20 OK OK 990 1008 987 989 1022 C4' A B 21 OK OK 1024 1041 1021 1023 1055 C4' G B 22 OK OK 1057 1075 1054 1056 1089 C4' C B 23 OK OK 1091 1106 1088 1090 1120 C4' C B 24 OK OK 1122 1137 1119 1121 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 382 C5' G B 1 OK OK 381 401 402 383 416 C5' G B 2 OK OK 415 435 436 417 450 C5' U B 3 OK OK 449 466 467 451 480 C5' U B 4 OK OK 479 496 497 481 510 C5' C B 5 OK OK 509 526 527 511 541 C5' A B 6 OK OK 540 559 560 542 574 C5' C B 7 OK OK 573 590 591 575 605 C5' C B 8 OK OK 604 621 622 606 636 C5' U B 9 OK OK 635 652 653 637 666 C5' C B 10 OK OK 665 682 683 667 697 C5' U B 11 OK OK 696 713 714 698 727 C5' A B 12 OK OK 726 745 746 728 760 C5' A B 13 OK OK 759 778 779 761 793 C5' C B 14 OK OK 792 809 810 794 824 C5' C B 15 OK OK 823 840 841 825 855 C5' G B 16 OK OK 854 874 875 856 889 C5' G B 17 OK OK 888 908 909 890 923 C5' G B 18 OK OK 922 942 943 924 957 C5' U B 19 OK OK 956 973 974 958 987 C5' G B 20 OK OK 986 1006 1007 988 1021 C5' A B 21 OK OK 1020 1039 1040 1022 1054 C5' G B 22 OK OK 1053 1073 1074 1055 1088 C5' C B 23 OK OK 1087 1104 1105 1089 1119 C5' C B 24 OK OK 1118 1135 1136 1120 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 378 P G B 1 OK OK 379 380 381 412 P G B 2 distorted distorted 386 413 414 415 446 P U B 3 distorted distorted 420 447 448 449 476 P U B 4 distorted distorted 454 477 478 479 506 P C B 5 distorted distorted 484 507 508 509 537 P A B 6 distorted distorted 514 538 539 540 570 P C B 7 distorted distorted 545 571 572 573 601 P C B 8 distorted distorted 578 602 603 604 632 P U B 9 distorted distorted 609 633 634 635 662 P C B 10 distorted distorted 640 663 664 665 693 P U B 11 distorted distorted 670 694 695 696 723 P A B 12 distorted distorted 701 724 725 726 756 P A B 13 distorted distorted 731 757 758 759 789 P C B 14 distorted distorted 764 790 791 792 820 P C B 15 distorted distorted 797 821 822 823 851 P G B 16 distorted distorted 828 852 853 854 885 P G B 17 distorted distorted 859 886 887 888 919 P G B 18 distorted distorted 893 920 921 922 953 P U B 19 distorted distorted 927 954 955 956 983 P G B 20 distorted distorted 961 984 985 986 1017 P A B 21 distorted distorted 991 1018 1019 1020 1050 P G B 22 distorted distorted 1025 1051 1052 1053 1084 P C B 23 distorted distorted 1058 1085 1086 1087 1115 P C B 24 distorted distorted 1092 1116 1117 1118 ---------------------------------------------------------------------------------