ID code: '1QFQ' 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' --------------------------------------------------------------------------------- 591 C1' G A 1 alpha beta 586 609 592 589 625 C1' C A 2 alpha beta 620 640 626 623 656 C1' C A 3 alpha beta 651 671 657 654 687 C1' C A 4 alpha beta 682 702 688 685 718 C1' U A 5 alpha beta 713 733 719 716 748 C1' G A 6 alpha beta 743 766 749 746 782 C1' A A 7 alpha beta 777 799 783 780 815 C1' A A 8 alpha beta 810 832 816 813 848 C1' A A 9 alpha beta 843 865 849 846 881 C1' A A 10 alpha beta 876 898 882 879 914 C1' A A 11 alpha beta 909 931 915 912 947 C1' G A 12 alpha beta 942 965 948 945 981 C1' G A 13 alpha beta 976 999 982 979 1015 C1' G A 14 alpha beta 1010 1033 1016 1013 1049 C1' C A 15 alpha beta 1044 1064 1050 1047 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 589 C2' G A 1 OK OK 591 587 607 590 623 C2' C A 2 OK OK 625 621 638 624 654 C2' C A 3 OK OK 656 652 669 655 685 C2' C A 4 OK OK 687 683 700 686 716 C2' U A 5 OK OK 718 714 731 717 746 C2' G A 6 OK OK 748 744 764 747 780 C2' A A 7 OK OK 782 778 797 781 813 C2' A A 8 OK OK 815 811 830 814 846 C2' A A 9 OK OK 848 844 863 847 879 C2' A A 10 OK OK 881 877 896 880 912 C2' A A 11 OK OK 914 910 929 913 945 C2' G A 12 OK OK 947 943 963 946 979 C2' G A 13 OK OK 981 977 997 980 1013 C2' G A 14 OK OK 1015 1011 1031 1014 1047 C2' C A 15 OK OK 1049 1045 1062 1048 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 587 C3' G A 1 OK OK 585 606 588 589 621 C3' C A 2 OK OK 619 637 622 623 652 C3' C A 3 OK OK 650 668 653 654 683 C3' C A 4 OK OK 681 699 684 685 714 C3' U A 5 OK OK 712 730 715 716 744 C3' G A 6 OK OK 742 763 745 746 778 C3' A A 7 OK OK 776 796 779 780 811 C3' A A 8 OK OK 809 829 812 813 844 C3' A A 9 OK OK 842 862 845 846 877 C3' A A 10 OK OK 875 895 878 879 910 C3' A A 11 OK OK 908 928 911 912 943 C3' G A 12 OK OK 941 962 944 945 977 C3' G A 13 OK OK 975 996 978 979 1011 C3' G A 14 OK OK 1009 1030 1012 1013 1045 C3' C A 15 OK OK 1043 1061 1046 1047 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 585 C4' G A 1 OK OK 587 605 584 586 619 C4' C A 2 OK OK 621 636 618 620 650 C4' C A 3 OK OK 652 667 649 651 681 C4' C A 4 OK OK 683 698 680 682 712 C4' U A 5 OK OK 714 729 711 713 742 C4' G A 6 OK OK 744 762 741 743 776 C4' A A 7 OK OK 778 795 775 777 809 C4' A A 8 OK OK 811 828 808 810 842 C4' A A 9 OK OK 844 861 841 843 875 C4' A A 10 OK OK 877 894 874 876 908 C4' A A 11 OK OK 910 927 907 909 941 C4' G A 12 OK OK 943 961 940 942 975 C4' G A 13 OK OK 977 995 974 976 1009 C4' G A 14 OK OK 1011 1029 1008 1010 1043 C4' C A 15 OK OK 1045 1060 1042 1044 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 584 C5' G A 1 OK OK 583 603 604 585 618 C5' C A 2 OK OK 617 634 635 619 649 C5' C A 3 OK OK 648 665 666 650 680 C5' C A 4 OK OK 679 696 697 681 711 C5' U A 5 OK OK 710 727 728 712 741 C5' G A 6 OK OK 740 760 761 742 775 C5' A A 7 OK OK 774 793 794 776 808 C5' A A 8 OK OK 807 826 827 809 841 C5' A A 9 OK OK 840 859 860 842 874 C5' A A 10 OK OK 873 892 893 875 907 C5' A A 11 OK OK 906 925 926 908 940 C5' G A 12 OK OK 939 959 960 941 974 C5' G A 13 OK OK 973 993 994 975 1008 C5' G A 14 OK OK 1007 1027 1028 1009 1042 C5' C A 15 OK OK 1041 1058 1059 1043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 580 P G A 1 distorted distorted 581 582 583 614 P C A 2 distorted distorted 588 615 616 617 645 P C A 3 distorted distorted 622 646 647 648 676 P C A 4 distorted distorted 653 677 678 679 707 P U A 5 distorted distorted 684 708 709 710 737 P G A 6 distorted distorted 715 738 739 740 771 P A A 7 distorted distorted 745 772 773 774 804 P A A 8 distorted distorted 779 805 806 807 837 P A A 9 distorted distorted 812 838 839 840 870 P A A 10 distorted distorted 845 871 872 873 903 P A A 11 distorted distorted 878 904 905 906 936 P G A 12 distorted distorted 911 937 938 939 970 P G A 13 distorted distorted 944 971 972 973 1004 P G A 14 distorted distorted 978 1005 1006 1007 1038 P C A 15 distorted distorted 1012 1039 1040 1041 ---------------------------------------------------------------------------------