ID code: '1S9M' 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' --------------------------------------------------------------------------------- 673 C1' G B 1 beta 669 674 672 695 C1' C B 2 beta 691 696 694 714 C1' A B 3 beta 710 715 713 735 C1' C B 4 beta 731 736 734 754 C1' A B 5 beta 750 755 753 775 C1' A B 6 beta 771 776 774 796 C1' A B 7 beta 792 797 795 817 C1' C B 8 beta 813 818 816 834 C1' G C 9 beta 830 835 833 856 C1' T C 10 beta 852 857 855 876 C1' T C 11 beta 872 877 875 896 C1' T C 12 beta 892 897 895 916 C1' G C 13 beta 912 917 915 938 C1' T C 14 beta 934 939 937 958 C1' G C 15 beta 954 959 957 980 C1' C C 16 beta 976 981 979 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 672 C2' G B 1 673 670 694 C2' C B 2 695 692 713 C2' A B 3 714 711 734 C2' C B 4 735 732 753 C2' A B 5 754 751 774 C2' A B 6 775 772 795 C2' A B 7 796 793 816 C2' C B 8 817 814 833 C2' G C 9 834 831 855 C2' T C 10 856 853 875 C2' T C 11 876 873 895 C2' T C 12 896 893 915 C2' G C 13 916 913 937 C2' T C 14 938 935 957 C2' G C 15 958 955 979 C2' C C 16 980 977 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 670 C3' G B 1 OK 668 671 672 692 C3' C B 2 OK 690 693 694 711 C3' A B 3 OK 709 712 713 732 C3' C B 4 OK 730 733 734 751 C3' A B 5 distorted 749 752 753 772 C3' A B 6 OK 770 773 774 793 C3' A B 7 OK 791 794 795 814 C3' C B 8 OK 812 815 816 831 C3' G C 9 distorted 829 832 833 853 C3' T C 10 OK 851 854 855 873 C3' T C 11 OK 871 874 875 893 C3' T C 12 OK 891 894 895 913 C3' G C 13 OK 911 914 915 935 C3' T C 14 OK 933 936 937 955 C3' G C 15 OK 953 956 957 977 C3' C C 16 OK 975 978 979 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 668 C4' G B 1 OK 670 667 669 690 C4' C B 2 OK 692 689 691 709 C4' A B 3 OK 711 708 710 730 C4' C B 4 OK 732 729 731 749 C4' A B 5 OK 751 748 750 770 C4' A B 6 OK 772 769 771 791 C4' A B 7 OK 793 790 792 812 C4' C B 8 OK 814 811 813 829 C4' G C 9 OK 831 828 830 851 C4' T C 10 OK 853 850 852 871 C4' T C 11 OK 873 870 872 891 C4' T C 12 OK 893 890 892 911 C4' G C 13 OK 913 910 912 933 C4' T C 14 OK 935 932 934 953 C4' G C 15 OK 955 952 954 975 C4' C C 16 OK 977 974 976 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 667 C5' G B 1 666 668 689 C5' C B 2 688 690 708 C5' A B 3 707 709 729 C5' C B 4 728 730 748 C5' A B 5 747 749 769 C5' A B 6 768 770 790 C5' A B 7 789 791 811 C5' C B 8 810 812 828 C5' G C 9 827 829 850 C5' T C 10 849 851 870 C5' T C 11 869 871 890 C5' T C 12 889 891 910 C5' G C 13 909 911 932 C5' T C 14 931 933 952 C5' G C 15 951 953 974 C5' C C 16 973 975 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 685 P C B 2 distorted distorted 671 686 687 688 704 P A B 3 distorted distorted 693 705 706 707 725 P C B 4 distorted distorted 712 726 727 728 744 P A B 5 distorted distorted 733 745 746 747 765 P A B 6 distorted distorted 752 766 767 768 786 P A B 7 distorted distorted 773 787 788 789 807 P C B 8 distorted distorted 794 808 809 810 846 P T C 10 distorted distorted 832 847 848 849 866 P T C 11 distorted distorted 854 867 868 869 886 P T C 12 distorted distorted 874 887 888 889 906 P G C 13 distorted distorted 894 907 908 909 928 P T C 14 distorted distorted 914 929 930 931 948 P G C 15 distorted distorted 936 949 950 951 970 P C C 16 distorted distorted 956 971 972 973 ---------------------------------------------------------------------------------