ID code: '1AZQ' 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' --------------------------------------------------------------------------------- 682 C1' G B 101 beta 678 683 681 708 C1' T B 102 beta 704 709 707 729 C1' A B 103 beta 725 730 728 752 C1' A B 104 beta 748 753 751 775 C1' T B 105 beta 771 776 774 796 C1' T B 106 beta 792 797 795 817 C1' A B 107 beta 813 818 816 840 C1' C B 108 beta 836 841 839 860 C1' G C 109 beta 856 861 859 886 C1' T C 110 beta 882 887 885 907 C1' A C 111 beta 903 908 906 930 C1' A C 112 beta 926 931 929 953 C1' T C 113 beta 949 954 952 974 C1' T C 114 beta 970 975 973 995 C1' A C 115 beta 991 996 994 1018 C1' C C 116 beta 1014 1019 1017 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 681 C2' G B 101 682 679 707 C2' T B 102 708 705 728 C2' A B 103 729 726 751 C2' A B 104 752 749 774 C2' T B 105 775 772 795 C2' T B 106 796 793 816 C2' A B 107 817 814 839 C2' C B 108 840 837 859 C2' G C 109 860 857 885 C2' T C 110 886 883 906 C2' A C 111 907 904 929 C2' A C 112 930 927 952 C2' T C 113 953 950 973 C2' T C 114 974 971 994 C2' A C 115 995 992 1017 C2' C C 116 1018 1015 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 679 C3' G B 101 OK 677 680 681 705 C3' T B 102 OK 703 706 707 726 C3' A B 103 OK 724 727 728 749 C3' A B 104 OK 747 750 751 772 C3' T B 105 OK 770 773 774 793 C3' T B 106 OK 791 794 795 814 C3' A B 107 OK 812 815 816 837 C3' C B 108 OK 835 838 839 857 C3' G C 109 OK 855 858 859 883 C3' T C 110 OK 881 884 885 904 C3' A C 111 OK 902 905 906 927 C3' A C 112 OK 925 928 929 950 C3' T C 113 OK 948 951 952 971 C3' T C 114 OK 969 972 973 992 C3' A C 115 OK 990 993 994 1015 C3' C C 116 OK 1013 1016 1017 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 677 C4' G B 101 OK 679 676 678 703 C4' T B 102 OK 705 702 704 724 C4' A B 103 OK 726 723 725 747 C4' A B 104 OK 749 746 748 770 C4' T B 105 OK 772 769 771 791 C4' T B 106 OK 793 790 792 812 C4' A B 107 OK 814 811 813 835 C4' C B 108 OK 837 834 836 855 C4' G C 109 OK 857 854 856 881 C4' T C 110 OK 883 880 882 902 C4' A C 111 OK 904 901 903 925 C4' A C 112 OK 927 924 926 948 C4' T C 113 OK 950 947 949 969 C4' T C 114 OK 971 968 970 990 C4' A C 115 OK 992 989 991 1013 C4' C C 116 OK 1015 1012 1014 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 676 C5' G B 101 675 677 702 C5' T B 102 701 703 723 C5' A B 103 722 724 746 C5' A B 104 745 747 769 C5' T B 105 768 770 790 C5' T B 106 789 791 811 C5' A B 107 810 812 834 C5' C B 108 833 835 854 C5' G C 109 853 855 880 C5' T C 110 879 881 901 C5' A C 111 900 902 924 C5' A C 112 923 925 947 C5' T C 113 946 948 968 C5' T C 114 967 969 989 C5' A C 115 988 990 1012 C5' C C 116 1011 1013 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 698 P T B 102 OK OK 680 699 700 701 719 P A B 103 OK OK 706 720 721 722 742 P A B 104 OK OK 727 743 744 745 765 P T B 105 OK OK 750 766 767 768 786 P T B 106 OK OK 773 787 788 789 807 P A B 107 OK OK 794 808 809 810 830 P C B 108 OK OK 815 831 832 833 876 P T C 110 OK OK 858 877 878 879 897 P A C 111 OK OK 884 898 899 900 920 P A C 112 OK OK 905 921 922 923 943 P T C 113 OK OK 928 944 945 946 964 P T C 114 OK OK 951 965 966 967 985 P A C 115 OK OK 972 986 987 988 1008 P C C 116 OK OK 993 1009 1010 1011 ---------------------------------------------------------------------------------