ID code: '1AZP' 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' C B 102 beta 704 709 707 729 C1' G B 103 beta 725 730 728 754 C1' A B 104 beta 750 755 753 777 C1' T B 105 beta 773 778 776 798 C1' C B 106 beta 794 799 797 819 C1' G B 107 beta 815 820 818 844 C1' C B 108 beta 840 845 843 864 C1' G C 109 beta 860 865 863 890 C1' C C 110 beta 886 891 889 911 C1' G C 111 beta 907 912 910 936 C1' A C 112 beta 932 937 935 959 C1' T C 113 beta 955 960 958 980 C1' C C 114 beta 976 981 979 1001 C1' G C 115 beta 997 1002 1000 1026 C1' C C 116 beta 1022 1027 1025 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C B 102 708 705 728 C2' G B 103 729 726 753 C2' A B 104 754 751 776 C2' T B 105 777 774 797 C2' C B 106 798 795 818 C2' G B 107 819 816 843 C2' C B 108 844 841 863 C2' G C 109 864 861 889 C2' C C 110 890 887 910 C2' G C 111 911 908 935 C2' A C 112 936 933 958 C2' T C 113 959 956 979 C2' C C 114 980 977 1000 C2' G C 115 1001 998 1025 C2' C C 116 1026 1023 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 679 C3' G B 101 OK 677 680 681 705 C3' C B 102 OK 703 706 707 726 C3' G B 103 OK 724 727 728 751 C3' A B 104 OK 749 752 753 774 C3' T B 105 OK 772 775 776 795 C3' C B 106 OK 793 796 797 816 C3' G B 107 OK 814 817 818 841 C3' C B 108 OK 839 842 843 861 C3' G C 109 OK 859 862 863 887 C3' C C 110 OK 885 888 889 908 C3' G C 111 OK 906 909 910 933 C3' A C 112 OK 931 934 935 956 C3' T C 113 OK 954 957 958 977 C3' C C 114 OK 975 978 979 998 C3' G C 115 OK 996 999 1000 1023 C3' C C 116 OK 1021 1024 1025 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 677 C4' G B 101 OK 679 676 678 703 C4' C B 102 OK 705 702 704 724 C4' G B 103 OK 726 723 725 749 C4' A B 104 OK 751 748 750 772 C4' T B 105 OK 774 771 773 793 C4' C B 106 OK 795 792 794 814 C4' G B 107 OK 816 813 815 839 C4' C B 108 OK 841 838 840 859 C4' G C 109 OK 861 858 860 885 C4' C C 110 OK 887 884 886 906 C4' G C 111 OK 908 905 907 931 C4' A C 112 OK 933 930 932 954 C4' T C 113 OK 956 953 955 975 C4' C C 114 OK 977 974 976 996 C4' G C 115 OK 998 995 997 1021 C4' C C 116 OK 1023 1020 1022 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 676 C5' G B 101 675 677 702 C5' C B 102 701 703 723 C5' G B 103 722 724 748 C5' A B 104 747 749 771 C5' T B 105 770 772 792 C5' C B 106 791 793 813 C5' G B 107 812 814 838 C5' C B 108 837 839 858 C5' G C 109 857 859 884 C5' C C 110 883 885 905 C5' G C 111 904 906 930 C5' A C 112 929 931 953 C5' T C 113 952 954 974 C5' C C 114 973 975 995 C5' G C 115 994 996 1020 C5' C C 116 1019 1021 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 698 P C B 102 OK OK 680 699 700 701 719 P G B 103 OK OK 706 720 721 722 744 P A B 104 OK OK 727 745 746 747 767 P T B 105 OK OK 752 768 769 770 788 P C B 106 OK OK 775 789 790 791 809 P G B 107 OK OK 796 810 811 812 834 P C B 108 OK OK 817 835 836 837 880 P C C 110 OK OK 862 881 882 883 901 P G C 111 OK OK 888 902 903 904 926 P A C 112 OK OK 909 927 928 929 949 P T C 113 OK OK 934 950 951 952 970 P C C 114 OK OK 957 971 972 973 991 P G C 115 OK OK 978 992 993 994 1016 P C C 116 OK OK 999 1017 1018 1019 ---------------------------------------------------------------------------------