ID code: '8ICF' 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' --------------------------------------------------------------------------------- 2647 C1' C T 1 beta 2643 2648 2646 2666 C1' A T 2 beta 2662 2667 2665 2687 C1' T T 3 beta 2683 2688 2686 2707 C1' T T 4 beta 2703 2708 2706 2727 C1' A T 5 beta 2723 2728 2726 2748 C1' G T 6 beta 2744 2749 2747 2770 C1' A T 7 beta 2766 2771 2769 2797 C1' T P 1 beta 2793 2798 2796 2817 C1' C P 2 beta 2813 2818 2816 2836 C1' T P 3 beta 2832 2837 2835 2856 C1' A P 4 beta 2852 2857 2855 2877 C1' A P 5 beta 2873 2878 2876 2898 C1' T P 6 beta 2894 2899 2897 2918 C1' G P 7 beta 2914 2919 2917 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2646 C2' C T 1 2647 2644 2665 C2' A T 2 2666 2663 2686 C2' T T 3 2687 2684 2706 C2' T T 4 2707 2704 2726 C2' A T 5 2727 2724 2747 C2' G T 6 2748 2745 2769 C2' A T 7 2770 2767 2796 C2' T P 1 2797 2794 2816 C2' C P 2 2817 2814 2835 C2' T P 3 2836 2833 2855 C2' A P 4 2856 2853 2876 C2' A P 5 2877 2874 2897 C2' T P 6 2898 2895 2917 C2' G P 7 2918 2915 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2644 C3' C T 1 OK 2642 2645 2646 2663 C3' A T 2 OK 2661 2664 2665 2684 C3' T T 3 OK 2682 2685 2686 2704 C3' T T 4 OK 2702 2705 2706 2724 C3' A T 5 OK 2722 2725 2726 2745 C3' G T 6 OK 2743 2746 2747 2767 C3' A T 7 OK 2765 2768 2769 2794 C3' T P 1 OK 2792 2795 2796 2814 C3' C P 2 OK 2812 2815 2816 2833 C3' T P 3 OK 2831 2834 2835 2853 C3' A P 4 OK 2851 2854 2855 2874 C3' A P 5 OK 2872 2875 2876 2895 C3' T P 6 OK 2893 2896 2897 2915 C3' G P 7 OK 2913 2916 2917 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2642 C4' C T 1 OK 2644 2641 2643 2661 C4' A T 2 OK 2663 2660 2662 2682 C4' T T 3 OK 2684 2681 2683 2702 C4' T T 4 OK 2704 2701 2703 2722 C4' A T 5 OK 2724 2721 2723 2743 C4' G T 6 OK 2745 2742 2744 2765 C4' A T 7 OK 2767 2764 2766 2792 C4' T P 1 OK 2794 2791 2793 2812 C4' C P 2 OK 2814 2811 2813 2831 C4' T P 3 OK 2833 2830 2832 2851 C4' A P 4 OK 2853 2850 2852 2872 C4' A P 5 OK 2874 2871 2873 2893 C4' T P 6 OK 2895 2892 2894 2913 C4' G P 7 OK 2915 2912 2914 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2641 C5' C T 1 2640 2642 2660 C5' A T 2 2659 2661 2681 C5' T T 3 2680 2682 2701 C5' T T 4 2700 2702 2721 C5' A T 5 2720 2722 2742 C5' G T 6 2741 2743 2764 C5' A T 7 2763 2765 2791 C5' T P 1 2790 2792 2811 C5' C P 2 2810 2812 2830 C5' T P 3 2829 2831 2850 C5' A P 4 2849 2851 2871 C5' A P 5 2870 2872 2892 C5' T P 6 2891 2893 2912 C5' G P 7 2911 2913 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2656 P A T 2 OK OK 2645 2657 2658 2659 2677 P T T 3 OK OK 2664 2678 2679 2680 2697 P T T 4 OK OK 2685 2698 2699 2700 2717 P A T 5 OK OK 2705 2718 2719 2720 2738 P G T 6 OK OK 2725 2739 2740 2741 2760 P A T 7 OK OK 2746 2761 2762 2763 2807 P C P 2 OK OK 2795 2808 2809 2810 2826 P T P 3 OK OK 2815 2827 2828 2829 2846 P A P 4 OK OK 2834 2847 2848 2849 2867 P A P 5 OK OK 2854 2868 2869 2870 2888 P T P 6 OK OK 2875 2889 2890 2891 2908 P G P 7 OK OK 2896 2909 2910 2911 ---------------------------------------------------------------------------------