ID code: '8ICV' 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' --------------------------------------------------------------------------------- 2648 C1' C T 1 beta 2644 2649 2647 2667 C1' A T 2 beta 2663 2668 2666 2688 C1' T T 3 beta 2684 2689 2687 2708 C1' T T 4 beta 2704 2709 2707 2728 C1' A T 5 beta 2724 2729 2727 2749 C1' G T 6 beta 2745 2750 2748 2771 C1' A T 7 beta 2767 2772 2770 2798 C1' T P 1 beta 2794 2799 2797 2818 C1' C P 2 beta 2814 2819 2817 2837 C1' T P 3 beta 2833 2838 2836 2857 C1' A P 4 beta 2853 2858 2856 2878 C1' A P 5 beta 2874 2879 2877 2899 C1' T P 6 beta 2895 2900 2898 2919 C1' G P 7 beta 2915 2920 2918 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2647 C2' C T 1 2648 2645 2666 C2' A T 2 2667 2664 2687 C2' T T 3 2688 2685 2707 C2' T T 4 2708 2705 2727 C2' A T 5 2728 2725 2748 C2' G T 6 2749 2746 2770 C2' A T 7 2771 2768 2797 C2' T P 1 2798 2795 2817 C2' C P 2 2818 2815 2836 C2' T P 3 2837 2834 2856 C2' A P 4 2857 2854 2877 C2' A P 5 2878 2875 2898 C2' T P 6 2899 2896 2918 C2' G P 7 2919 2916 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2645 C3' C T 1 OK 2643 2646 2647 2664 C3' A T 2 OK 2662 2665 2666 2685 C3' T T 3 OK 2683 2686 2687 2705 C3' T T 4 OK 2703 2706 2707 2725 C3' A T 5 OK 2723 2726 2727 2746 C3' G T 6 OK 2744 2747 2748 2768 C3' A T 7 OK 2766 2769 2770 2795 C3' T P 1 OK 2793 2796 2797 2815 C3' C P 2 OK 2813 2816 2817 2834 C3' T P 3 OK 2832 2835 2836 2854 C3' A P 4 OK 2852 2855 2856 2875 C3' A P 5 OK 2873 2876 2877 2896 C3' T P 6 OK 2894 2897 2898 2916 C3' G P 7 OK 2914 2917 2918 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2643 C4' C T 1 OK 2645 2642 2644 2662 C4' A T 2 OK 2664 2661 2663 2683 C4' T T 3 OK 2685 2682 2684 2703 C4' T T 4 OK 2705 2702 2704 2723 C4' A T 5 OK 2725 2722 2724 2744 C4' G T 6 OK 2746 2743 2745 2766 C4' A T 7 OK 2768 2765 2767 2793 C4' T P 1 OK 2795 2792 2794 2813 C4' C P 2 OK 2815 2812 2814 2832 C4' T P 3 OK 2834 2831 2833 2852 C4' A P 4 OK 2854 2851 2853 2873 C4' A P 5 OK 2875 2872 2874 2894 C4' T P 6 OK 2896 2893 2895 2914 C4' G P 7 OK 2916 2913 2915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2642 C5' C T 1 2641 2643 2661 C5' A T 2 2660 2662 2682 C5' T T 3 2681 2683 2702 C5' T T 4 2701 2703 2722 C5' A T 5 2721 2723 2743 C5' G T 6 2742 2744 2765 C5' A T 7 2764 2766 2792 C5' T P 1 2791 2793 2812 C5' C P 2 2811 2813 2831 C5' T P 3 2830 2832 2851 C5' A P 4 2850 2852 2872 C5' A P 5 2871 2873 2893 C5' T P 6 2892 2894 2913 C5' G P 7 2912 2914 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2657 P A T 2 OK OK 2646 2658 2659 2660 2678 P T T 3 OK OK 2665 2679 2680 2681 2698 P T T 4 OK OK 2686 2699 2700 2701 2718 P A T 5 OK OK 2706 2719 2720 2721 2739 P G T 6 OK OK 2726 2740 2741 2742 2761 P A T 7 OK OK 2747 2762 2763 2764 2808 P C P 2 OK OK 2796 2809 2810 2811 2827 P T P 3 OK OK 2816 2828 2829 2830 2847 P A P 4 OK OK 2835 2848 2849 2850 2868 P A P 5 OK OK 2855 2869 2870 2871 2889 P T P 6 OK OK 2876 2890 2891 2892 2909 P G P 7 OK OK 2897 2910 2911 2912 ---------------------------------------------------------------------------------