ID code: '8ICK' 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' --------------------------------------------------------------------------------- 2645 C1' C T 1 beta 2641 2646 2644 2664 C1' A T 2 beta 2660 2665 2663 2685 C1' T T 3 beta 2681 2686 2684 2705 C1' T T 4 beta 2701 2706 2704 2725 C1' A T 5 beta 2721 2726 2724 2746 C1' G T 6 beta 2742 2747 2745 2768 C1' A T 7 beta 2764 2769 2767 2795 C1' T P 1 beta 2791 2796 2794 2815 C1' C P 2 beta 2811 2816 2814 2834 C1' T P 3 beta 2830 2835 2833 2854 C1' A P 4 beta 2850 2855 2853 2875 C1' A P 5 beta 2871 2876 2874 2896 C1' T P 6 beta 2892 2897 2895 2916 C1' G P 7 beta 2912 2917 2915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2644 C2' C T 1 2645 2642 2663 C2' A T 2 2664 2661 2684 C2' T T 3 2685 2682 2704 C2' T T 4 2705 2702 2724 C2' A T 5 2725 2722 2745 C2' G T 6 2746 2743 2767 C2' A T 7 2768 2765 2794 C2' T P 1 2795 2792 2814 C2' C P 2 2815 2812 2833 C2' T P 3 2834 2831 2853 C2' A P 4 2854 2851 2874 C2' A P 5 2875 2872 2895 C2' T P 6 2896 2893 2915 C2' G P 7 2916 2913 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2642 C3' C T 1 OK 2640 2643 2644 2661 C3' A T 2 OK 2659 2662 2663 2682 C3' T T 3 OK 2680 2683 2684 2702 C3' T T 4 OK 2700 2703 2704 2722 C3' A T 5 OK 2720 2723 2724 2743 C3' G T 6 OK 2741 2744 2745 2765 C3' A T 7 OK 2763 2766 2767 2792 C3' T P 1 OK 2790 2793 2794 2812 C3' C P 2 OK 2810 2813 2814 2831 C3' T P 3 OK 2829 2832 2833 2851 C3' A P 4 OK 2849 2852 2853 2872 C3' A P 5 OK 2870 2873 2874 2893 C3' T P 6 OK 2891 2894 2895 2913 C3' G P 7 OK 2911 2914 2915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2640 C4' C T 1 OK 2642 2639 2641 2659 C4' A T 2 OK 2661 2658 2660 2680 C4' T T 3 OK 2682 2679 2681 2700 C4' T T 4 OK 2702 2699 2701 2720 C4' A T 5 OK 2722 2719 2721 2741 C4' G T 6 OK 2743 2740 2742 2763 C4' A T 7 OK 2765 2762 2764 2790 C4' T P 1 OK 2792 2789 2791 2810 C4' C P 2 OK 2812 2809 2811 2829 C4' T P 3 OK 2831 2828 2830 2849 C4' A P 4 OK 2851 2848 2850 2870 C4' A P 5 OK 2872 2869 2871 2891 C4' T P 6 OK 2893 2890 2892 2911 C4' G P 7 OK 2913 2910 2912 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2639 C5' C T 1 2638 2640 2658 C5' A T 2 2657 2659 2679 C5' T T 3 2678 2680 2699 C5' T T 4 2698 2700 2719 C5' A T 5 2718 2720 2740 C5' G T 6 2739 2741 2762 C5' A T 7 2761 2763 2789 C5' T P 1 2788 2790 2809 C5' C P 2 2808 2810 2828 C5' T P 3 2827 2829 2848 C5' A P 4 2847 2849 2869 C5' A P 5 2868 2870 2890 C5' T P 6 2889 2891 2910 C5' G P 7 2909 2911 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2654 P A T 2 OK OK 2643 2655 2656 2657 2675 P T T 3 OK OK 2662 2676 2677 2678 2695 P T T 4 OK OK 2683 2696 2697 2698 2715 P A T 5 OK OK 2703 2716 2717 2718 2736 P G T 6 OK OK 2723 2737 2738 2739 2758 P A T 7 OK OK 2744 2759 2760 2761 2805 P C P 2 OK OK 2793 2806 2807 2808 2824 P T P 3 OK OK 2813 2825 2826 2827 2844 P A P 4 OK OK 2832 2845 2846 2847 2865 P A P 5 OK OK 2852 2866 2867 2868 2886 P T P 6 OK OK 2873 2887 2888 2889 2906 P G P 7 OK OK 2894 2907 2908 2909 ---------------------------------------------------------------------------------