ID code: '9ICC' 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' --------------------------------------------------------------------------------- 2655 C1' C T 1 beta 2651 2656 2654 2674 C1' A T 2 beta 2670 2675 2673 2695 C1' T T 3 beta 2691 2696 2694 2715 C1' T T 4 beta 2711 2716 2714 2735 C1' A T 5 beta 2731 2736 2734 2756 C1' G T 6 beta 2752 2757 2755 2778 C1' A T 7 beta 2774 2779 2777 2805 C1' T P 1 beta 2801 2806 2804 2825 C1' C P 2 beta 2821 2826 2824 2844 C1' T P 3 beta 2840 2845 2843 2864 C1' A P 4 beta 2860 2865 2863 2885 C1' A P 5 beta 2881 2886 2884 2906 C1' T P 6 beta 2902 2907 2905 2926 C1' G P 7 beta 2922 2927 2925 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2654 C2' C T 1 2655 2652 2673 C2' A T 2 2674 2671 2694 C2' T T 3 2695 2692 2714 C2' T T 4 2715 2712 2734 C2' A T 5 2735 2732 2755 C2' G T 6 2756 2753 2777 C2' A T 7 2778 2775 2804 C2' T P 1 2805 2802 2824 C2' C P 2 2825 2822 2843 C2' T P 3 2844 2841 2863 C2' A P 4 2864 2861 2884 C2' A P 5 2885 2882 2905 C2' T P 6 2906 2903 2925 C2' G P 7 2926 2923 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2652 C3' C T 1 OK 2650 2653 2654 2671 C3' A T 2 OK 2669 2672 2673 2692 C3' T T 3 OK 2690 2693 2694 2712 C3' T T 4 OK 2710 2713 2714 2732 C3' A T 5 OK 2730 2733 2734 2753 C3' G T 6 OK 2751 2754 2755 2775 C3' A T 7 OK 2773 2776 2777 2802 C3' T P 1 OK 2800 2803 2804 2822 C3' C P 2 OK 2820 2823 2824 2841 C3' T P 3 OK 2839 2842 2843 2861 C3' A P 4 OK 2859 2862 2863 2882 C3' A P 5 OK 2880 2883 2884 2903 C3' T P 6 OK 2901 2904 2905 2923 C3' G P 7 OK 2921 2924 2925 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2650 C4' C T 1 OK 2652 2649 2651 2669 C4' A T 2 OK 2671 2668 2670 2690 C4' T T 3 OK 2692 2689 2691 2710 C4' T T 4 OK 2712 2709 2711 2730 C4' A T 5 OK 2732 2729 2731 2751 C4' G T 6 OK 2753 2750 2752 2773 C4' A T 7 OK 2775 2772 2774 2800 C4' T P 1 OK 2802 2799 2801 2820 C4' C P 2 OK 2822 2819 2821 2839 C4' T P 3 OK 2841 2838 2840 2859 C4' A P 4 OK 2861 2858 2860 2880 C4' A P 5 OK 2882 2879 2881 2901 C4' T P 6 OK 2903 2900 2902 2921 C4' G P 7 OK 2923 2920 2922 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2649 C5' C T 1 2648 2650 2668 C5' A T 2 2667 2669 2689 C5' T T 3 2688 2690 2709 C5' T T 4 2708 2710 2729 C5' A T 5 2728 2730 2750 C5' G T 6 2749 2751 2772 C5' A T 7 2771 2773 2799 C5' T P 1 2798 2800 2819 C5' C P 2 2818 2820 2838 C5' T P 3 2837 2839 2858 C5' A P 4 2857 2859 2879 C5' A P 5 2878 2880 2900 C5' T P 6 2899 2901 2920 C5' G P 7 2919 2921 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2664 P A T 2 OK OK 2653 2665 2666 2667 2685 P T T 3 OK OK 2672 2686 2687 2688 2705 P T T 4 OK OK 2693 2706 2707 2708 2725 P A T 5 OK OK 2713 2726 2727 2728 2746 P G T 6 OK OK 2733 2747 2748 2749 2768 P A T 7 OK OK 2754 2769 2770 2771 2815 P C P 2 OK OK 2803 2816 2817 2818 2834 P T P 3 OK OK 2823 2835 2836 2837 2854 P A P 4 OK OK 2842 2855 2856 2857 2875 P A P 5 OK OK 2862 2876 2877 2878 2896 P T P 6 OK OK 2883 2897 2898 2899 2916 P G P 7 OK OK 2904 2917 2918 2919 ---------------------------------------------------------------------------------