ID code: '9ICY' 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' --------------------------------------------------------------------------------- 2639 C1' C T 1 beta 2635 2640 2638 2658 C1' A T 2 beta 2654 2659 2657 2679 C1' T T 3 beta 2675 2680 2678 2699 C1' T T 4 beta 2695 2700 2698 2719 C1' A T 5 beta 2715 2720 2718 2740 C1' G T 6 beta 2736 2741 2739 2762 C1' A T 7 beta 2758 2763 2761 2785 C1' T P 1 beta 2781 2786 2784 2805 C1' C P 2 beta 2801 2806 2804 2824 C1' T P 3 beta 2820 2825 2823 2844 C1' A P 4 beta 2840 2845 2843 2865 C1' A P 5 beta 2861 2866 2864 2886 C1' T P 6 beta 2882 2887 2885 2906 C1' G P 7 beta 2902 2907 2905 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2638 C2' C T 1 2639 2636 2657 C2' A T 2 2658 2655 2678 C2' T T 3 2679 2676 2698 C2' T T 4 2699 2696 2718 C2' A T 5 2719 2716 2739 C2' G T 6 2740 2737 2761 C2' A T 7 2762 2759 2784 C2' T P 1 2785 2782 2804 C2' C P 2 2805 2802 2823 C2' T P 3 2824 2821 2843 C2' A P 4 2844 2841 2864 C2' A P 5 2865 2862 2885 C2' T P 6 2886 2883 2905 C2' G P 7 2906 2903 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2636 C3' C T 1 OK 2634 2637 2638 2655 C3' A T 2 OK 2653 2656 2657 2676 C3' T T 3 OK 2674 2677 2678 2696 C3' T T 4 OK 2694 2697 2698 2716 C3' A T 5 OK 2714 2717 2718 2737 C3' G T 6 OK 2735 2738 2739 2759 C3' A T 7 OK 2757 2760 2761 2782 C3' T P 1 OK 2780 2783 2784 2802 C3' C P 2 OK 2800 2803 2804 2821 C3' T P 3 OK 2819 2822 2823 2841 C3' A P 4 OK 2839 2842 2843 2862 C3' A P 5 OK 2860 2863 2864 2883 C3' T P 6 OK 2881 2884 2885 2903 C3' G P 7 OK 2901 2904 2905 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2634 C4' C T 1 OK 2636 2633 2635 2653 C4' A T 2 OK 2655 2652 2654 2674 C4' T T 3 OK 2676 2673 2675 2694 C4' T T 4 OK 2696 2693 2695 2714 C4' A T 5 OK 2716 2713 2715 2735 C4' G T 6 OK 2737 2734 2736 2757 C4' A T 7 OK 2759 2756 2758 2780 C4' T P 1 OK 2782 2779 2781 2800 C4' C P 2 OK 2802 2799 2801 2819 C4' T P 3 OK 2821 2818 2820 2839 C4' A P 4 OK 2841 2838 2840 2860 C4' A P 5 OK 2862 2859 2861 2881 C4' T P 6 OK 2883 2880 2882 2901 C4' G P 7 OK 2903 2900 2902 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2633 C5' C T 1 2632 2634 2652 C5' A T 2 2651 2653 2673 C5' T T 3 2672 2674 2693 C5' T T 4 2692 2694 2713 C5' A T 5 2712 2714 2734 C5' G T 6 2733 2735 2756 C5' A T 7 2755 2757 2779 C5' T P 1 2778 2780 2799 C5' C P 2 2798 2800 2818 C5' T P 3 2817 2819 2838 C5' A P 4 2837 2839 2859 C5' A P 5 2858 2860 2880 C5' T P 6 2879 2881 2900 C5' G P 7 2899 2901 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2648 P A T 2 OK OK 2637 2649 2650 2651 2669 P T T 3 OK OK 2656 2670 2671 2672 2689 P T T 4 OK OK 2677 2690 2691 2692 2709 P A T 5 OK OK 2697 2710 2711 2712 2730 P G T 6 OK OK 2717 2731 2732 2733 2752 P A T 7 OK OK 2738 2753 2754 2755 2795 P C P 2 OK OK 2783 2796 2797 2798 2814 P T P 3 OK OK 2803 2815 2816 2817 2834 P A P 4 OK OK 2822 2835 2836 2837 2855 P A P 5 OK OK 2842 2856 2857 2858 2876 P T P 6 OK OK 2863 2877 2878 2879 2896 P G P 7 OK OK 2884 2897 2898 2899 ---------------------------------------------------------------------------------