ID code: '8ICH' 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' --------------------------------------------------------------------------------- 2634 C1' C T 1 beta 2630 2635 2633 2653 C1' A T 2 beta 2649 2654 2652 2674 C1' T T 3 beta 2670 2675 2673 2694 C1' T T 4 beta 2690 2695 2693 2714 C1' A T 5 beta 2710 2715 2713 2735 C1' G T 6 beta 2731 2736 2734 2757 C1' A T 7 beta 2753 2758 2756 2784 C1' T P 1 beta 2780 2785 2783 2804 C1' C P 2 beta 2800 2805 2803 2823 C1' T P 3 beta 2819 2824 2822 2843 C1' A P 4 beta 2839 2844 2842 2864 C1' A P 5 beta 2860 2865 2863 2885 C1' T P 6 beta 2881 2886 2884 2905 C1' G P 7 beta 2901 2906 2904 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2633 C2' C T 1 2634 2631 2652 C2' A T 2 2653 2650 2673 C2' T T 3 2674 2671 2693 C2' T T 4 2694 2691 2713 C2' A T 5 2714 2711 2734 C2' G T 6 2735 2732 2756 C2' A T 7 2757 2754 2783 C2' T P 1 2784 2781 2803 C2' C P 2 2804 2801 2822 C2' T P 3 2823 2820 2842 C2' A P 4 2843 2840 2863 C2' A P 5 2864 2861 2884 C2' T P 6 2885 2882 2904 C2' G P 7 2905 2902 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2631 C3' C T 1 OK 2629 2632 2633 2650 C3' A T 2 OK 2648 2651 2652 2671 C3' T T 3 OK 2669 2672 2673 2691 C3' T T 4 OK 2689 2692 2693 2711 C3' A T 5 OK 2709 2712 2713 2732 C3' G T 6 OK 2730 2733 2734 2754 C3' A T 7 OK 2752 2755 2756 2781 C3' T P 1 OK 2779 2782 2783 2801 C3' C P 2 OK 2799 2802 2803 2820 C3' T P 3 OK 2818 2821 2822 2840 C3' A P 4 OK 2838 2841 2842 2861 C3' A P 5 OK 2859 2862 2863 2882 C3' T P 6 OK 2880 2883 2884 2902 C3' G P 7 OK 2900 2903 2904 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2629 C4' C T 1 OK 2631 2628 2630 2648 C4' A T 2 OK 2650 2647 2649 2669 C4' T T 3 OK 2671 2668 2670 2689 C4' T T 4 OK 2691 2688 2690 2709 C4' A T 5 OK 2711 2708 2710 2730 C4' G T 6 OK 2732 2729 2731 2752 C4' A T 7 OK 2754 2751 2753 2779 C4' T P 1 OK 2781 2778 2780 2799 C4' C P 2 OK 2801 2798 2800 2818 C4' T P 3 OK 2820 2817 2819 2838 C4' A P 4 OK 2840 2837 2839 2859 C4' A P 5 OK 2861 2858 2860 2880 C4' T P 6 OK 2882 2879 2881 2900 C4' G P 7 OK 2902 2899 2901 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2628 C5' C T 1 2627 2629 2647 C5' A T 2 2646 2648 2668 C5' T T 3 2667 2669 2688 C5' T T 4 2687 2689 2708 C5' A T 5 2707 2709 2729 C5' G T 6 2728 2730 2751 C5' A T 7 2750 2752 2778 C5' T P 1 2777 2779 2798 C5' C P 2 2797 2799 2817 C5' T P 3 2816 2818 2837 C5' A P 4 2836 2838 2858 C5' A P 5 2857 2859 2879 C5' T P 6 2878 2880 2899 C5' G P 7 2898 2900 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2643 P A T 2 OK OK 2632 2644 2645 2646 2664 P T T 3 OK OK 2651 2665 2666 2667 2684 P T T 4 OK OK 2672 2685 2686 2687 2704 P A T 5 OK OK 2692 2705 2706 2707 2725 P G T 6 OK OK 2712 2726 2727 2728 2747 P A T 7 OK OK 2733 2748 2749 2750 2794 P C P 2 OK OK 2782 2795 2796 2797 2813 P T P 3 OK OK 2802 2814 2815 2816 2833 P A P 4 OK OK 2821 2834 2835 2836 2854 P A P 5 OK OK 2841 2855 2856 2857 2875 P T P 6 OK OK 2862 2876 2877 2878 2895 P G P 7 OK OK 2883 2896 2897 2898 ---------------------------------------------------------------------------------