ID code: '8ICT' 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' --------------------------------------------------------------------------------- 2656 C1' C T 1 beta 2652 2657 2655 2675 C1' A T 2 beta 2671 2676 2674 2696 C1' T T 3 beta 2692 2697 2695 2716 C1' T T 4 beta 2712 2717 2715 2736 C1' A T 5 beta 2732 2737 2735 2757 C1' G T 6 beta 2753 2758 2756 2779 C1' A T 7 beta 2775 2780 2778 2806 C1' T P 1 beta 2802 2807 2805 2826 C1' C P 2 beta 2822 2827 2825 2845 C1' T P 3 beta 2841 2846 2844 2865 C1' A P 4 beta 2861 2866 2864 2886 C1' A P 5 beta 2882 2887 2885 2907 C1' T P 6 beta 2903 2908 2906 2927 C1' G P 7 beta 2923 2928 2926 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2655 C2' C T 1 2656 2653 2674 C2' A T 2 2675 2672 2695 C2' T T 3 2696 2693 2715 C2' T T 4 2716 2713 2735 C2' A T 5 2736 2733 2756 C2' G T 6 2757 2754 2778 C2' A T 7 2779 2776 2805 C2' T P 1 2806 2803 2825 C2' C P 2 2826 2823 2844 C2' T P 3 2845 2842 2864 C2' A P 4 2865 2862 2885 C2' A P 5 2886 2883 2906 C2' T P 6 2907 2904 2926 C2' G P 7 2927 2924 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2653 C3' C T 1 OK 2651 2654 2655 2672 C3' A T 2 OK 2670 2673 2674 2693 C3' T T 3 OK 2691 2694 2695 2713 C3' T T 4 OK 2711 2714 2715 2733 C3' A T 5 OK 2731 2734 2735 2754 C3' G T 6 OK 2752 2755 2756 2776 C3' A T 7 OK 2774 2777 2778 2803 C3' T P 1 OK 2801 2804 2805 2823 C3' C P 2 OK 2821 2824 2825 2842 C3' T P 3 OK 2840 2843 2844 2862 C3' A P 4 OK 2860 2863 2864 2883 C3' A P 5 OK 2881 2884 2885 2904 C3' T P 6 OK 2902 2905 2906 2924 C3' G P 7 OK 2922 2925 2926 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2651 C4' C T 1 OK 2653 2650 2652 2670 C4' A T 2 OK 2672 2669 2671 2691 C4' T T 3 OK 2693 2690 2692 2711 C4' T T 4 OK 2713 2710 2712 2731 C4' A T 5 OK 2733 2730 2732 2752 C4' G T 6 OK 2754 2751 2753 2774 C4' A T 7 OK 2776 2773 2775 2801 C4' T P 1 OK 2803 2800 2802 2821 C4' C P 2 OK 2823 2820 2822 2840 C4' T P 3 OK 2842 2839 2841 2860 C4' A P 4 OK 2862 2859 2861 2881 C4' A P 5 OK 2883 2880 2882 2902 C4' T P 6 OK 2904 2901 2903 2922 C4' G P 7 OK 2924 2921 2923 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2650 C5' C T 1 2649 2651 2669 C5' A T 2 2668 2670 2690 C5' T T 3 2689 2691 2710 C5' T T 4 2709 2711 2730 C5' A T 5 2729 2731 2751 C5' G T 6 2750 2752 2773 C5' A T 7 2772 2774 2800 C5' T P 1 2799 2801 2820 C5' C P 2 2819 2821 2839 C5' T P 3 2838 2840 2859 C5' A P 4 2858 2860 2880 C5' A P 5 2879 2881 2901 C5' T P 6 2900 2902 2921 C5' G P 7 2920 2922 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2665 P A T 2 OK OK 2654 2666 2667 2668 2686 P T T 3 OK OK 2673 2687 2688 2689 2706 P T T 4 OK OK 2694 2707 2708 2709 2726 P A T 5 OK OK 2714 2727 2728 2729 2747 P G T 6 OK OK 2734 2748 2749 2750 2769 P A T 7 OK OK 2755 2770 2771 2772 2816 P C P 2 OK OK 2804 2817 2818 2819 2835 P T P 3 OK OK 2824 2836 2837 2838 2855 P A P 4 OK OK 2843 2856 2857 2858 2876 P A P 5 OK OK 2863 2877 2878 2879 2897 P T P 6 OK OK 2884 2898 2899 2900 2917 P G P 7 OK OK 2905 2918 2919 2920 ---------------------------------------------------------------------------------