ID code: '1ZQQ' 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' --------------------------------------------------------------------------------- 2636 C1' C T 1 beta 2632 2637 2635 2655 C1' A T 2 beta 2651 2656 2654 2676 C1' T T 3 beta 2672 2677 2675 2696 C1' T T 4 beta 2692 2697 2695 2716 C1' A T 5 beta 2712 2717 2715 2737 C1' G T 6 beta 2733 2738 2736 2759 C1' A T 7 beta 2755 2760 2758 2786 C1' T P 1 beta 2782 2787 2785 2806 C1' C P 2 beta 2802 2807 2805 2825 C1' T P 3 beta 2821 2826 2824 2845 C1' A P 4 beta 2841 2846 2844 2866 C1' A P 5 beta 2862 2867 2865 2887 C1' T P 6 beta 2883 2888 2886 2907 C1' G P 7 beta 2903 2908 2906 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2635 C2' C T 1 2636 2633 2654 C2' A T 2 2655 2652 2675 C2' T T 3 2676 2673 2695 C2' T T 4 2696 2693 2715 C2' A T 5 2716 2713 2736 C2' G T 6 2737 2734 2758 C2' A T 7 2759 2756 2785 C2' T P 1 2786 2783 2805 C2' C P 2 2806 2803 2824 C2' T P 3 2825 2822 2844 C2' A P 4 2845 2842 2865 C2' A P 5 2866 2863 2886 C2' T P 6 2887 2884 2906 C2' G P 7 2907 2904 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2633 C3' C T 1 OK 2631 2634 2635 2652 C3' A T 2 OK 2650 2653 2654 2673 C3' T T 3 OK 2671 2674 2675 2693 C3' T T 4 OK 2691 2694 2695 2713 C3' A T 5 OK 2711 2714 2715 2734 C3' G T 6 OK 2732 2735 2736 2756 C3' A T 7 OK 2754 2757 2758 2783 C3' T P 1 OK 2781 2784 2785 2803 C3' C P 2 OK 2801 2804 2805 2822 C3' T P 3 OK 2820 2823 2824 2842 C3' A P 4 OK 2840 2843 2844 2863 C3' A P 5 OK 2861 2864 2865 2884 C3' T P 6 OK 2882 2885 2886 2904 C3' G P 7 OK 2902 2905 2906 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2631 C4' C T 1 OK 2633 2630 2632 2650 C4' A T 2 OK 2652 2649 2651 2671 C4' T T 3 OK 2673 2670 2672 2691 C4' T T 4 OK 2693 2690 2692 2711 C4' A T 5 OK 2713 2710 2712 2732 C4' G T 6 OK 2734 2731 2733 2754 C4' A T 7 OK 2756 2753 2755 2781 C4' T P 1 OK 2783 2780 2782 2801 C4' C P 2 OK 2803 2800 2802 2820 C4' T P 3 OK 2822 2819 2821 2840 C4' A P 4 OK 2842 2839 2841 2861 C4' A P 5 OK 2863 2860 2862 2882 C4' T P 6 OK 2884 2881 2883 2902 C4' G P 7 OK 2904 2901 2903 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2630 C5' C T 1 2629 2631 2649 C5' A T 2 2648 2650 2670 C5' T T 3 2669 2671 2690 C5' T T 4 2689 2691 2710 C5' A T 5 2709 2711 2731 C5' G T 6 2730 2732 2753 C5' A T 7 2752 2754 2780 C5' T P 1 2779 2781 2800 C5' C P 2 2799 2801 2819 C5' T P 3 2818 2820 2839 C5' A P 4 2838 2840 2860 C5' A P 5 2859 2861 2881 C5' T P 6 2880 2882 2901 C5' G P 7 2900 2902 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2645 P A T 2 OK OK 2634 2646 2647 2648 2666 P T T 3 OK OK 2653 2667 2668 2669 2686 P T T 4 OK OK 2674 2687 2688 2689 2706 P A T 5 OK OK 2694 2707 2708 2709 2727 P G T 6 OK OK 2714 2728 2729 2730 2749 P A T 7 OK OK 2735 2750 2751 2752 2796 P C P 2 OK OK 2784 2797 2798 2799 2815 P T P 3 OK OK 2804 2816 2817 2818 2835 P A P 4 OK OK 2823 2836 2837 2838 2856 P A P 5 OK OK 2843 2857 2858 2859 2877 P T P 6 OK OK 2864 2878 2879 2880 2897 P G P 7 OK OK 2885 2898 2899 2900 ---------------------------------------------------------------------------------