ID code: '8ICZ' 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 2789 C1' T P 1 beta 2785 2790 2788 2809 C1' C P 2 beta 2805 2810 2808 2828 C1' T P 3 beta 2824 2829 2827 2848 C1' A P 4 beta 2844 2849 2847 2869 C1' A P 5 beta 2865 2870 2868 2890 C1' T P 6 beta 2886 2891 2889 2910 C1' G P 7 beta 2906 2911 2909 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 2788 C2' T P 1 2789 2786 2808 C2' C P 2 2809 2806 2827 C2' T P 3 2828 2825 2847 C2' A P 4 2848 2845 2868 C2' A P 5 2869 2866 2889 C2' T P 6 2890 2887 2909 C2' G P 7 2910 2907 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 2786 C3' T P 1 OK 2784 2787 2788 2806 C3' C P 2 OK 2804 2807 2808 2825 C3' T P 3 OK 2823 2826 2827 2845 C3' A P 4 OK 2843 2846 2847 2866 C3' A P 5 OK 2864 2867 2868 2887 C3' T P 6 OK 2885 2888 2889 2907 C3' G P 7 OK 2905 2908 2909 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 2784 C4' T P 1 OK 2786 2783 2785 2804 C4' C P 2 OK 2806 2803 2805 2823 C4' T P 3 OK 2825 2822 2824 2843 C4' A P 4 OK 2845 2842 2844 2864 C4' A P 5 OK 2866 2863 2865 2885 C4' T P 6 OK 2887 2884 2886 2905 C4' G P 7 OK 2907 2904 2906 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 2783 C5' T P 1 2782 2784 2803 C5' C P 2 2802 2804 2822 C5' T P 3 2821 2823 2842 C5' A P 4 2841 2843 2863 C5' A P 5 2862 2864 2884 C5' T P 6 2883 2885 2904 C5' G P 7 2903 2905 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 2799 P C P 2 OK OK 2787 2800 2801 2802 2818 P T P 3 OK OK 2807 2819 2820 2821 2838 P A P 4 OK OK 2826 2839 2840 2841 2859 P A P 5 OK OK 2846 2860 2861 2862 2880 P T P 6 OK OK 2867 2881 2882 2883 2900 P G P 7 OK OK 2888 2901 2902 2903 ---------------------------------------------------------------------------------