ID code: '2PVI' 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' --------------------------------------------------------------------------------- 2623 C1' G C 3 beta 2619 2624 2622 2645 C1' A C 4 beta 2641 2646 2644 2666 C1' C C 5 beta 2662 2667 2665 2685 C1' C C 6 beta 2681 2686 2684 2704 C1' A C 7 beta 2700 2705 2703 2725 C1' G C 8 beta 2721 2726 2724 2744 C1' CYI C 9 beta 2743 2745 2754 2767 C1' T C 10 beta 2763 2768 2766 2787 C1' G C 11 beta 2783 2788 2786 2809 C1' G C 12 beta 2805 2810 2808 2831 C1' T C 13 beta 2827 2832 2830 2851 C1' C C 14 beta 2847 2852 2850 2888 C1' G D 3 beta 2884 2889 2887 2910 C1' A D 4 beta 2906 2911 2909 2931 C1' C D 5 beta 2927 2932 2930 2950 C1' C D 6 beta 2946 2951 2949 2969 C1' A D 7 beta 2965 2970 2968 2990 C1' G D 8 beta 2986 2991 2989 3009 C1' CYI D 9 beta 3008 3010 3019 3032 C1' T D 10 beta 3028 3033 3031 3052 C1' G D 11 beta 3048 3053 3051 3074 C1' G D 12 beta 3070 3075 3073 3096 C1' T D 13 beta 3092 3097 3095 3116 C1' C D 14 beta 3112 3117 3115 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2622 C2' G C 3 2623 2620 2644 C2' A C 4 2645 2642 2665 C2' C C 5 2666 2663 2684 C2' C C 6 2685 2682 2703 C2' A C 7 2704 2701 2724 C2' G C 8 2725 2722 2754 C2' CYI C 9 2744 2755 2766 C2' T C 10 2767 2764 2786 C2' G C 11 2787 2784 2808 C2' G C 12 2809 2806 2830 C2' T C 13 2831 2828 2850 C2' C C 14 2851 2848 2887 C2' G D 3 2888 2885 2909 C2' A D 4 2910 2907 2930 C2' C D 5 2931 2928 2949 C2' C D 6 2950 2947 2968 C2' A D 7 2969 2966 2989 C2' G D 8 2990 2987 3019 C2' CYI D 9 3009 3020 3031 C2' T D 10 3032 3029 3051 C2' G D 11 3052 3049 3073 C2' G D 12 3074 3071 3095 C2' T D 13 3096 3093 3115 C2' C D 14 3116 3113 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2620 C3' G C 3 OK 2618 2621 2622 2642 C3' A C 4 OK 2640 2643 2644 2663 C3' C C 5 OK 2661 2664 2665 2682 C3' C C 6 OK 2680 2683 2684 2701 C3' A C 7 OK 2699 2702 2703 2722 C3' G C 8 OK 2720 2723 2724 2755 C3' CYI C 9 OK 2742 2756 2754 2764 C3' T C 10 OK 2762 2765 2766 2784 C3' G C 11 OK 2782 2785 2786 2806 C3' G C 12 OK 2804 2807 2808 2828 C3' T C 13 OK 2826 2829 2830 2848 C3' C C 14 OK 2846 2849 2850 2885 C3' G D 3 OK 2883 2886 2887 2907 C3' A D 4 OK 2905 2908 2909 2928 C3' C D 5 OK 2926 2929 2930 2947 C3' C D 6 OK 2945 2948 2949 2966 C3' A D 7 OK 2964 2967 2968 2987 C3' G D 8 OK 2985 2988 2989 3020 C3' CYI D 9 OK 3007 3021 3019 3029 C3' T D 10 OK 3027 3030 3031 3049 C3' G D 11 OK 3047 3050 3051 3071 C3' G D 12 OK 3069 3072 3073 3093 C3' T D 13 OK 3091 3094 3095 3113 C3' C D 14 OK 3111 3114 3115 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2618 C4' G C 3 OK 2620 2617 2619 2640 C4' A C 4 OK 2642 2639 2641 2661 C4' C C 5 OK 2663 2660 2662 2680 C4' C C 6 OK 2682 2679 2681 2699 C4' A C 7 OK 2701 2698 2700 2720 C4' G C 8 OK 2722 2719 2721 2742 C4' CYI C 9 OK 2755 2741 2743 2762 C4' T C 10 OK 2764 2761 2763 2782 C4' G C 11 OK 2784 2781 2783 2804 C4' G C 12 OK 2806 2803 2805 2826 C4' T C 13 OK 2828 2825 2827 2846 C4' C C 14 OK 2848 2845 2847 2883 C4' G D 3 OK 2885 2882 2884 2905 C4' A D 4 OK 2907 2904 2906 2926 C4' C D 5 OK 2928 2925 2927 2945 C4' C D 6 OK 2947 2944 2946 2964 C4' A D 7 OK 2966 2963 2965 2985 C4' G D 8 OK 2987 2984 2986 3007 C4' CYI D 9 OK 3020 3006 3008 3027 C4' T D 10 OK 3029 3026 3028 3047 C4' G D 11 OK 3049 3046 3048 3069 C4' G D 12 OK 3071 3068 3070 3091 C4' T D 13 OK 3093 3090 3092 3111 C4' C D 14 OK 3113 3110 3112 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2617 C5' G C 3 2616 2618 2639 C5' A C 4 2638 2640 2660 C5' C C 5 2659 2661 2679 C5' C C 6 2678 2680 2698 C5' A C 7 2697 2699 2719 C5' G C 8 2718 2720 2741 C5' CYI C 9 2740 2742 2761 C5' T C 10 2760 2762 2781 C5' G C 11 2780 2782 2803 C5' G C 12 2802 2804 2825 C5' T C 13 2824 2826 2845 C5' C C 14 2844 2846 2882 C5' G D 3 2881 2883 2904 C5' A D 4 2903 2905 2925 C5' C D 5 2924 2926 2944 C5' C D 6 2943 2945 2963 C5' A D 7 2962 2964 2984 C5' G D 8 2983 2985 3006 C5' CYI D 9 3005 3007 3026 C5' T D 10 3025 3027 3046 C5' G D 11 3045 3047 3068 C5' G D 12 3067 3069 3090 C5' T D 13 3089 3091 3110 C5' C D 14 3109 3111 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2635 P A C 4 OK OK 2621 2636 2637 2638 2656 P C C 5 OK OK 2643 2657 2658 2659 2675 P C C 6 OK OK 2664 2676 2677 2678 2694 P A C 7 OK OK 2683 2695 2696 2697 2715 P G C 8 OK OK 2702 2716 2717 2718 2737 P CYI C 9 OK OK 2723 2738 2739 2740 2757 P T C 10 OK OK 2756 2758 2759 2760 2777 P G C 11 OK OK 2765 2778 2779 2780 2799 P G C 12 OK OK 2785 2800 2801 2802 2821 P T C 13 OK OK 2807 2822 2823 2824 2841 P C C 14 OK OK 2829 2842 2843 2844 2900 P A D 4 OK OK 2886 2901 2902 2903 2921 P C D 5 OK OK 2908 2922 2923 2924 2940 P C D 6 OK OK 2929 2941 2942 2943 2959 P A D 7 OK OK 2948 2960 2961 2962 2980 P G D 8 OK OK 2967 2981 2982 2983 3002 P CYI D 9 OK OK 2988 3003 3004 3005 3022 P T D 10 OK OK 3021 3023 3024 3025 3042 P G D 11 OK OK 3030 3043 3044 3045 3064 P G D 12 OK OK 3050 3065 3066 3067 3086 P T D 13 OK OK 3072 3087 3088 3089 3106 P C D 14 OK OK 3094 3107 3108 3109 ---------------------------------------------------------------------------------