ID code: '4RT3' 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' --------------------------------------------------------------------------------- 2617 C1' DC T 1 beta 2613 2618 2616 2636 C1' DC T 2 beta 2632 2637 2635 2655 C1' DG T 3 beta 2651 2656 2654 2677 C1' DA T 4 beta 2673 2678 2676 2698 C1' DC T 5 beta 2694 2699 2697 2717 C1' DA T 6 beta 2713 2718 2716 2738 C1' DG T 7 beta 2734 2739 2737 2760 C1' DC T 8 beta 2756 2761 2759 2779 C1' DG T 9 beta 2775 2780 2778 2801 C1' DC T 10 beta 2797 2802 2800 2820 C1' DA T 11 beta 2816 2821 2819 2841 C1' DT T 12 beta 2837 2842 2840 2861 C1' DC T 13 beta 2857 2862 2860 2880 C1' DA T 14 beta 2876 2881 2879 2901 C1' DG T 15 beta 2897 2902 2900 2923 C1' DC T 16 beta 2919 2924 2922 2940 C1' DG P 1 beta 2936 2941 2939 2962 C1' DC P 2 beta 2958 2963 2961 2981 C1' DT P 3 beta 2977 2982 2980 3001 C1' DG P 4 beta 2997 3002 3000 3023 C1' DA P 5 beta 3019 3024 3022 3044 C1' DT P 6 beta 3040 3045 3043 3064 C1' DG P 7 beta 3060 3065 3063 3086 C1' DC P 8 beta 3082 3087 3085 3105 C1' DG P 9 beta 3101 3106 3104 3125 C1' DOC P 10 beta 3129 3117 3126 3147 C1' DG D 1 beta 3143 3148 3146 3169 C1' DT D 2 beta 3165 3170 3168 3189 C1' DC D 3 beta 3185 3190 3188 3208 C1' DG D 4 beta 3204 3209 3207 3230 C1' DG D 5 beta 3226 3231 3229 3259 C1' C6T A 408 beta 3263 3258 3260 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2616 C2' DC T 1 2617 2614 2635 C2' DC T 2 2636 2633 2654 C2' DG T 3 2655 2652 2676 C2' DA T 4 2677 2674 2697 C2' DC T 5 2698 2695 2716 C2' DA T 6 2717 2714 2737 C2' DG T 7 2738 2735 2759 C2' DC T 8 2760 2757 2778 C2' DG T 9 2779 2776 2800 C2' DC T 10 2801 2798 2819 C2' DA T 11 2820 2817 2840 C2' DT T 12 2841 2838 2860 C2' DC T 13 2861 2858 2879 C2' DA T 14 2880 2877 2900 C2' DG T 15 2901 2898 2922 C2' DC T 16 2923 2920 2939 C2' DG P 1 2940 2937 2961 C2' DC P 2 2962 2959 2980 C2' DT P 3 2981 2978 3000 C2' DG P 4 3001 2998 3022 C2' DA P 5 3023 3020 3043 C2' DT P 6 3044 3041 3063 C2' DG P 7 3064 3061 3085 C2' DC P 8 3086 3083 3104 C2' DG P 9 3105 3102 3126 C2' DOC P 10 3125 3127 3146 C2' DG D 1 3147 3144 3168 C2' DT D 2 3169 3166 3188 C2' DC D 3 3189 3186 3207 C2' DG D 4 3208 3205 3229 C2' DG D 5 3230 3227 3260 C2' C6T A 408 3259 3261 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2614 C3' DC T 1 OK 2612 2615 2616 2633 C3' DC T 2 OK 2631 2634 2635 2652 C3' DG T 3 OK 2650 2653 2654 2674 C3' DA T 4 OK 2672 2675 2676 2695 C3' DC T 5 OK 2693 2696 2697 2714 C3' DA T 6 OK 2712 2715 2716 2735 C3' DG T 7 OK 2733 2736 2737 2757 C3' DC T 8 OK 2755 2758 2759 2776 C3' DG T 9 OK 2774 2777 2778 2798 C3' DC T 10 OK 2796 2799 2800 2817 C3' DA T 11 OK 2815 2818 2819 2838 C3' DT T 12 OK 2836 2839 2840 2858 C3' DC T 13 OK 2856 2859 2860 2877 C3' DA T 14 OK 2875 2878 2879 2898 C3' DG T 15 OK 2896 2899 2900 2920 C3' DC T 16 OK 2918 2921 2922 2937 C3' DG P 1 OK 2935 2938 2939 2959 C3' DC P 2 OK 2957 2960 2961 2978 C3' DT P 3 OK 2976 2979 2980 2998 C3' DG P 4 OK 2996 2999 3000 3020 C3' DA P 5 OK 3018 3021 3022 3041 C3' DT P 6 OK 3039 3042 3043 3061 C3' DG P 7 OK 3059 3062 3063 3083 C3' DC P 8 OK 3081 3084 3085 3102 C3' DG P 9 OK 3100 3103 3104 3127 C3' DOC P 10 3128 3126 3144 C3' DG D 1 OK 3142 3145 3146 3166 C3' DT D 2 OK 3164 3167 3168 3186 C3' DC D 3 OK 3184 3187 3188 3205 C3' DG D 4 OK 3203 3206 3207 3227 C3' DG D 5 OK 3225 3228 3229 3261 C3' C6T A 408 OK 3264 3262 3260 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2612 C4' DC T 1 OK 2614 2611 2613 2631 C4' DC T 2 OK 2633 2630 2632 2650 C4' DG T 3 OK 2652 2649 2651 2672 C4' DA T 4 OK 2674 2671 2673 2693 C4' DC T 5 OK 2695 2692 2694 2712 C4' DA T 6 OK 2714 2711 2713 2733 C4' DG T 7 OK 2735 2732 2734 2755 C4' DC T 8 OK 2757 2754 2756 2774 C4' DG T 9 OK 2776 2773 2775 2796 C4' DC T 10 OK 2798 2795 2797 2815 C4' DA T 11 OK 2817 2814 2816 2836 C4' DT T 12 OK 2838 2835 2837 2856 C4' DC T 13 OK 2858 2855 2857 2875 C4' DA T 14 OK 2877 2874 2876 2896 C4' DG T 15 OK 2898 2895 2897 2918 C4' DC T 16 OK 2920 2917 2919 2935 C4' DG P 1 OK 2937 2934 2936 2957 C4' DC P 2 OK 2959 2956 2958 2976 C4' DT P 3 OK 2978 2975 2977 2996 C4' DG P 4 OK 2998 2995 2997 3018 C4' DA P 5 OK 3020 3017 3019 3039 C4' DT P 6 OK 3041 3038 3040 3059 C4' DG P 7 OK 3061 3058 3060 3081 C4' DC P 8 OK 3083 3080 3082 3100 C4' DG P 9 OK 3102 3099 3101 3128 C4' DOC P 10 OK 3127 3130 3129 3142 C4' DG D 1 OK 3144 3141 3143 3164 C4' DT D 2 OK 3166 3163 3165 3184 C4' DC D 3 OK 3186 3183 3185 3203 C4' DG D 4 OK 3205 3202 3204 3225 C4' DG D 5 OK 3227 3224 3226 3264 C4' C6T A 408 OK 3261 3265 3263 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2611 C5' DC T 1 2610 2612 2630 C5' DC T 2 2629 2631 2649 C5' DG T 3 2648 2650 2671 C5' DA T 4 2670 2672 2692 C5' DC T 5 2691 2693 2711 C5' DA T 6 2710 2712 2732 C5' DG T 7 2731 2733 2754 C5' DC T 8 2753 2755 2773 C5' DG T 9 2772 2774 2795 C5' DC T 10 2794 2796 2814 C5' DA T 11 2813 2815 2835 C5' DT T 12 2834 2836 2855 C5' DC T 13 2854 2856 2874 C5' DA T 14 2873 2875 2895 C5' DG T 15 2894 2896 2917 C5' DC T 16 2916 2918 2934 C5' DG P 1 2933 2935 2956 C5' DC P 2 2955 2957 2975 C5' DT P 3 2974 2976 2995 C5' DG P 4 2994 2996 3017 C5' DA P 5 3016 3018 3038 C5' DT P 6 3037 3039 3058 C5' DG P 7 3057 3059 3080 C5' DC P 8 3079 3081 3099 C5' DG P 9 3098 3100 3130 C5' DOC P 10 3131 3128 3141 C5' DG D 1 3140 3142 3163 C5' DT D 2 3162 3164 3183 C5' DC D 3 3182 3184 3202 C5' DG D 4 3201 3203 3224 C5' DG D 5 3223 3225 3265 C5' C6T A 408 3266 3264 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2626 P DC T 2 distorted distorted 2615 2627 2628 2629 2645 P DG T 3 distorted distorted 2634 2646 2647 2648 2667 P DA T 4 distorted distorted 2653 2668 2669 2670 2688 P DC T 5 distorted distorted 2675 2689 2690 2691 2707 P DA T 6 distorted distorted 2696 2708 2709 2710 2728 P DG T 7 distorted distorted 2715 2729 2730 2731 2750 P DC T 8 distorted distorted 2736 2751 2752 2753 2769 P DG T 9 distorted distorted 2758 2770 2771 2772 2791 P DC T 10 distorted distorted 2777 2792 2793 2794 2810 P DA T 11 distorted distorted 2799 2811 2812 2813 2831 P DT T 12 distorted distorted 2818 2832 2833 2834 2851 P DC T 13 distorted distorted 2839 2852 2853 2854 2870 P DA T 14 distorted distorted 2859 2871 2872 2873 2891 P DG T 15 distorted distorted 2878 2892 2893 2894 2913 P DC T 16 distorted distorted 2899 2914 2915 2916 2952 P DC P 2 distorted distorted 2938 2953 2954 2955 2971 P DT P 3 distorted distorted 2960 2972 2973 2974 2991 P DG P 4 distorted distorted 2979 2992 2993 2994 3013 P DA P 5 distorted distorted 2999 3014 3015 3016 3034 P DT P 6 distorted distorted 3021 3035 3036 3037 3054 P DG P 7 distorted distorted 3042 3055 3056 3057 3076 P DC P 8 distorted distorted 3062 3077 3078 3079 3095 P DG P 9 distorted distorted 3084 3096 3097 3098 3132 P DOC P 10 distorted distorted 3103 3133 3134 3131 3137 P DG D 1 distorted distorted 3138 3139 3140 3159 P DT D 2 distorted distorted 3145 3160 3161 3162 3179 P DC D 3 distorted distorted 3167 3180 3181 3182 3198 P DG D 4 distorted distorted 3187 3199 3200 3201 3220 P DG D 5 distorted distorted 3206 3221 3222 3223 ---------------------------------------------------------------------------------