ID code: '3JPN' 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' --------------------------------------------------------------------------------- 2633 C1' DG D 1 beta 2629 2634 2632 2655 C1' DT D 2 beta 2651 2656 2654 2675 C1' DC D 3 beta 2671 2676 2674 2694 C1' DG D 4 beta 2690 2695 2693 2716 C1' DG D 5 beta 2712 2717 2715 2736 C1' DG P 1 beta 2732 2737 2735 2758 C1' DC P 2 beta 2754 2759 2757 2777 C1' DT P 3 beta 2773 2778 2776 2797 C1' DG P 4 beta 2793 2798 2796 2819 C1' DA P 5 beta 2815 2820 2818 2840 C1' DT P 6 beta 2836 2841 2839 2860 C1' DG P 7 beta 2856 2861 2859 2882 C1' DC P 8 beta 2878 2883 2881 2901 C1' DG P 9 beta 2897 2902 2900 2921 C1' DOC P 10 beta 2925 2913 2922 2939 C1' DC T 1 beta 2935 2940 2938 2958 C1' DC T 2 beta 2954 2959 2957 2977 C1' DG T 3 beta 2973 2978 2976 2999 C1' DA T 4 beta 2995 3000 2998 3020 C1' DC T 5 beta 3016 3021 3019 3039 C1' DC T 6 beta 3035 3040 3038 3058 C1' DG T 7 beta 3054 3059 3057 3080 C1' DC T 8 beta 3076 3081 3079 3099 C1' DG T 9 beta 3095 3100 3098 3121 C1' DC T 10 beta 3117 3122 3120 3140 C1' DA T 11 beta 3136 3141 3139 3161 C1' DT T 12 beta 3157 3162 3160 3181 C1' DC T 13 beta 3177 3182 3180 3200 C1' DA T 14 beta 3196 3201 3199 3221 C1' DG T 15 beta 3217 3222 3220 3243 C1' DC T 16 beta 3239 3244 3242 3267 C1' G2C A 338 beta 3283 3263 3272 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2632 C2' DG D 1 2633 2630 2654 C2' DT D 2 2655 2652 2674 C2' DC D 3 2675 2672 2693 C2' DG D 4 2694 2691 2715 C2' DG D 5 2716 2713 2735 C2' DG P 1 2736 2733 2757 C2' DC P 2 2758 2755 2776 C2' DT P 3 2777 2774 2796 C2' DG P 4 2797 2794 2818 C2' DA P 5 2819 2816 2839 C2' DT P 6 2840 2837 2859 C2' DG P 7 2860 2857 2881 C2' DC P 8 2882 2879 2900 C2' DG P 9 2901 2898 2922 C2' DOC P 10 2921 2923 2938 C2' DC T 1 2939 2936 2957 C2' DC T 2 2958 2955 2976 C2' DG T 3 2977 2974 2998 C2' DA T 4 2999 2996 3019 C2' DC T 5 3020 3017 3038 C2' DC T 6 3039 3036 3057 C2' DG T 7 3058 3055 3079 C2' DC T 8 3080 3077 3098 C2' DG T 9 3099 3096 3120 C2' DC T 10 3121 3118 3139 C2' DA T 11 3140 3137 3160 C2' DT T 12 3161 3158 3180 C2' DC T 13 3181 3178 3199 C2' DA T 14 3200 3197 3220 C2' DG T 15 3221 3218 3242 C2' DC T 16 3243 3240 3272 C2' G2C A 338 3267 3277 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2630 C3' DG D 1 OK 2628 2631 2632 2652 C3' DT D 2 OK 2650 2653 2654 2672 C3' DC D 3 OK 2670 2673 2674 2691 C3' DG D 4 OK 2689 2692 2693 2713 C3' DG D 5 OK 2711 2714 2715 2733 C3' DG P 1 OK 2731 2734 2735 2755 C3' DC P 2 OK 2753 2756 2757 2774 C3' DT P 3 OK 2772 2775 2776 2794 C3' DG P 4 OK 2792 2795 2796 2816 C3' DA P 5 OK 2814 2817 2818 2837 C3' DT P 6 OK 2835 2838 2839 2857 C3' DG P 7 OK 2855 2858 2859 2879 C3' DC P 8 OK 2877 2880 2881 2898 C3' DG P 9 OK 2896 2899 2900 2923 C3' DOC P 10 2924 2922 2936 C3' DC T 1 OK 2934 2937 2938 2955 C3' DC T 2 OK 2953 2956 2957 2974 C3' DG T 3 OK 2972 2975 2976 2996 C3' DA T 4 OK 2994 2997 2998 3017 C3' DC T 5 OK 3015 3018 3019 3036 C3' DC T 6 OK 3034 3037 3038 3055 C3' DG T 7 OK 3053 3056 3057 3077 C3' DC T 8 OK 3075 3078 3079 3096 C3' DG T 9 OK 3094 3097 3098 3118 C3' DC T 10 OK 3116 3119 3120 3137 C3' DA T 11 OK 3135 3138 3139 3158 C3' DT T 12 OK 3156 3159 3160 3178 C3' DC T 13 OK 3176 3179 3180 3197 C3' DA T 14 OK 3195 3198 3199 3218 C3' DG T 15 OK 3216 3219 3220 3240 C3' DC T 16 OK 3238 3241 3242 3277 C3' G2C A 338 OK 3282 3278 3272 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2628 C4' DG D 1 OK 2630 2627 2629 2650 C4' DT D 2 OK 2652 2649 2651 2670 C4' DC D 3 OK 2672 2669 2671 2689 C4' DG D 4 OK 2691 2688 2690 2711 C4' DG D 5 OK 2713 2710 2712 2731 C4' DG P 1 OK 2733 2730 2732 2753 C4' DC P 2 OK 2755 2752 2754 2772 C4' DT P 3 OK 2774 2771 2773 2792 C4' DG P 4 OK 2794 2791 2793 2814 C4' DA P 5 OK 2816 2813 2815 2835 C4' DT P 6 OK 2837 2834 2836 2855 C4' DG P 7 OK 2857 2854 2856 2877 C4' DC P 8 OK 2879 2876 2878 2896 C4' DG P 9 OK 2898 2895 2897 2924 C4' DOC P 10 OK 2923 2926 2925 2934 C4' DC T 1 OK 2936 2933 2935 2953 C4' DC T 2 OK 2955 2952 2954 2972 C4' DG T 3 OK 2974 2971 2973 2994 C4' DA T 4 OK 2996 2993 2995 3015 C4' DC T 5 OK 3017 3014 3016 3034 C4' DC T 6 OK 3036 3033 3035 3053 C4' DG T 7 OK 3055 3052 3054 3075 C4' DC T 8 OK 3077 3074 3076 3094 C4' DG T 9 OK 3096 3093 3095 3116 C4' DC T 10 OK 3118 3115 3117 3135 C4' DA T 11 OK 3137 3134 3136 3156 C4' DT T 12 OK 3158 3155 3157 3176 C4' DC T 13 OK 3178 3175 3177 3195 C4' DA T 14 OK 3197 3194 3196 3216 C4' DG T 15 OK 3218 3215 3217 3238 C4' DC T 16 OK 3240 3237 3239 3282 C4' G2C A 338 OK 3277 3284 3283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2627 C5' DG D 1 2626 2628 2649 C5' DT D 2 2648 2650 2669 C5' DC D 3 2668 2670 2688 C5' DG D 4 2687 2689 2710 C5' DG D 5 2709 2711 2730 C5' DG P 1 2729 2731 2752 C5' DC P 2 2751 2753 2771 C5' DT P 3 2770 2772 2791 C5' DG P 4 2790 2792 2813 C5' DA P 5 2812 2814 2834 C5' DT P 6 2833 2835 2854 C5' DG P 7 2853 2855 2876 C5' DC P 8 2875 2877 2895 C5' DG P 9 2894 2896 2926 C5' DOC P 10 2927 2924 2933 C5' DC T 1 2932 2934 2952 C5' DC T 2 2951 2953 2971 C5' DG T 3 2970 2972 2993 C5' DA T 4 2992 2994 3014 C5' DC T 5 3013 3015 3033 C5' DC T 6 3032 3034 3052 C5' DG T 7 3051 3053 3074 C5' DC T 8 3073 3075 3093 C5' DG T 9 3092 3094 3115 C5' DC T 10 3114 3116 3134 C5' DA T 11 3133 3135 3155 C5' DT T 12 3154 3156 3175 C5' DC T 13 3174 3176 3194 C5' DA T 14 3193 3195 3215 C5' DG T 15 3214 3216 3237 C5' DC T 16 3236 3238 3284 C5' G2C A 338 3285 3282 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2623 P DG D 1 OK OK 2624 2625 2626 2645 P DT D 2 distorted distorted 2631 2646 2647 2648 2665 P DC D 3 distorted distorted 2653 2666 2667 2668 2684 P DG D 4 distorted distorted 2673 2685 2686 2687 2706 P DG D 5 distorted distorted 2692 2707 2708 2709 2748 P DC P 2 distorted distorted 2734 2749 2750 2751 2767 P DT P 3 distorted distorted 2756 2768 2769 2770 2787 P DG P 4 distorted distorted 2775 2788 2789 2790 2809 P DA P 5 distorted distorted 2795 2810 2811 2812 2830 P DT P 6 distorted distorted 2817 2831 2832 2833 2850 P DG P 7 distorted distorted 2838 2851 2852 2853 2872 P DC P 8 distorted distorted 2858 2873 2874 2875 2891 P DG P 9 distorted distorted 2880 2892 2893 2894 2928 P DOC P 10 distorted distorted 2899 2929 2930 2927 2948 P DC T 2 distorted distorted 2937 2949 2950 2951 2967 P DG T 3 distorted distorted 2956 2968 2969 2970 2989 P DA T 4 distorted distorted 2975 2990 2991 2992 3010 P DC T 5 distorted distorted 2997 3011 3012 3013 3029 P DC T 6 distorted distorted 3018 3030 3031 3032 3048 P DG T 7 distorted distorted 3037 3049 3050 3051 3070 P DC T 8 distorted distorted 3056 3071 3072 3073 3089 P DG T 9 distorted distorted 3078 3090 3091 3092 3111 P DC T 10 distorted distorted 3097 3112 3113 3114 3130 P DA T 11 distorted distorted 3119 3131 3132 3133 3151 P DT T 12 distorted distorted 3138 3152 3153 3154 3171 P DC T 13 distorted distorted 3159 3172 3173 3174 3190 P DA T 14 distorted distorted 3179 3191 3192 3193 3211 P DG T 15 distorted distorted 3198 3212 3213 3214 3233 P DC T 16 distorted distorted 3219 3234 3235 3236 ---------------------------------------------------------------------------------