ID code: '2PXI' 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' --------------------------------------------------------------------------------- 2643 C1' DC T 1 beta 2639 2644 2642 2662 C1' DC T 2 beta 2658 2663 2661 2681 C1' DG T 3 beta 2677 2682 2680 2703 C1' DA T 4 beta 2699 2704 2702 2724 C1' DC T 5 beta 2720 2725 2723 2743 C1' DC T 6 beta 2739 2744 2742 2762 C1' DG T 7 beta 2758 2763 2761 2784 C1' DC T 8 beta 2780 2785 2783 2803 C1' DG T 9 beta 2799 2804 2802 2825 C1' DC T 10 beta 2821 2826 2824 2844 C1' DA T 11 beta 2840 2845 2843 2865 C1' DT T 12 beta 2861 2866 2864 2885 C1' DC T 13 beta 2881 2886 2884 2904 C1' DA T 14 beta 2900 2905 2903 2925 C1' DG T 15 beta 2921 2926 2924 2947 C1' DC T 16 beta 2943 2948 2946 2964 C1' DG P 1 beta 2960 2965 2963 2986 C1' DC P 2 beta 2982 2987 2985 3005 C1' DT P 3 beta 3001 3006 3004 3025 C1' DG P 4 beta 3021 3026 3024 3047 C1' DA P 5 beta 3043 3048 3046 3068 C1' DT P 6 beta 3064 3069 3067 3088 C1' DG P 7 beta 3084 3089 3087 3110 C1' DC P 8 beta 3106 3111 3109 3129 C1' DG P 9 beta 3125 3130 3128 3149 C1' DOC P 10 beta 3153 3141 3150 3171 C1' DG D 1 beta 3167 3172 3170 3193 C1' DT D 2 beta 3189 3194 3192 3213 C1' DC D 3 beta 3209 3214 3212 3232 C1' DG D 4 beta 3228 3233 3231 3254 C1' DG D 5 beta 3250 3255 3253 3293 C1' GFH A 338 beta 3292 3294 3305 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2642 C2' DC T 1 2643 2640 2661 C2' DC T 2 2662 2659 2680 C2' DG T 3 2681 2678 2702 C2' DA T 4 2703 2700 2723 C2' DC T 5 2724 2721 2742 C2' DC T 6 2743 2740 2761 C2' DG T 7 2762 2759 2783 C2' DC T 8 2784 2781 2802 C2' DG T 9 2803 2800 2824 C2' DC T 10 2825 2822 2843 C2' DA T 11 2844 2841 2864 C2' DT T 12 2865 2862 2884 C2' DC T 13 2885 2882 2903 C2' DA T 14 2904 2901 2924 C2' DG T 15 2925 2922 2946 C2' DC T 16 2947 2944 2963 C2' DG P 1 2964 2961 2985 C2' DC P 2 2986 2983 3004 C2' DT P 3 3005 3002 3024 C2' DG P 4 3025 3022 3046 C2' DA P 5 3047 3044 3067 C2' DT P 6 3068 3065 3087 C2' DG P 7 3088 3085 3109 C2' DC P 8 3110 3107 3128 C2' DG P 9 3129 3126 3150 C2' DOC P 10 3149 3151 3170 C2' DG D 1 3171 3168 3192 C2' DT D 2 3193 3190 3212 C2' DC D 3 3213 3210 3231 C2' DG D 4 3232 3229 3253 C2' DG D 5 3254 3251 3305 C2' GFH A 338 3293 3306 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2640 C3' DC T 1 OK 2638 2641 2642 2659 C3' DC T 2 OK 2657 2660 2661 2678 C3' DG T 3 OK 2676 2679 2680 2700 C3' DA T 4 OK 2698 2701 2702 2721 C3' DC T 5 OK 2719 2722 2723 2740 C3' DC T 6 OK 2738 2741 2742 2759 C3' DG T 7 OK 2757 2760 2761 2781 C3' DC T 8 OK 2779 2782 2783 2800 C3' DG T 9 OK 2798 2801 2802 2822 C3' DC T 10 OK 2820 2823 2824 2841 C3' DA T 11 OK 2839 2842 2843 2862 C3' DT T 12 OK 2860 2863 2864 2882 C3' DC T 13 OK 2880 2883 2884 2901 C3' DA T 14 OK 2899 2902 2903 2922 C3' DG T 15 OK 2920 2923 2924 2944 C3' DC T 16 OK 2942 2945 2946 2961 C3' DG P 1 OK 2959 2962 2963 2983 C3' DC P 2 OK 2981 2984 2985 3002 C3' DT P 3 OK 3000 3003 3004 3022 C3' DG P 4 OK 3020 3023 3024 3044 C3' DA P 5 OK 3042 3045 3046 3065 C3' DT P 6 OK 3063 3066 3067 3085 C3' DG P 7 OK 3083 3086 3087 3107 C3' DC P 8 OK 3105 3108 3109 3126 C3' DG P 9 OK 3124 3127 3128 3151 C3' DOC P 10 3152 3150 3168 C3' DG D 1 OK 3166 3169 3170 3190 C3' DT D 2 OK 3188 3191 3192 3210 C3' DC D 3 OK 3208 3211 3212 3229 C3' DG D 4 OK 3227 3230 3231 3251 C3' DG D 5 OK 3249 3252 3253 3306 C3' GFH A 338 OK 3291 3307 3305 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2638 C4' DC T 1 OK 2640 2637 2639 2657 C4' DC T 2 OK 2659 2656 2658 2676 C4' DG T 3 OK 2678 2675 2677 2698 C4' DA T 4 OK 2700 2697 2699 2719 C4' DC T 5 OK 2721 2718 2720 2738 C4' DC T 6 OK 2740 2737 2739 2757 C4' DG T 7 OK 2759 2756 2758 2779 C4' DC T 8 OK 2781 2778 2780 2798 C4' DG T 9 OK 2800 2797 2799 2820 C4' DC T 10 OK 2822 2819 2821 2839 C4' DA T 11 OK 2841 2838 2840 2860 C4' DT T 12 OK 2862 2859 2861 2880 C4' DC T 13 OK 2882 2879 2881 2899 C4' DA T 14 OK 2901 2898 2900 2920 C4' DG T 15 OK 2922 2919 2921 2942 C4' DC T 16 OK 2944 2941 2943 2959 C4' DG P 1 OK 2961 2958 2960 2981 C4' DC P 2 OK 2983 2980 2982 3000 C4' DT P 3 OK 3002 2999 3001 3020 C4' DG P 4 OK 3022 3019 3021 3042 C4' DA P 5 OK 3044 3041 3043 3063 C4' DT P 6 OK 3065 3062 3064 3083 C4' DG P 7 OK 3085 3082 3084 3105 C4' DC P 8 OK 3107 3104 3106 3124 C4' DG P 9 OK 3126 3123 3125 3152 C4' DOC P 10 OK 3151 3154 3153 3166 C4' DG D 1 OK 3168 3165 3167 3188 C4' DT D 2 OK 3190 3187 3189 3208 C4' DC D 3 OK 3210 3207 3209 3227 C4' DG D 4 OK 3229 3226 3228 3249 C4' DG D 5 OK 3251 3248 3250 3291 C4' GFH A 338 OK 3306 3290 3292 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2637 C5' DC T 1 2636 2638 2656 C5' DC T 2 2655 2657 2675 C5' DG T 3 2674 2676 2697 C5' DA T 4 2696 2698 2718 C5' DC T 5 2717 2719 2737 C5' DC T 6 2736 2738 2756 C5' DG T 7 2755 2757 2778 C5' DC T 8 2777 2779 2797 C5' DG T 9 2796 2798 2819 C5' DC T 10 2818 2820 2838 C5' DA T 11 2837 2839 2859 C5' DT T 12 2858 2860 2879 C5' DC T 13 2878 2880 2898 C5' DA T 14 2897 2899 2919 C5' DG T 15 2918 2920 2941 C5' DC T 16 2940 2942 2958 C5' DG P 1 2957 2959 2980 C5' DC P 2 2979 2981 2999 C5' DT P 3 2998 3000 3019 C5' DG P 4 3018 3020 3041 C5' DA P 5 3040 3042 3062 C5' DT P 6 3061 3063 3082 C5' DG P 7 3081 3083 3104 C5' DC P 8 3103 3105 3123 C5' DG P 9 3122 3124 3154 C5' DOC P 10 3155 3152 3165 C5' DG D 1 3164 3166 3187 C5' DT D 2 3186 3188 3207 C5' DC D 3 3206 3208 3226 C5' DG D 4 3225 3227 3248 C5' DG D 5 3247 3249 3290 C5' GFH A 338 3280 3291 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2652 P DC T 2 distorted distorted 2641 2653 2654 2655 2671 P DG T 3 distorted distorted 2660 2672 2673 2674 2693 P DA T 4 distorted distorted 2679 2694 2695 2696 2714 P DC T 5 distorted distorted 2701 2715 2716 2717 2733 P DC T 6 distorted distorted 2722 2734 2735 2736 2752 P DG T 7 distorted distorted 2741 2753 2754 2755 2774 P DC T 8 distorted distorted 2760 2775 2776 2777 2793 P DG T 9 distorted distorted 2782 2794 2795 2796 2815 P DC T 10 distorted distorted 2801 2816 2817 2818 2834 P DA T 11 distorted distorted 2823 2835 2836 2837 2855 P DT T 12 distorted distorted 2842 2856 2857 2858 2875 P DC T 13 distorted distorted 2863 2876 2877 2878 2894 P DA T 14 distorted distorted 2883 2895 2896 2897 2915 P DG T 15 distorted distorted 2902 2916 2917 2918 2937 P DC T 16 distorted distorted 2923 2938 2939 2940 2976 P DC P 2 distorted distorted 2962 2977 2978 2979 2995 P DT P 3 distorted distorted 2984 2996 2997 2998 3015 P DG P 4 distorted distorted 3003 3016 3017 3018 3037 P DA P 5 distorted distorted 3023 3038 3039 3040 3058 P DT P 6 distorted distorted 3045 3059 3060 3061 3078 P DG P 7 distorted distorted 3066 3079 3080 3081 3100 P DC P 8 distorted distorted 3086 3101 3102 3103 3119 P DG P 9 distorted distorted 3108 3120 3121 3122 3156 P DOC P 10 distorted distorted 3127 3157 3158 3155 3161 P DG D 1 OK OK 3162 3163 3164 3183 P DT D 2 distorted distorted 3169 3184 3185 3186 3203 P DC D 3 distorted distorted 3191 3204 3205 3206 3222 P DG D 4 distorted distorted 3211 3223 3224 3225 3244 P DG D 5 distorted distorted 3230 3245 3246 3247 ---------------------------------------------------------------------------------