ID code: '3JPR' 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' --------------------------------------------------------------------------------- 2621 C1' DG D 1 beta 2617 2622 2620 2643 C1' DT D 2 beta 2639 2644 2642 2663 C1' DC D 3 beta 2659 2664 2662 2682 C1' DG D 4 beta 2678 2683 2681 2704 C1' DG D 5 beta 2700 2705 2703 2724 C1' DG P 1 beta 2720 2725 2723 2746 C1' DC P 2 beta 2742 2747 2745 2765 C1' DT P 3 beta 2761 2766 2764 2785 C1' DG P 4 beta 2781 2786 2784 2807 C1' DA P 5 beta 2803 2808 2806 2828 C1' DT P 6 beta 2824 2829 2827 2848 C1' DG P 7 beta 2844 2849 2847 2870 C1' DC P 8 beta 2866 2871 2869 2889 C1' DG P 9 beta 2885 2890 2888 2909 C1' DOC P 10 beta 2913 2901 2910 2927 C1' DC T 1 beta 2923 2928 2926 2946 C1' DC T 2 beta 2942 2947 2945 2965 C1' DG T 3 beta 2961 2966 2964 2987 C1' DA T 4 beta 2983 2988 2986 3008 C1' DC T 5 beta 3004 3009 3007 3027 C1' DC T 6 beta 3023 3028 3026 3046 C1' DG T 7 beta 3042 3047 3045 3068 C1' DC T 8 beta 3064 3069 3067 3087 C1' DG T 9 beta 3083 3088 3086 3109 C1' DC T 10 beta 3105 3110 3108 3128 C1' DA T 11 beta 3124 3129 3127 3149 C1' DT T 12 beta 3145 3150 3148 3169 C1' DC T 13 beta 3165 3170 3168 3188 C1' DA T 14 beta 3184 3189 3187 3209 C1' DG T 15 beta 3205 3210 3208 3231 C1' DC T 16 beta 3227 3232 3230 3255 C1' G2M A 338 beta 3271 3251 3259 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2620 C2' DG D 1 2621 2618 2642 C2' DT D 2 2643 2640 2662 C2' DC D 3 2663 2660 2681 C2' DG D 4 2682 2679 2703 C2' DG D 5 2704 2701 2723 C2' DG P 1 2724 2721 2745 C2' DC P 2 2746 2743 2764 C2' DT P 3 2765 2762 2784 C2' DG P 4 2785 2782 2806 C2' DA P 5 2807 2804 2827 C2' DT P 6 2828 2825 2847 C2' DG P 7 2848 2845 2869 C2' DC P 8 2870 2867 2888 C2' DG P 9 2889 2886 2910 C2' DOC P 10 2909 2911 2926 C2' DC T 1 2927 2924 2945 C2' DC T 2 2946 2943 2964 C2' DG T 3 2965 2962 2986 C2' DA T 4 2987 2984 3007 C2' DC T 5 3008 3005 3026 C2' DC T 6 3027 3024 3045 C2' DG T 7 3046 3043 3067 C2' DC T 8 3068 3065 3086 C2' DG T 9 3087 3084 3108 C2' DC T 10 3109 3106 3127 C2' DA T 11 3128 3125 3148 C2' DT T 12 3149 3146 3168 C2' DC T 13 3169 3166 3187 C2' DA T 14 3188 3185 3208 C2' DG T 15 3209 3206 3230 C2' DC T 16 3231 3228 3259 C2' G2M A 338 3255 3263 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2618 C3' DG D 1 OK 2616 2619 2620 2640 C3' DT D 2 OK 2638 2641 2642 2660 C3' DC D 3 OK 2658 2661 2662 2679 C3' DG D 4 OK 2677 2680 2681 2701 C3' DG D 5 OK 2699 2702 2703 2721 C3' DG P 1 OK 2719 2722 2723 2743 C3' DC P 2 OK 2741 2744 2745 2762 C3' DT P 3 OK 2760 2763 2764 2782 C3' DG P 4 OK 2780 2783 2784 2804 C3' DA P 5 OK 2802 2805 2806 2825 C3' DT P 6 OK 2823 2826 2827 2845 C3' DG P 7 OK 2843 2846 2847 2867 C3' DC P 8 OK 2865 2868 2869 2886 C3' DG P 9 OK 2884 2887 2888 2911 C3' DOC P 10 2912 2910 2924 C3' DC T 1 OK 2922 2925 2926 2943 C3' DC T 2 OK 2941 2944 2945 2962 C3' DG T 3 OK 2960 2963 2964 2984 C3' DA T 4 OK 2982 2985 2986 3005 C3' DC T 5 OK 3003 3006 3007 3024 C3' DC T 6 OK 3022 3025 3026 3043 C3' DG T 7 OK 3041 3044 3045 3065 C3' DC T 8 OK 3063 3066 3067 3084 C3' DG T 9 OK 3082 3085 3086 3106 C3' DC T 10 OK 3104 3107 3108 3125 C3' DA T 11 OK 3123 3126 3127 3146 C3' DT T 12 OK 3144 3147 3148 3166 C3' DC T 13 OK 3164 3167 3168 3185 C3' DA T 14 OK 3183 3186 3187 3206 C3' DG T 15 OK 3204 3207 3208 3228 C3' DC T 16 OK 3226 3229 3230 3263 C3' G2M A 338 OK 3270 3264 3259 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2616 C4' DG D 1 OK 2618 2615 2617 2638 C4' DT D 2 OK 2640 2637 2639 2658 C4' DC D 3 OK 2660 2657 2659 2677 C4' DG D 4 OK 2679 2676 2678 2699 C4' DG D 5 OK 2701 2698 2700 2719 C4' DG P 1 OK 2721 2718 2720 2741 C4' DC P 2 OK 2743 2740 2742 2760 C4' DT P 3 OK 2762 2759 2761 2780 C4' DG P 4 OK 2782 2779 2781 2802 C4' DA P 5 OK 2804 2801 2803 2823 C4' DT P 6 OK 2825 2822 2824 2843 C4' DG P 7 OK 2845 2842 2844 2865 C4' DC P 8 OK 2867 2864 2866 2884 C4' DG P 9 OK 2886 2883 2885 2912 C4' DOC P 10 OK 2911 2914 2913 2922 C4' DC T 1 OK 2924 2921 2923 2941 C4' DC T 2 OK 2943 2940 2942 2960 C4' DG T 3 OK 2962 2959 2961 2982 C4' DA T 4 OK 2984 2981 2983 3003 C4' DC T 5 OK 3005 3002 3004 3022 C4' DC T 6 OK 3024 3021 3023 3041 C4' DG T 7 OK 3043 3040 3042 3063 C4' DC T 8 OK 3065 3062 3064 3082 C4' DG T 9 OK 3084 3081 3083 3104 C4' DC T 10 OK 3106 3103 3105 3123 C4' DA T 11 OK 3125 3122 3124 3144 C4' DT T 12 OK 3146 3143 3145 3164 C4' DC T 13 OK 3166 3163 3165 3183 C4' DA T 14 OK 3185 3182 3184 3204 C4' DG T 15 OK 3206 3203 3205 3226 C4' DC T 16 OK 3228 3225 3227 3270 C4' G2M A 338 OK 3263 3272 3271 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2615 C5' DG D 1 2614 2616 2637 C5' DT D 2 2636 2638 2657 C5' DC D 3 2656 2658 2676 C5' DG D 4 2675 2677 2698 C5' DG D 5 2697 2699 2718 C5' DG P 1 2717 2719 2740 C5' DC P 2 2739 2741 2759 C5' DT P 3 2758 2760 2779 C5' DG P 4 2778 2780 2801 C5' DA P 5 2800 2802 2822 C5' DT P 6 2821 2823 2842 C5' DG P 7 2841 2843 2864 C5' DC P 8 2863 2865 2883 C5' DG P 9 2882 2884 2914 C5' DOC P 10 2915 2912 2921 C5' DC T 1 2920 2922 2940 C5' DC T 2 2939 2941 2959 C5' DG T 3 2958 2960 2981 C5' DA T 4 2980 2982 3002 C5' DC T 5 3001 3003 3021 C5' DC T 6 3020 3022 3040 C5' DG T 7 3039 3041 3062 C5' DC T 8 3061 3063 3081 C5' DG T 9 3080 3082 3103 C5' DC T 10 3102 3104 3122 C5' DA T 11 3121 3123 3143 C5' DT T 12 3142 3144 3163 C5' DC T 13 3162 3164 3182 C5' DA T 14 3181 3183 3203 C5' DG T 15 3202 3204 3225 C5' DC T 16 3224 3226 3272 C5' G2M A 338 3273 3270 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2611 P DG D 1 OK OK 2612 2613 2614 2633 P DT D 2 distorted distorted 2619 2634 2635 2636 2653 P DC D 3 distorted distorted 2641 2654 2655 2656 2672 P DG D 4 distorted distorted 2661 2673 2674 2675 2694 P DG D 5 distorted distorted 2680 2695 2696 2697 2736 P DC P 2 distorted distorted 2722 2737 2738 2739 2755 P DT P 3 distorted distorted 2744 2756 2757 2758 2775 P DG P 4 distorted distorted 2763 2776 2777 2778 2797 P DA P 5 distorted distorted 2783 2798 2799 2800 2818 P DT P 6 distorted distorted 2805 2819 2820 2821 2838 P DG P 7 distorted distorted 2826 2839 2840 2841 2860 P DC P 8 distorted distorted 2846 2861 2862 2863 2879 P DG P 9 distorted distorted 2868 2880 2881 2882 2916 P DOC P 10 distorted distorted 2887 2917 2918 2915 2936 P DC T 2 distorted distorted 2925 2937 2938 2939 2955 P DG T 3 distorted distorted 2944 2956 2957 2958 2977 P DA T 4 distorted distorted 2963 2978 2979 2980 2998 P DC T 5 distorted distorted 2985 2999 3000 3001 3017 P DC T 6 distorted distorted 3006 3018 3019 3020 3036 P DG T 7 distorted distorted 3025 3037 3038 3039 3058 P DC T 8 distorted distorted 3044 3059 3060 3061 3077 P DG T 9 distorted distorted 3066 3078 3079 3080 3099 P DC T 10 distorted distorted 3085 3100 3101 3102 3118 P DA T 11 distorted distorted 3107 3119 3120 3121 3139 P DT T 12 distorted distorted 3126 3140 3141 3142 3159 P DC T 13 distorted distorted 3147 3160 3161 3162 3178 P DA T 14 distorted distorted 3167 3179 3180 3181 3199 P DG T 15 distorted distorted 3186 3200 3201 3202 3221 P DC T 16 distorted distorted 3207 3222 3223 3224 ---------------------------------------------------------------------------------