ID code: '1QP4' 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' --------------------------------------------------------------------------------- 2680 C1' A M 700 beta 2676 2681 2679 2701 C1' C M 701 beta 2697 2702 2700 2720 C1' G M 702 beta 2716 2721 2719 2742 C1' C M 703 beta 2738 2743 2741 2761 C1' A M 704 beta 2757 2762 2760 2782 C1' A M 705 beta 2778 2783 2781 2803 C1' T M 706 beta 2799 2804 2802 2823 C1' C M 707 beta 2819 2824 2822 2842 C1' G M 708 beta 2838 2843 2841 2864 C1' A M 709 beta 2860 2865 2863 2885 C1' T M 710 beta 2881 2886 2884 2905 C1' T M 711 beta 2901 2906 2904 2925 C1' G M 712 beta 2921 2926 2924 2947 C1' C M 713 beta 2943 2948 2946 2966 C1' G M 714 beta 2962 2967 2965 2988 C1' T M 715 beta 2984 2989 2987 3027 C1' A B 700 beta 3023 3028 3026 3048 C1' C B 701 beta 3044 3049 3047 3067 C1' G B 702 beta 3063 3068 3066 3089 C1' C B 703 beta 3085 3090 3088 3108 C1' A B 704 beta 3104 3109 3107 3129 C1' A B 705 beta 3125 3130 3128 3150 C1' T B 706 beta 3146 3151 3149 3170 C1' C B 707 beta 3166 3171 3169 3189 C1' G B 708 beta 3185 3190 3188 3211 C1' A B 709 beta 3207 3212 3210 3232 C1' T B 710 beta 3228 3233 3231 3252 C1' T B 711 beta 3248 3253 3251 3272 C1' G B 712 beta 3268 3273 3271 3294 C1' C B 713 beta 3290 3295 3293 3313 C1' G B 714 beta 3309 3314 3312 3335 C1' T B 715 beta 3331 3336 3334 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2679 C2' A M 700 2680 2677 2700 C2' C M 701 2701 2698 2719 C2' G M 702 2720 2717 2741 C2' C M 703 2742 2739 2760 C2' A M 704 2761 2758 2781 C2' A M 705 2782 2779 2802 C2' T M 706 2803 2800 2822 C2' C M 707 2823 2820 2841 C2' G M 708 2842 2839 2863 C2' A M 709 2864 2861 2884 C2' T M 710 2885 2882 2904 C2' T M 711 2905 2902 2924 C2' G M 712 2925 2922 2946 C2' C M 713 2947 2944 2965 C2' G M 714 2966 2963 2987 C2' T M 715 2988 2985 3026 C2' A B 700 3027 3024 3047 C2' C B 701 3048 3045 3066 C2' G B 702 3067 3064 3088 C2' C B 703 3089 3086 3107 C2' A B 704 3108 3105 3128 C2' A B 705 3129 3126 3149 C2' T B 706 3150 3147 3169 C2' C B 707 3170 3167 3188 C2' G B 708 3189 3186 3210 C2' A B 709 3211 3208 3231 C2' T B 710 3232 3229 3251 C2' T B 711 3252 3249 3271 C2' G B 712 3272 3269 3293 C2' C B 713 3294 3291 3312 C2' G B 714 3313 3310 3334 C2' T B 715 3335 3332 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2677 C3' A M 700 OK 2675 2678 2679 2698 C3' C M 701 OK 2696 2699 2700 2717 C3' G M 702 OK 2715 2718 2719 2739 C3' C M 703 OK 2737 2740 2741 2758 C3' A M 704 OK 2756 2759 2760 2779 C3' A M 705 OK 2777 2780 2781 2800 C3' T M 706 OK 2798 2801 2802 2820 C3' C M 707 OK 2818 2821 2822 2839 C3' G M 708 OK 2837 2840 2841 2861 C3' A M 709 OK 2859 2862 2863 2882 C3' T M 710 OK 2880 2883 2884 2902 C3' T M 711 OK 2900 2903 2904 2922 C3' G M 712 OK 2920 2923 2924 2944 C3' C M 713 OK 2942 2945 2946 2963 C3' G M 714 OK 2961 2964 2965 2985 C3' T M 715 OK 2983 2986 2987 3024 C3' A B 700 OK 3022 3025 3026 3045 C3' C B 701 OK 3043 3046 3047 3064 C3' G B 702 OK 3062 3065 3066 3086 C3' C B 703 OK 3084 3087 3088 3105 C3' A B 704 OK 3103 3106 3107 3126 C3' A B 705 OK 3124 3127 3128 3147 C3' T B 706 OK 3145 3148 3149 3167 C3' C B 707 OK 3165 3168 3169 3186 C3' G B 708 OK 3184 3187 3188 3208 C3' A B 709 OK 3206 3209 3210 3229 C3' T B 710 OK 3227 3230 3231 3249 C3' T B 711 OK 3247 3250 3251 3269 C3' G B 712 OK 3267 3270 3271 3291 C3' C B 713 OK 3289 3292 3293 3310 C3' G B 714 OK 3308 3311 3312 3332 C3' T B 715 OK 3330 3333 3334 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2675 C4' A M 700 OK 2677 2674 2676 2696 C4' C M 701 OK 2698 2695 2697 2715 C4' G M 702 OK 2717 2714 2716 2737 C4' C M 703 OK 2739 2736 2738 2756 C4' A M 704 OK 2758 2755 2757 2777 C4' A M 705 OK 2779 2776 2778 2798 C4' T M 706 OK 2800 2797 2799 2818 C4' C M 707 OK 2820 2817 2819 2837 C4' G M 708 OK 2839 2836 2838 2859 C4' A M 709 OK 2861 2858 2860 2880 C4' T M 710 OK 2882 2879 2881 2900 C4' T M 711 OK 2902 2899 2901 2920 C4' G M 712 OK 2922 2919 2921 2942 C4' C M 713 OK 2944 2941 2943 2961 C4' G M 714 OK 2963 2960 2962 2983 C4' T M 715 OK 2985 2982 2984 3022 C4' A B 700 OK 3024 3021 3023 3043 C4' C B 701 OK 3045 3042 3044 3062 C4' G B 702 OK 3064 3061 3063 3084 C4' C B 703 OK 3086 3083 3085 3103 C4' A B 704 OK 3105 3102 3104 3124 C4' A B 705 OK 3126 3123 3125 3145 C4' T B 706 OK 3147 3144 3146 3165 C4' C B 707 OK 3167 3164 3166 3184 C4' G B 708 OK 3186 3183 3185 3206 C4' A B 709 OK 3208 3205 3207 3227 C4' T B 710 OK 3229 3226 3228 3247 C4' T B 711 OK 3249 3246 3248 3267 C4' G B 712 OK 3269 3266 3268 3289 C4' C B 713 OK 3291 3288 3290 3308 C4' G B 714 OK 3310 3307 3309 3330 C4' T B 715 OK 3332 3329 3331 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2674 C5' A M 700 2673 2675 2695 C5' C M 701 2694 2696 2714 C5' G M 702 2713 2715 2736 C5' C M 703 2735 2737 2755 C5' A M 704 2754 2756 2776 C5' A M 705 2775 2777 2797 C5' T M 706 2796 2798 2817 C5' C M 707 2816 2818 2836 C5' G M 708 2835 2837 2858 C5' A M 709 2857 2859 2879 C5' T M 710 2878 2880 2899 C5' T M 711 2898 2900 2919 C5' G M 712 2918 2920 2941 C5' C M 713 2940 2942 2960 C5' G M 714 2959 2961 2982 C5' T M 715 2981 2983 3021 C5' A B 700 3020 3022 3042 C5' C B 701 3041 3043 3061 C5' G B 702 3060 3062 3083 C5' C B 703 3082 3084 3102 C5' A B 704 3101 3103 3123 C5' A B 705 3122 3124 3144 C5' T B 706 3143 3145 3164 C5' C B 707 3163 3165 3183 C5' G B 708 3182 3184 3205 C5' A B 709 3204 3206 3226 C5' T B 710 3225 3227 3246 C5' T B 711 3245 3247 3266 C5' G B 712 3265 3267 3288 C5' C B 713 3287 3289 3307 C5' G B 714 3306 3308 3329 C5' T B 715 3328 3330 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2691 P C M 701 distorted distorted 2678 2692 2693 2694 2710 P G M 702 distorted distorted 2699 2711 2712 2713 2732 P C M 703 distorted distorted 2718 2733 2734 2735 2751 P A M 704 distorted distorted 2740 2752 2753 2754 2772 P A M 705 distorted distorted 2759 2773 2774 2775 2793 P T M 706 distorted distorted 2780 2794 2795 2796 2813 P C M 707 distorted distorted 2801 2814 2815 2816 2832 P G M 708 distorted distorted 2821 2833 2834 2835 2854 P A M 709 distorted distorted 2840 2855 2856 2857 2875 P T M 710 distorted distorted 2862 2876 2877 2878 2895 P T M 711 distorted distorted 2883 2896 2897 2898 2915 P G M 712 distorted distorted 2903 2916 2917 2918 2937 P C M 713 distorted distorted 2923 2938 2939 2940 2956 P G M 714 distorted distorted 2945 2957 2958 2959 2978 P T M 715 distorted distorted 2964 2979 2980 2981 3038 P C B 701 distorted distorted 3025 3039 3040 3041 3057 P G B 702 distorted distorted 3046 3058 3059 3060 3079 P C B 703 distorted distorted 3065 3080 3081 3082 3098 P A B 704 distorted distorted 3087 3099 3100 3101 3119 P A B 705 distorted distorted 3106 3120 3121 3122 3140 P T B 706 distorted distorted 3127 3141 3142 3143 3160 P C B 707 distorted distorted 3148 3161 3162 3163 3179 P G B 708 distorted distorted 3168 3180 3181 3182 3201 P A B 709 distorted distorted 3187 3202 3203 3204 3222 P T B 710 distorted distorted 3209 3223 3224 3225 3242 P T B 711 distorted distorted 3230 3243 3244 3245 3262 P G B 712 distorted distorted 3250 3263 3264 3265 3284 P C B 713 distorted distorted 3270 3285 3286 3287 3303 P G B 714 distorted distorted 3292 3304 3305 3306 3325 P T B 715 distorted distorted 3311 3326 3327 3328 ---------------------------------------------------------------------------------