ID code: '3GIK' 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' --------------------------------------------------------------------------------- 2749 C1' DG D 1 beta 2745 2750 2748 2771 C1' DT D 2 beta 2767 2772 2770 2791 C1' DT D 3 beta 2787 2792 2790 2811 C1' DG D 4 beta 2807 2812 2810 2833 C1' DG D 5 beta 2829 2834 2832 2855 C1' DA D 6 beta 2851 2856 2854 2876 C1' DT D 7 beta 2872 2877 2875 2896 C1' DG D 8 beta 2892 2897 2895 2918 C1' DG D 9 beta 2914 2919 2917 2940 C1' DT D 10 beta 2936 2941 2939 2960 C1' DA D 11 beta 2956 2961 2959 2981 C1' DG D 12 beta 2977 2982 2980 3001 C1' DOC D 13 beta 3005 2993 3002 3019 C1' DC E 901 beta 3015 3020 3018 3038 C1' DT E 902 beta 3034 3039 3037 3058 C1' DA E 903 beta 3054 3059 3057 3079 C1' DA E 904 beta 3075 3080 3078 3100 C1' DC E 905 beta 3096 3101 3099 3119 C1' 8OG E 906 beta 3115 3120 3118 3142 C1' DC E 907 beta 3138 3143 3141 3161 C1' DT E 908 beta 3157 3162 3160 3181 C1' DA E 909 beta 3177 3182 3180 3202 C1' DC E 910 beta 3198 3203 3201 3221 C1' DC E 911 beta 3217 3222 3220 3240 C1' DA E 912 beta 3236 3241 3239 3261 C1' DT E 913 beta 3257 3262 3260 3281 C1' DC E 914 beta 3277 3282 3280 3300 C1' DC E 915 beta 3296 3301 3299 3319 C1' DA E 916 beta 3315 3320 3318 3340 C1' DA E 917 beta 3336 3341 3339 3361 C1' DC E 918 beta 3357 3362 3360 3390 C1' DGT A 414 beta 3386 3391 3389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2748 C2' DG D 1 2749 2746 2770 C2' DT D 2 2771 2768 2790 C2' DT D 3 2791 2788 2810 C2' DG D 4 2811 2808 2832 C2' DG D 5 2833 2830 2854 C2' DA D 6 2855 2852 2875 C2' DT D 7 2876 2873 2895 C2' DG D 8 2896 2893 2917 C2' DG D 9 2918 2915 2939 C2' DT D 10 2940 2937 2959 C2' DA D 11 2960 2957 2980 C2' DG D 12 2981 2978 3002 C2' DOC D 13 3001 3003 3018 C2' DC E 901 3019 3016 3037 C2' DT E 902 3038 3035 3057 C2' DA E 903 3058 3055 3078 C2' DA E 904 3079 3076 3099 C2' DC E 905 3100 3097 3118 C2' 8OG E 906 3119 3116 3141 C2' DC E 907 3142 3139 3160 C2' DT E 908 3161 3158 3180 C2' DA E 909 3181 3178 3201 C2' DC E 910 3202 3199 3220 C2' DC E 911 3221 3218 3239 C2' DA E 912 3240 3237 3260 C2' DT E 913 3261 3258 3280 C2' DC E 914 3281 3278 3299 C2' DC E 915 3300 3297 3318 C2' DA E 916 3319 3316 3339 C2' DA E 917 3340 3337 3360 C2' DC E 918 3361 3358 3389 C2' DGT A 414 3390 3387 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2746 C3' DG D 1 OK 2744 2747 2748 2768 C3' DT D 2 OK 2766 2769 2770 2788 C3' DT D 3 OK 2786 2789 2790 2808 C3' DG D 4 OK 2806 2809 2810 2830 C3' DG D 5 OK 2828 2831 2832 2852 C3' DA D 6 OK 2850 2853 2854 2873 C3' DT D 7 OK 2871 2874 2875 2893 C3' DG D 8 OK 2891 2894 2895 2915 C3' DG D 9 OK 2913 2916 2917 2937 C3' DT D 10 OK 2935 2938 2939 2957 C3' DA D 11 OK 2955 2958 2959 2978 C3' DG D 12 OK 2976 2979 2980 3003 C3' DOC D 13 3004 3002 3016 C3' DC E 901 OK 3014 3017 3018 3035 C3' DT E 902 OK 3033 3036 3037 3055 C3' DA E 903 OK 3053 3056 3057 3076 C3' DA E 904 OK 3074 3077 3078 3097 C3' DC E 905 OK 3095 3098 3099 3116 C3' 8OG E 906 OK 3114 3117 3118 3139 C3' DC E 907 OK 3137 3140 3141 3158 C3' DT E 908 OK 3156 3159 3160 3178 C3' DA E 909 OK 3176 3179 3180 3199 C3' DC E 910 OK 3197 3200 3201 3218 C3' DC E 911 OK 3216 3219 3220 3237 C3' DA E 912 OK 3235 3238 3239 3258 C3' DT E 913 OK 3256 3259 3260 3278 C3' DC E 914 OK 3276 3279 3280 3297 C3' DC E 915 OK 3295 3298 3299 3316 C3' DA E 916 OK 3314 3317 3318 3337 C3' DA E 917 OK 3335 3338 3339 3358 C3' DC E 918 OK 3356 3359 3360 3387 C3' DGT A 414 OK 3385 3388 3389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2744 C4' DG D 1 OK 2746 2743 2745 2766 C4' DT D 2 OK 2768 2765 2767 2786 C4' DT D 3 OK 2788 2785 2787 2806 C4' DG D 4 OK 2808 2805 2807 2828 C4' DG D 5 OK 2830 2827 2829 2850 C4' DA D 6 OK 2852 2849 2851 2871 C4' DT D 7 OK 2873 2870 2872 2891 C4' DG D 8 OK 2893 2890 2892 2913 C4' DG D 9 OK 2915 2912 2914 2935 C4' DT D 10 OK 2937 2934 2936 2955 C4' DA D 11 OK 2957 2954 2956 2976 C4' DG D 12 OK 2978 2975 2977 3004 C4' DOC D 13 OK 3003 3006 3005 3014 C4' DC E 901 OK 3016 3013 3015 3033 C4' DT E 902 OK 3035 3032 3034 3053 C4' DA E 903 OK 3055 3052 3054 3074 C4' DA E 904 OK 3076 3073 3075 3095 C4' DC E 905 OK 3097 3094 3096 3114 C4' 8OG E 906 OK 3116 3113 3115 3137 C4' DC E 907 OK 3139 3136 3138 3156 C4' DT E 908 OK 3158 3155 3157 3176 C4' DA E 909 OK 3178 3175 3177 3197 C4' DC E 910 OK 3199 3196 3198 3216 C4' DC E 911 OK 3218 3215 3217 3235 C4' DA E 912 OK 3237 3234 3236 3256 C4' DT E 913 OK 3258 3255 3257 3276 C4' DC E 914 OK 3278 3275 3277 3295 C4' DC E 915 OK 3297 3294 3296 3314 C4' DA E 916 OK 3316 3313 3315 3335 C4' DA E 917 OK 3337 3334 3336 3356 C4' DC E 918 OK 3358 3355 3357 3385 C4' DGT A 414 OK 3387 3384 3386 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2743 C5' DG D 1 2742 2744 2765 C5' DT D 2 2764 2766 2785 C5' DT D 3 2784 2786 2805 C5' DG D 4 2804 2806 2827 C5' DG D 5 2826 2828 2849 C5' DA D 6 2848 2850 2870 C5' DT D 7 2869 2871 2890 C5' DG D 8 2889 2891 2912 C5' DG D 9 2911 2913 2934 C5' DT D 10 2933 2935 2954 C5' DA D 11 2953 2955 2975 C5' DG D 12 2974 2976 3006 C5' DOC D 13 3007 3004 3013 C5' DC E 901 3012 3014 3032 C5' DT E 902 3031 3033 3052 C5' DA E 903 3051 3053 3073 C5' DA E 904 3072 3074 3094 C5' DC E 905 3093 3095 3113 C5' 8OG E 906 3112 3114 3136 C5' DC E 907 3135 3137 3155 C5' DT E 908 3154 3156 3175 C5' DA E 909 3174 3176 3196 C5' DC E 910 3195 3197 3215 C5' DC E 911 3214 3216 3234 C5' DA E 912 3233 3235 3255 C5' DT E 913 3254 3256 3275 C5' DC E 914 3274 3276 3294 C5' DC E 915 3293 3295 3313 C5' DA E 916 3312 3314 3334 C5' DA E 917 3333 3335 3355 C5' DC E 918 3354 3356 3384 C5' DGT A 414 3383 3385 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2761 P DT D 2 distorted distorted 2747 2762 2763 2764 2781 P DT D 3 distorted distorted 2769 2782 2783 2784 2801 P DG D 4 distorted distorted 2789 2802 2803 2804 2823 P DG D 5 distorted distorted 2809 2824 2825 2826 2845 P DA D 6 distorted distorted 2831 2846 2847 2848 2866 P DT D 7 distorted distorted 2853 2867 2868 2869 2886 P DG D 8 distorted distorted 2874 2887 2888 2889 2908 P DG D 9 distorted distorted 2894 2909 2910 2911 2930 P DT D 10 distorted distorted 2916 2931 2932 2933 2950 P DA D 11 distorted distorted 2938 2951 2952 2953 2971 P DG D 12 distorted distorted 2958 2972 2973 2974 3008 P DOC D 13 distorted distorted 2979 3009 3010 3007 3028 P DT E 902 distorted distorted 3017 3029 3030 3031 3048 P DA E 903 distorted distorted 3036 3049 3050 3051 3069 P DA E 904 distorted distorted 3056 3070 3071 3072 3090 P DC E 905 distorted distorted 3077 3091 3092 3093 3109 P 8OG E 906 distorted distorted 3098 3110 3111 3112 3132 P DC E 907 distorted distorted 3117 3133 3134 3135 3151 P DT E 908 distorted distorted 3140 3152 3153 3154 3171 P DA E 909 distorted distorted 3159 3172 3173 3174 3192 P DC E 910 distorted distorted 3179 3193 3194 3195 3211 P DC E 911 distorted distorted 3200 3212 3213 3214 3230 P DA E 912 distorted distorted 3219 3231 3232 3233 3251 P DT E 913 distorted distorted 3238 3252 3253 3254 3271 P DC E 914 distorted distorted 3259 3272 3273 3274 3290 P DC E 915 distorted distorted 3279 3291 3292 3293 3309 P DA E 916 distorted distorted 3298 3310 3311 3312 3330 P DA E 917 distorted distorted 3317 3331 3332 3333 3351 P DC E 918 distorted distorted 3338 3352 3353 3354 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