ID code: '4QWB' 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' --------------------------------------------------------------------------------- 2799 C1' DG B 1 beta 2795 2800 2798 2821 C1' DG B 2 beta 2817 2822 2820 2843 C1' DC B 3 beta 2839 2844 2842 2862 C1' DT B 4 beta 2858 2863 2861 2882 C1' DA B 5 beta 2878 2883 2881 2903 C1' DC B 6 beta 2899 2904 2902 2922 C1' DA B 7 beta 2918 2923 2921 2943 C1' DG B 8 beta 2939 2944 2942 2965 C1' DG B 9 beta 2961 2966 2964 2987 C1' DA B 10 beta 2983 2988 2986 3008 C1' DC B 11 beta 3004 3009 3007 3027 C1' DT B 12 beta 3023 3028 3026 3045 C1' DOC B 13 beta 3049 3037 3046 3066 C1' DA C 4 beta 3062 3067 3065 3087 C1' DG C 5 beta 3083 3088 3086 3109 C1' DG C 6 beta 3105 3110 3108 3131 C1' DA C 7 beta 3127 3132 3130 3152 C1' DG C 8 beta 3148 3153 3151 3174 C1' DT C 9 beta 3170 3175 3173 3194 C1' DC C 10 beta 3190 3195 3193 3213 C1' DC C 11 beta 3209 3214 3212 3232 C1' DT C 12 beta 3228 3233 3231 3252 C1' DG C 13 beta 3248 3253 3251 3274 C1' DT C 14 beta 3270 3275 3273 3294 C1' DA C 15 beta 3290 3295 3293 3315 C1' DG C 16 beta 3311 3316 3314 3337 C1' DC C 17 beta 3333 3338 3336 3356 C1' DC C 18 beta 3352 3357 3355 3381 C1' YYY A 401 beta 3377 3382 3380 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2798 C2' DG B 1 2799 2796 2820 C2' DG B 2 2821 2818 2842 C2' DC B 3 2843 2840 2861 C2' DT B 4 2862 2859 2881 C2' DA B 5 2882 2879 2902 C2' DC B 6 2903 2900 2921 C2' DA B 7 2922 2919 2942 C2' DG B 8 2943 2940 2964 C2' DG B 9 2965 2962 2986 C2' DA B 10 2987 2984 3007 C2' DC B 11 3008 3005 3026 C2' DT B 12 3027 3024 3046 C2' DOC B 13 3045 3047 3065 C2' DA C 4 3066 3063 3086 C2' DG C 5 3087 3084 3108 C2' DG C 6 3109 3106 3130 C2' DA C 7 3131 3128 3151 C2' DG C 8 3152 3149 3173 C2' DT C 9 3174 3171 3193 C2' DC C 10 3194 3191 3212 C2' DC C 11 3213 3210 3231 C2' DT C 12 3232 3229 3251 C2' DG C 13 3252 3249 3273 C2' DT C 14 3274 3271 3293 C2' DA C 15 3294 3291 3314 C2' DG C 16 3315 3312 3336 C2' DC C 17 3337 3334 3355 C2' DC C 18 3356 3353 3380 C2' YYY A 401 3381 3378 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2796 C3' DG B 1 OK 2794 2797 2798 2818 C3' DG B 2 OK 2816 2819 2820 2840 C3' DC B 3 OK 2838 2841 2842 2859 C3' DT B 4 OK 2857 2860 2861 2879 C3' DA B 5 OK 2877 2880 2881 2900 C3' DC B 6 OK 2898 2901 2902 2919 C3' DA B 7 OK 2917 2920 2921 2940 C3' DG B 8 OK 2938 2941 2942 2962 C3' DG B 9 OK 2960 2963 2964 2984 C3' DA B 10 OK 2982 2985 2986 3005 C3' DC B 11 OK 3003 3006 3007 3024 C3' DT B 12 OK 3022 3025 3026 3047 C3' DOC B 13 3048 3046 3063 C3' DA C 4 OK 3061 3064 3065 3084 C3' DG C 5 OK 3082 3085 3086 3106 C3' DG C 6 OK 3104 3107 3108 3128 C3' DA C 7 OK 3126 3129 3130 3149 C3' DG C 8 OK 3147 3150 3151 3171 C3' DT C 9 OK 3169 3172 3173 3191 C3' DC C 10 OK 3189 3192 3193 3210 C3' DC C 11 OK 3208 3211 3212 3229 C3' DT C 12 OK 3227 3230 3231 3249 C3' DG C 13 OK 3247 3250 3251 3271 C3' DT C 14 OK 3269 3272 3273 3291 C3' DA C 15 OK 3289 3292 3293 3312 C3' DG C 16 OK 3310 3313 3314 3334 C3' DC C 17 OK 3332 3335 3336 3353 C3' DC C 18 OK 3351 3354 3355 3378 C3' YYY A 401 OK 3376 3379 3380 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2794 C4' DG B 1 OK 2796 2793 2795 2816 C4' DG B 2 OK 2818 2815 2817 2838 C4' DC B 3 OK 2840 2837 2839 2857 C4' DT B 4 OK 2859 2856 2858 2877 C4' DA B 5 OK 2879 2876 2878 2898 C4' DC B 6 OK 2900 2897 2899 2917 C4' DA B 7 OK 2919 2916 2918 2938 C4' DG B 8 OK 2940 2937 2939 2960 C4' DG B 9 OK 2962 2959 2961 2982 C4' DA B 10 OK 2984 2981 2983 3003 C4' DC B 11 OK 3005 3002 3004 3022 C4' DT B 12 OK 3024 3021 3023 3048 C4' DOC B 13 OK 3047 3050 3049 3061 C4' DA C 4 OK 3063 3060 3062 3082 C4' DG C 5 OK 3084 3081 3083 3104 C4' DG C 6 OK 3106 3103 3105 3126 C4' DA C 7 OK 3128 3125 3127 3147 C4' DG C 8 OK 3149 3146 3148 3169 C4' DT C 9 OK 3171 3168 3170 3189 C4' DC C 10 OK 3191 3188 3190 3208 C4' DC C 11 OK 3210 3207 3209 3227 C4' DT C 12 OK 3229 3226 3228 3247 C4' DG C 13 OK 3249 3246 3248 3269 C4' DT C 14 OK 3271 3268 3270 3289 C4' DA C 15 OK 3291 3288 3290 3310 C4' DG C 16 OK 3312 3309 3311 3332 C4' DC C 17 OK 3334 3331 3333 3351 C4' DC C 18 OK 3353 3350 3352 3376 C4' YYY A 401 OK 3378 3375 3377 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2793 C5' DG B 1 2792 2794 2815 C5' DG B 2 2814 2816 2837 C5' DC B 3 2836 2838 2856 C5' DT B 4 2855 2857 2876 C5' DA B 5 2875 2877 2897 C5' DC B 6 2896 2898 2916 C5' DA B 7 2915 2917 2937 C5' DG B 8 2936 2938 2959 C5' DG B 9 2958 2960 2981 C5' DA B 10 2980 2982 3002 C5' DC B 11 3001 3003 3021 C5' DT B 12 3020 3022 3050 C5' DOC B 13 3051 3048 3060 C5' DA C 4 3059 3061 3081 C5' DG C 5 3080 3082 3103 C5' DG C 6 3102 3104 3125 C5' DA C 7 3124 3126 3146 C5' DG C 8 3145 3147 3168 C5' DT C 9 3167 3169 3188 C5' DC C 10 3187 3189 3207 C5' DC C 11 3206 3208 3226 C5' DT C 12 3225 3227 3246 C5' DG C 13 3245 3247 3268 C5' DT C 14 3267 3269 3288 C5' DA C 15 3287 3289 3309 C5' DG C 16 3308 3310 3331 C5' DC C 17 3330 3332 3350 C5' DC C 18 3349 3351 3375 C5' YYY A 401 3374 3376 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2811 P DG B 2 distorted distorted 2797 2812 2813 2814 2833 P DC B 3 distorted distorted 2819 2834 2835 2836 2852 P DT B 4 distorted distorted 2841 2853 2854 2855 2872 P DA B 5 distorted distorted 2860 2873 2874 2875 2893 P DC B 6 distorted distorted 2880 2894 2895 2896 2912 P DA B 7 distorted distorted 2901 2913 2914 2915 2933 P DG B 8 distorted distorted 2920 2934 2935 2936 2955 P DG B 9 distorted distorted 2941 2956 2957 2958 2977 P DA B 10 distorted distorted 2963 2978 2979 2980 2998 P DC B 11 distorted distorted 2985 2999 3000 3001 3017 P DT B 12 distorted distorted 3006 3018 3019 3020 3052 P DOC B 13 distorted distorted 3025 3053 3054 3051 3056 P DA C 4 distorted distorted 3057 3058 3059 3077 P DG C 5 distorted distorted 3064 3078 3079 3080 3099 P DG C 6 distorted distorted 3085 3100 3101 3102 3121 P DA C 7 distorted distorted 3107 3122 3123 3124 3142 P DG C 8 distorted distorted 3129 3143 3144 3145 3164 P DT C 9 distorted distorted 3150 3165 3166 3167 3184 P DC C 10 distorted distorted 3172 3185 3186 3187 3203 P DC C 11 distorted distorted 3192 3204 3205 3206 3222 P DT C 12 distorted distorted 3211 3223 3224 3225 3242 P DG C 13 distorted distorted 3230 3243 3244 3245 3264 P DT C 14 distorted distorted 3250 3265 3266 3267 3284 P DA C 15 distorted distorted 3272 3285 3286 3287 3305 P DG C 16 distorted distorted 3292 3306 3307 3308 3327 P DC C 17 distorted distorted 3313 3328 3329 3330 3346 P DC C 18 distorted distorted 3335 3347 3348 3349 ---------------------------------------------------------------------------------