ID code: '2W9A' 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' --------------------------------------------------------------------------------- 2774 C1' DG P 1 beta 2770 2775 2773 2796 C1' DG P 2 beta 2792 2797 2795 2818 C1' DG P 3 beta 2814 2819 2817 2840 C1' DG P 4 beta 2836 2841 2839 2862 C1' DG P 5 beta 2858 2863 2861 2884 C1' DA P 6 beta 2880 2885 2883 2905 C1' DA P 7 beta 2901 2906 2904 2926 C1' DG P 8 beta 2922 2927 2925 2948 C1' DG P 9 beta 2944 2949 2947 2970 C1' DA P 10 beta 2966 2971 2969 2991 C1' DT P 11 beta 2987 2992 2990 3011 C1' DT P 12 beta 3007 3012 3010 3031 C1' DC P 13 beta 3027 3032 3030 3048 C1' DOC P 14 beta 3052 3040 3049 3066 C1' DA T 3 beta 3062 3067 3065 3087 C1' DC T 4 beta 3083 3088 3086 3106 C1' O2G T 5 beta 3102 3107 3105 3130 C1' DG T 6 beta 3126 3131 3129 3152 C1' DA T 7 beta 3148 3153 3151 3173 C1' DA T 8 beta 3169 3174 3172 3194 C1' DT T 9 beta 3190 3195 3193 3214 C1' DC T 10 beta 3210 3215 3213 3233 C1' DC T 11 beta 3229 3234 3232 3252 C1' DT T 12 beta 3248 3253 3251 3272 C1' DT T 13 beta 3268 3273 3271 3292 C1' DC T 14 beta 3288 3293 3291 3311 C1' DC T 15 beta 3307 3312 3310 3330 C1' DC T 16 beta 3326 3331 3329 3349 C1' DC T 17 beta 3345 3350 3348 3368 C1' DC T 18 beta 3364 3369 3367 3397 C1' DGT A 594 beta 3393 3398 3396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2773 C2' DG P 1 2774 2771 2795 C2' DG P 2 2796 2793 2817 C2' DG P 3 2818 2815 2839 C2' DG P 4 2840 2837 2861 C2' DG P 5 2862 2859 2883 C2' DA P 6 2884 2881 2904 C2' DA P 7 2905 2902 2925 C2' DG P 8 2926 2923 2947 C2' DG P 9 2948 2945 2969 C2' DA P 10 2970 2967 2990 C2' DT P 11 2991 2988 3010 C2' DT P 12 3011 3008 3030 C2' DC P 13 3031 3028 3049 C2' DOC P 14 3048 3050 3065 C2' DA T 3 3066 3063 3086 C2' DC T 4 3087 3084 3105 C2' O2G T 5 3106 3103 3129 C2' DG T 6 3130 3127 3151 C2' DA T 7 3152 3149 3172 C2' DA T 8 3173 3170 3193 C2' DT T 9 3194 3191 3213 C2' DC T 10 3214 3211 3232 C2' DC T 11 3233 3230 3251 C2' DT T 12 3252 3249 3271 C2' DT T 13 3272 3269 3291 C2' DC T 14 3292 3289 3310 C2' DC T 15 3311 3308 3329 C2' DC T 16 3330 3327 3348 C2' DC T 17 3349 3346 3367 C2' DC T 18 3368 3365 3396 C2' DGT A 594 3397 3394 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2771 C3' DG P 1 OK 2769 2772 2773 2793 C3' DG P 2 OK 2791 2794 2795 2815 C3' DG P 3 OK 2813 2816 2817 2837 C3' DG P 4 OK 2835 2838 2839 2859 C3' DG P 5 OK 2857 2860 2861 2881 C3' DA P 6 OK 2879 2882 2883 2902 C3' DA P 7 OK 2900 2903 2904 2923 C3' DG P 8 OK 2921 2924 2925 2945 C3' DG P 9 OK 2943 2946 2947 2967 C3' DA P 10 OK 2965 2968 2969 2988 C3' DT P 11 OK 2986 2989 2990 3008 C3' DT P 12 OK 3006 3009 3010 3028 C3' DC P 13 OK 3026 3029 3030 3050 C3' DOC P 14 3051 3049 3063 C3' DA T 3 OK 3061 3064 3065 3084 C3' DC T 4 OK 3082 3085 3086 3103 C3' O2G T 5 OK 3101 3104 3105 3127 C3' DG T 6 OK 3125 3128 3129 3149 C3' DA T 7 OK 3147 3150 3151 3170 C3' DA T 8 OK 3168 3171 3172 3191 C3' DT T 9 OK 3189 3192 3193 3211 C3' DC T 10 OK 3209 3212 3213 3230 C3' DC T 11 OK 3228 3231 3232 3249 C3' DT T 12 OK 3247 3250 3251 3269 C3' DT T 13 OK 3267 3270 3271 3289 C3' DC T 14 OK 3287 3290 3291 3308 C3' DC T 15 OK 3306 3309 3310 3327 C3' DC T 16 OK 3325 3328 3329 3346 C3' DC T 17 OK 3344 3347 3348 3365 C3' DC T 18 OK 3363 3366 3367 3394 C3' DGT A 594 OK 3392 3395 3396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2769 C4' DG P 1 OK 2771 2768 2770 2791 C4' DG P 2 OK 2793 2790 2792 2813 C4' DG P 3 OK 2815 2812 2814 2835 C4' DG P 4 OK 2837 2834 2836 2857 C4' DG P 5 OK 2859 2856 2858 2879 C4' DA P 6 OK 2881 2878 2880 2900 C4' DA P 7 OK 2902 2899 2901 2921 C4' DG P 8 OK 2923 2920 2922 2943 C4' DG P 9 OK 2945 2942 2944 2965 C4' DA P 10 OK 2967 2964 2966 2986 C4' DT P 11 OK 2988 2985 2987 3006 C4' DT P 12 OK 3008 3005 3007 3026 C4' DC P 13 OK 3028 3025 3027 3051 C4' DOC P 14 OK 3050 3053 3052 3061 C4' DA T 3 OK 3063 3060 3062 3082 C4' DC T 4 OK 3084 3081 3083 3101 C4' O2G T 5 OK 3103 3100 3102 3125 C4' DG T 6 OK 3127 3124 3126 3147 C4' DA T 7 OK 3149 3146 3148 3168 C4' DA T 8 OK 3170 3167 3169 3189 C4' DT T 9 OK 3191 3188 3190 3209 C4' DC T 10 OK 3211 3208 3210 3228 C4' DC T 11 OK 3230 3227 3229 3247 C4' DT T 12 OK 3249 3246 3248 3267 C4' DT T 13 OK 3269 3266 3268 3287 C4' DC T 14 OK 3289 3286 3288 3306 C4' DC T 15 OK 3308 3305 3307 3325 C4' DC T 16 OK 3327 3324 3326 3344 C4' DC T 17 OK 3346 3343 3345 3363 C4' DC T 18 OK 3365 3362 3364 3392 C4' DGT A 594 OK 3394 3391 3393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2768 C5' DG P 1 2767 2769 2790 C5' DG P 2 2789 2791 2812 C5' DG P 3 2811 2813 2834 C5' DG P 4 2833 2835 2856 C5' DG P 5 2855 2857 2878 C5' DA P 6 2877 2879 2899 C5' DA P 7 2898 2900 2920 C5' DG P 8 2919 2921 2942 C5' DG P 9 2941 2943 2964 C5' DA P 10 2963 2965 2985 C5' DT P 11 2984 2986 3005 C5' DT P 12 3004 3006 3025 C5' DC P 13 3024 3026 3053 C5' DOC P 14 3054 3051 3060 C5' DA T 3 3059 3061 3081 C5' DC T 4 3080 3082 3100 C5' O2G T 5 3099 3101 3124 C5' DG T 6 3123 3125 3146 C5' DA T 7 3145 3147 3167 C5' DA T 8 3166 3168 3188 C5' DT T 9 3187 3189 3208 C5' DC T 10 3207 3209 3227 C5' DC T 11 3226 3228 3246 C5' DT T 12 3245 3247 3266 C5' DT T 13 3265 3267 3286 C5' DC T 14 3285 3287 3305 C5' DC T 15 3304 3306 3324 C5' DC T 16 3323 3325 3343 C5' DC T 17 3342 3344 3362 C5' DC T 18 3361 3363 3391 C5' DGT A 594 3390 3392 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2786 P DG P 2 distorted distorted 2772 2787 2788 2789 2808 P DG P 3 distorted distorted 2794 2809 2810 2811 2830 P DG P 4 distorted distorted 2816 2831 2832 2833 2852 P DG P 5 distorted distorted 2838 2853 2854 2855 2874 P DA P 6 distorted distorted 2860 2875 2876 2877 2895 P DA P 7 distorted distorted 2882 2896 2897 2898 2916 P DG P 8 distorted distorted 2903 2917 2918 2919 2938 P DG P 9 distorted distorted 2924 2939 2940 2941 2960 P DA P 10 distorted distorted 2946 2961 2962 2963 2981 P DT P 11 distorted distorted 2968 2982 2983 2984 3001 P DT P 12 distorted distorted 2989 3002 3003 3004 3021 P DC P 13 distorted distorted 3009 3022 3023 3024 3055 P DOC P 14 distorted distorted 3029 3056 3057 3054 3077 P DC T 4 distorted distorted 3064 3078 3079 3080 3096 P O2G T 5 OK OK 3085 3097 3098 3099 3120 P DG T 6 distorted distorted 3104 3121 3122 3123 3142 P DA T 7 distorted distorted 3128 3143 3144 3145 3163 P DA T 8 distorted distorted 3150 3164 3165 3166 3184 P DT T 9 distorted distorted 3171 3185 3186 3187 3204 P DC T 10 distorted distorted 3192 3205 3206 3207 3223 P DC T 11 distorted distorted 3212 3224 3225 3226 3242 P DT T 12 distorted distorted 3231 3243 3244 3245 3262 P DT T 13 distorted distorted 3250 3263 3264 3265 3282 P DC T 14 distorted distorted 3270 3283 3284 3285 3301 P DC T 15 distorted distorted 3290 3302 3303 3304 3320 P DC T 16 distorted distorted 3309 3321 3322 3323 3339 P DC T 17 distorted distorted 3328 3340 3341 3342 3358 P DC T 18 distorted distorted 3347 3359 3360 3361 ---------------------------------------------------------------------------------