ID code: '2W8K' 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' --------------------------------------------------------------------------------- 2763 C1' DG P 1 beta 2759 2764 2762 2785 C1' DG P 2 beta 2781 2786 2784 2807 C1' DG P 3 beta 2803 2808 2806 2829 C1' DG P 4 beta 2825 2830 2828 2851 C1' DG P 5 beta 2847 2852 2850 2873 C1' DA P 6 beta 2869 2874 2872 2894 C1' DA P 7 beta 2890 2895 2893 2915 C1' DG P 8 beta 2911 2916 2914 2937 C1' DG P 9 beta 2933 2938 2936 2959 C1' DA P 10 beta 2955 2960 2958 2980 C1' DT P 11 beta 2976 2981 2979 2999 C1' DT P 12 beta 2995 3000 2998 3018 C1' DC P 13 beta 3014 3019 3017 3035 C1' DOC P 14 beta 3039 3027 3036 3053 C1' DA T 3 beta 3049 3054 3052 3074 C1' DC T 4 beta 3070 3075 3073 3126 C1' DG T 6 beta 3122 3127 3125 3148 C1' DA T 7 beta 3144 3149 3147 3169 C1' DA T 8 beta 3165 3170 3168 3190 C1' DT T 9 beta 3186 3191 3189 3209 C1' DC T 10 beta 3205 3210 3208 3228 C1' DC T 11 beta 3224 3229 3227 3247 C1' DT T 12 beta 3243 3248 3246 3266 C1' DT T 13 beta 3262 3267 3265 3285 C1' DC T 14 beta 3281 3286 3284 3304 C1' DC T 15 beta 3300 3305 3303 3323 C1' DC T 16 beta 3319 3324 3322 3342 C1' DC T 17 beta 3338 3343 3341 3361 C1' DC T 18 beta 3357 3362 3360 3390 C1' DGT A1342 beta 3386 3391 3389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2762 C2' DG P 1 2763 2760 2784 C2' DG P 2 2785 2782 2806 C2' DG P 3 2807 2804 2828 C2' DG P 4 2829 2826 2850 C2' DG P 5 2851 2848 2872 C2' DA P 6 2873 2870 2893 C2' DA P 7 2894 2891 2914 C2' DG P 8 2915 2912 2936 C2' DG P 9 2937 2934 2958 C2' DA P 10 2959 2956 2979 C2' DT P 11 2980 2977 2998 C2' DT P 12 2999 2996 3017 C2' DC P 13 3018 3015 3036 C2' DOC P 14 3035 3037 3052 C2' DA T 3 3053 3050 3073 C2' DC T 4 3074 3071 3125 C2' DG T 6 3126 3123 3147 C2' DA T 7 3148 3145 3168 C2' DA T 8 3169 3166 3189 C2' DT T 9 3190 3187 3208 C2' DC T 10 3209 3206 3227 C2' DC T 11 3228 3225 3246 C2' DT T 12 3247 3244 3265 C2' DT T 13 3266 3263 3284 C2' DC T 14 3285 3282 3303 C2' DC T 15 3304 3301 3322 C2' DC T 16 3323 3320 3341 C2' DC T 17 3342 3339 3360 C2' DC T 18 3361 3358 3389 C2' DGT A1342 3390 3387 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2760 C3' DG P 1 OK 2758 2761 2762 2782 C3' DG P 2 OK 2780 2783 2784 2804 C3' DG P 3 OK 2802 2805 2806 2826 C3' DG P 4 OK 2824 2827 2828 2848 C3' DG P 5 OK 2846 2849 2850 2870 C3' DA P 6 OK 2868 2871 2872 2891 C3' DA P 7 OK 2889 2892 2893 2912 C3' DG P 8 OK 2910 2913 2914 2934 C3' DG P 9 OK 2932 2935 2936 2956 C3' DA P 10 OK 2954 2957 2958 2977 C3' DT P 11 OK 2975 2978 2979 2996 C3' DT P 12 OK 2994 2997 2998 3015 C3' DC P 13 OK 3013 3016 3017 3037 C3' DOC P 14 3038 3036 3050 C3' DA T 3 OK 3048 3051 3052 3071 C3' DC T 4 OK 3069 3072 3073 3123 C3' DG T 6 OK 3121 3124 3125 3145 C3' DA T 7 OK 3143 3146 3147 3166 C3' DA T 8 OK 3164 3167 3168 3187 C3' DT T 9 OK 3185 3188 3189 3206 C3' DC T 10 OK 3204 3207 3208 3225 C3' DC T 11 OK 3223 3226 3227 3244 C3' DT T 12 OK 3242 3245 3246 3263 C3' DT T 13 OK 3261 3264 3265 3282 C3' DC T 14 OK 3280 3283 3284 3301 C3' DC T 15 OK 3299 3302 3303 3320 C3' DC T 16 OK 3318 3321 3322 3339 C3' DC T 17 OK 3337 3340 3341 3358 C3' DC T 18 OK 3356 3359 3360 3387 C3' DGT A1342 OK 3385 3388 3389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2758 C4' DG P 1 OK 2760 2757 2759 2780 C4' DG P 2 OK 2782 2779 2781 2802 C4' DG P 3 OK 2804 2801 2803 2824 C4' DG P 4 OK 2826 2823 2825 2846 C4' DG P 5 OK 2848 2845 2847 2868 C4' DA P 6 OK 2870 2867 2869 2889 C4' DA P 7 OK 2891 2888 2890 2910 C4' DG P 8 OK 2912 2909 2911 2932 C4' DG P 9 OK 2934 2931 2933 2954 C4' DA P 10 OK 2956 2953 2955 2975 C4' DT P 11 OK 2977 2974 2976 2994 C4' DT P 12 OK 2996 2993 2995 3013 C4' DC P 13 OK 3015 3012 3014 3038 C4' DOC P 14 OK 3037 3040 3039 3048 C4' DA T 3 OK 3050 3047 3049 3069 C4' DC T 4 OK 3071 3068 3070 3121 C4' DG T 6 OK 3123 3120 3122 3143 C4' DA T 7 OK 3145 3142 3144 3164 C4' DA T 8 OK 3166 3163 3165 3185 C4' DT T 9 OK 3187 3184 3186 3204 C4' DC T 10 OK 3206 3203 3205 3223 C4' DC T 11 OK 3225 3222 3224 3242 C4' DT T 12 OK 3244 3241 3243 3261 C4' DT T 13 OK 3263 3260 3262 3280 C4' DC T 14 OK 3282 3279 3281 3299 C4' DC T 15 OK 3301 3298 3300 3318 C4' DC T 16 OK 3320 3317 3319 3337 C4' DC T 17 OK 3339 3336 3338 3356 C4' DC T 18 OK 3358 3355 3357 3385 C4' DGT A1342 OK 3387 3384 3386 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2757 C5' DG P 1 2756 2758 2779 C5' DG P 2 2778 2780 2801 C5' DG P 3 2800 2802 2823 C5' DG P 4 2822 2824 2845 C5' DG P 5 2844 2846 2867 C5' DA P 6 2866 2868 2888 C5' DA P 7 2887 2889 2909 C5' DG P 8 2908 2910 2931 C5' DG P 9 2930 2932 2953 C5' DA P 10 2952 2954 2974 C5' DT P 11 2973 2975 2993 C5' DT P 12 2992 2994 3012 C5' DC P 13 3011 3013 3040 C5' DOC P 14 3041 3038 3047 C5' DA T 3 3046 3048 3068 C5' DC T 4 3067 3069 3120 C5' DG T 6 3119 3121 3142 C5' DA T 7 3141 3143 3163 C5' DA T 8 3162 3164 3184 C5' DT T 9 3183 3185 3203 C5' DC T 10 3202 3204 3222 C5' DC T 11 3221 3223 3241 C5' DT T 12 3240 3242 3260 C5' DT T 13 3259 3261 3279 C5' DC T 14 3278 3280 3298 C5' DC T 15 3297 3299 3317 C5' DC T 16 3316 3318 3336 C5' DC T 17 3335 3337 3355 C5' DC T 18 3354 3356 3384 C5' DGT A1342 3383 3385 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2775 P DG P 2 distorted distorted 2761 2776 2777 2778 2797 P DG P 3 distorted distorted 2783 2798 2799 2800 2819 P DG P 4 distorted distorted 2805 2820 2821 2822 2841 P DG P 5 distorted distorted 2827 2842 2843 2844 2863 P DA P 6 distorted distorted 2849 2864 2865 2866 2884 P DA P 7 distorted distorted 2871 2885 2886 2887 2905 P DG P 8 distorted distorted 2892 2906 2907 2908 2927 P DG P 9 distorted distorted 2913 2928 2929 2930 2949 P DA P 10 distorted distorted 2935 2950 2951 2952 2970 P DT P 11 distorted distorted 2957 2971 2972 2973 2989 P DT P 12 distorted distorted 2978 2990 2991 2992 3008 P DC P 13 distorted distorted 2997 3009 3010 3011 3042 P DOC P 14 distorted distorted 3016 3043 3044 3041 3064 P DC T 4 distorted distorted 3051 3065 3066 3067 3083 P N2G T 5 OK OK 3072 3084 3085 3086 3116 P DG T 6 OK OK 3115 3117 3118 3119 3138 P DA T 7 distorted distorted 3124 3139 3140 3141 3159 P DA T 8 distorted distorted 3146 3160 3161 3162 3180 P DT T 9 distorted distorted 3167 3181 3182 3183 3199 P DC T 10 distorted distorted 3188 3200 3201 3202 3218 P DC T 11 distorted distorted 3207 3219 3220 3221 3237 P DT T 12 distorted distorted 3226 3238 3239 3240 3256 P DT T 13 distorted distorted 3245 3257 3258 3259 3275 P DC T 14 distorted distorted 3264 3276 3277 3278 3294 P DC T 15 distorted distorted 3283 3295 3296 3297 3313 P DC T 16 distorted distorted 3302 3314 3315 3316 3332 P DC T 17 distorted distorted 3321 3333 3334 3335 3351 P DC T 18 distorted distorted 3340 3352 3353 3354 ---------------------------------------------------------------------------------