ID code: '2XCA' 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' --------------------------------------------------------------------------------- 2764 C1' DG P 1 beta 2760 2765 2763 2786 C1' DG P 2 beta 2782 2787 2785 2808 C1' DG P 3 beta 2804 2809 2807 2830 C1' DG P 4 beta 2826 2831 2829 2852 C1' DG P 5 beta 2848 2853 2851 2874 C1' DA P 6 beta 2870 2875 2873 2895 C1' DA P 7 beta 2891 2896 2894 2916 C1' DG P 8 beta 2912 2917 2915 2938 C1' DG P 9 beta 2934 2939 2937 2960 C1' DA P 10 beta 2956 2961 2959 2981 C1' DT P 11 beta 2977 2982 2980 3001 C1' DT P 12 beta 2997 3002 3000 3019 C1' DOC P 13 beta 3023 3011 3020 3037 C1' DC T 2 beta 3033 3038 3036 3056 C1' DA T 3 beta 3052 3057 3055 3077 C1' DC T 4 beta 3073 3078 3076 3096 C1' 8OG T 5 beta 3092 3097 3095 3119 C1' DG T 6 beta 3115 3120 3118 3141 C1' DA T 7 beta 3137 3142 3140 3162 C1' DA T 8 beta 3158 3163 3161 3183 C1' DT T 9 beta 3179 3184 3182 3203 C1' DC T 10 beta 3199 3204 3202 3222 C1' DC T 11 beta 3218 3223 3221 3241 C1' DT T 12 beta 3237 3242 3240 3261 C1' DT T 13 beta 3257 3262 3260 3281 C1' DC T 14 beta 3277 3282 3280 3300 C1' DC T 15 beta 3296 3301 3299 3319 C1' DC T 16 beta 3315 3320 3318 3338 C1' DC T 17 beta 3334 3339 3337 3357 C1' DC T 18 beta 3353 3358 3356 3386 C1' DGT A1000 beta 3382 3387 3385 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2763 C2' DG P 1 2764 2761 2785 C2' DG P 2 2786 2783 2807 C2' DG P 3 2808 2805 2829 C2' DG P 4 2830 2827 2851 C2' DG P 5 2852 2849 2873 C2' DA P 6 2874 2871 2894 C2' DA P 7 2895 2892 2915 C2' DG P 8 2916 2913 2937 C2' DG P 9 2938 2935 2959 C2' DA P 10 2960 2957 2980 C2' DT P 11 2981 2978 3000 C2' DT P 12 3001 2998 3020 C2' DOC P 13 3019 3021 3036 C2' DC T 2 3037 3034 3055 C2' DA T 3 3056 3053 3076 C2' DC T 4 3077 3074 3095 C2' 8OG T 5 3096 3093 3118 C2' DG T 6 3119 3116 3140 C2' DA T 7 3141 3138 3161 C2' DA T 8 3162 3159 3182 C2' DT T 9 3183 3180 3202 C2' DC T 10 3203 3200 3221 C2' DC T 11 3222 3219 3240 C2' DT T 12 3241 3238 3260 C2' DT T 13 3261 3258 3280 C2' DC T 14 3281 3278 3299 C2' DC T 15 3300 3297 3318 C2' DC T 16 3319 3316 3337 C2' DC T 17 3338 3335 3356 C2' DC T 18 3357 3354 3385 C2' DGT A1000 3386 3383 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2761 C3' DG P 1 OK 2759 2762 2763 2783 C3' DG P 2 OK 2781 2784 2785 2805 C3' DG P 3 OK 2803 2806 2807 2827 C3' DG P 4 OK 2825 2828 2829 2849 C3' DG P 5 OK 2847 2850 2851 2871 C3' DA P 6 OK 2869 2872 2873 2892 C3' DA P 7 OK 2890 2893 2894 2913 C3' DG P 8 OK 2911 2914 2915 2935 C3' DG P 9 OK 2933 2936 2937 2957 C3' DA P 10 OK 2955 2958 2959 2978 C3' DT P 11 OK 2976 2979 2980 2998 C3' DT P 12 OK 2996 2999 3000 3021 C3' DOC P 13 3022 3020 3034 C3' DC T 2 OK 3032 3035 3036 3053 C3' DA T 3 OK 3051 3054 3055 3074 C3' DC T 4 OK 3072 3075 3076 3093 C3' 8OG T 5 OK 3091 3094 3095 3116 C3' DG T 6 OK 3114 3117 3118 3138 C3' DA T 7 OK 3136 3139 3140 3159 C3' DA T 8 OK 3157 3160 3161 3180 C3' DT T 9 OK 3178 3181 3182 3200 C3' DC T 10 OK 3198 3201 3202 3219 C3' DC T 11 OK 3217 3220 3221 3238 C3' DT T 12 OK 3236 3239 3240 3258 C3' DT T 13 OK 3256 3259 3260 3278 C3' DC T 14 OK 3276 3279 3280 3297 C3' DC T 15 OK 3295 3298 3299 3316 C3' DC T 16 OK 3314 3317 3318 3335 C3' DC T 17 OK 3333 3336 3337 3354 C3' DC T 18 OK 3352 3355 3356 3383 C3' DGT A1000 OK 3381 3384 3385 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2759 C4' DG P 1 OK 2761 2758 2760 2781 C4' DG P 2 OK 2783 2780 2782 2803 C4' DG P 3 OK 2805 2802 2804 2825 C4' DG P 4 OK 2827 2824 2826 2847 C4' DG P 5 OK 2849 2846 2848 2869 C4' DA P 6 OK 2871 2868 2870 2890 C4' DA P 7 OK 2892 2889 2891 2911 C4' DG P 8 OK 2913 2910 2912 2933 C4' DG P 9 OK 2935 2932 2934 2955 C4' DA P 10 OK 2957 2954 2956 2976 C4' DT P 11 OK 2978 2975 2977 2996 C4' DT P 12 OK 2998 2995 2997 3022 C4' DOC P 13 OK 3021 3024 3023 3032 C4' DC T 2 OK 3034 3031 3033 3051 C4' DA T 3 OK 3053 3050 3052 3072 C4' DC T 4 OK 3074 3071 3073 3091 C4' 8OG T 5 OK 3093 3090 3092 3114 C4' DG T 6 OK 3116 3113 3115 3136 C4' DA T 7 OK 3138 3135 3137 3157 C4' DA T 8 OK 3159 3156 3158 3178 C4' DT T 9 OK 3180 3177 3179 3198 C4' DC T 10 OK 3200 3197 3199 3217 C4' DC T 11 OK 3219 3216 3218 3236 C4' DT T 12 OK 3238 3235 3237 3256 C4' DT T 13 OK 3258 3255 3257 3276 C4' DC T 14 OK 3278 3275 3277 3295 C4' DC T 15 OK 3297 3294 3296 3314 C4' DC T 16 OK 3316 3313 3315 3333 C4' DC T 17 OK 3335 3332 3334 3352 C4' DC T 18 OK 3354 3351 3353 3381 C4' DGT A1000 OK 3383 3380 3382 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2758 C5' DG P 1 2757 2759 2780 C5' DG P 2 2779 2781 2802 C5' DG P 3 2801 2803 2824 C5' DG P 4 2823 2825 2846 C5' DG P 5 2845 2847 2868 C5' DA P 6 2867 2869 2889 C5' DA P 7 2888 2890 2910 C5' DG P 8 2909 2911 2932 C5' DG P 9 2931 2933 2954 C5' DA P 10 2953 2955 2975 C5' DT P 11 2974 2976 2995 C5' DT P 12 2994 2996 3024 C5' DOC P 13 3025 3022 3031 C5' DC T 2 3030 3032 3050 C5' DA T 3 3049 3051 3071 C5' DC T 4 3070 3072 3090 C5' 8OG T 5 3089 3091 3113 C5' DG T 6 3112 3114 3135 C5' DA T 7 3134 3136 3156 C5' DA T 8 3155 3157 3177 C5' DT T 9 3176 3178 3197 C5' DC T 10 3196 3198 3216 C5' DC T 11 3215 3217 3235 C5' DT T 12 3234 3236 3255 C5' DT T 13 3254 3256 3275 C5' DC T 14 3274 3276 3294 C5' DC T 15 3293 3295 3313 C5' DC T 16 3312 3314 3332 C5' DC T 17 3331 3333 3351 C5' DC T 18 3350 3352 3380 C5' DGT A1000 3379 3381 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2776 P DG P 2 distorted distorted 2762 2777 2778 2779 2798 P DG P 3 distorted distorted 2784 2799 2800 2801 2820 P DG P 4 distorted distorted 2806 2821 2822 2823 2842 P DG P 5 distorted distorted 2828 2843 2844 2845 2864 P DA P 6 distorted distorted 2850 2865 2866 2867 2885 P DA P 7 distorted distorted 2872 2886 2887 2888 2906 P DG P 8 distorted distorted 2893 2907 2908 2909 2928 P DG P 9 distorted distorted 2914 2929 2930 2931 2950 P DA P 10 distorted distorted 2936 2951 2952 2953 2971 P DT P 11 distorted distorted 2958 2972 2973 2974 2991 P DT P 12 distorted distorted 2979 2992 2993 2994 3026 P DOC P 13 distorted distorted 2999 3027 3028 3025 3046 P DA T 3 distorted distorted 3035 3047 3048 3049 3067 P DC T 4 distorted distorted 3054 3068 3069 3070 3086 P 8OG T 5 OK OK 3075 3087 3088 3089 3109 P DG T 6 distorted distorted 3094 3110 3111 3112 3131 P DA T 7 distorted distorted 3117 3132 3133 3134 3152 P DA T 8 distorted distorted 3139 3153 3154 3155 3173 P DT T 9 distorted distorted 3160 3174 3175 3176 3193 P DC T 10 distorted distorted 3181 3194 3195 3196 3212 P DC T 11 distorted distorted 3201 3213 3214 3215 3231 P DT T 12 distorted distorted 3220 3232 3233 3234 3251 P DT T 13 distorted distorted 3239 3252 3253 3254 3271 P DC T 14 distorted distorted 3259 3272 3273 3274 3290 P DC T 15 distorted distorted 3279 3291 3292 3293 3309 P DC T 16 distorted distorted 3298 3310 3311 3312 3328 P DC T 17 distorted distorted 3317 3329 3330 3331 3347 P DC T 18 distorted distorted 3336 3348 3349 3350 ---------------------------------------------------------------------------------