ID code: '1RKJ' 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' --------------------------------------------------------------------------------- 2743 C1' G B 1 alpha beta 2738 2761 2744 2741 2778 C1' G B 2 alpha beta 2773 2796 2779 2776 2812 C1' A B 3 alpha beta 2807 2829 2813 2810 2845 C1' U B 4 alpha beta 2840 2860 2846 2843 2875 C1' G B 5 alpha beta 2870 2893 2876 2873 2909 C1' C B 6 alpha beta 2904 2924 2910 2907 2940 C1' C B 7 alpha beta 2935 2955 2941 2938 2971 C1' U B 8 alpha beta 2966 2986 2972 2969 3001 C1' C B 9 alpha beta 2996 3016 3002 2999 3032 C1' C B 10 alpha beta 3027 3047 3033 3030 3063 C1' C B 11 alpha beta 3058 3078 3064 3061 3094 C1' G B 12 alpha beta 3089 3112 3095 3092 3128 C1' A B 13 alpha beta 3123 3145 3129 3126 3161 C1' G B 14 alpha beta 3156 3179 3162 3159 3195 C1' U B 15 alpha beta 3190 3210 3196 3193 3225 C1' G B 16 alpha beta 3220 3243 3226 3223 3259 C1' C B 17 alpha beta 3254 3274 3260 3257 3290 C1' A B 18 alpha beta 3285 3307 3291 3288 3323 C1' U B 19 alpha beta 3318 3338 3324 3321 3353 C1' C B 20 alpha beta 3348 3368 3354 3351 3384 C1' C B 21 alpha beta 3379 3400 3385 3382 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2741 C2' G B 1 OK OK 2743 2739 2759 2742 2776 C2' G B 2 OK OK 2778 2774 2794 2777 2810 C2' A B 3 OK OK 2812 2808 2827 2811 2843 C2' U B 4 OK OK 2845 2841 2858 2844 2873 C2' G B 5 OK OK 2875 2871 2891 2874 2907 C2' C B 6 OK OK 2909 2905 2922 2908 2938 C2' C B 7 OK OK 2940 2936 2953 2939 2969 C2' U B 8 OK OK 2971 2967 2984 2970 2999 C2' C B 9 OK OK 3001 2997 3014 3000 3030 C2' C B 10 OK OK 3032 3028 3045 3031 3061 C2' C B 11 OK OK 3063 3059 3076 3062 3092 C2' G B 12 OK OK 3094 3090 3110 3093 3126 C2' A B 13 OK OK 3128 3124 3143 3127 3159 C2' G B 14 OK OK 3161 3157 3177 3160 3193 C2' U B 15 OK OK 3195 3191 3208 3194 3223 C2' G B 16 OK OK 3225 3221 3241 3224 3257 C2' C B 17 OK OK 3259 3255 3272 3258 3288 C2' A B 18 OK OK 3290 3286 3305 3289 3321 C2' U B 19 OK OK 3323 3319 3336 3322 3351 C2' C B 20 OK OK 3353 3349 3366 3352 3382 C2' C B 21 OK OK 3384 3380 3398 3383 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2739 C3' G B 1 OK OK 2737 2758 2740 2741 2774 C3' G B 2 OK OK 2772 2793 2775 2776 2808 C3' A B 3 OK OK 2806 2826 2809 2810 2841 C3' U B 4 OK OK 2839 2857 2842 2843 2871 C3' G B 5 OK OK 2869 2890 2872 2873 2905 C3' C B 6 OK OK 2903 2921 2906 2907 2936 C3' C B 7 OK OK 2934 2952 2937 2938 2967 C3' U B 8 OK OK 2965 2983 2968 2969 2997 C3' C B 9 OK OK 2995 3013 2998 2999 3028 C3' C B 10 OK OK 3026 3044 3029 3030 3059 C3' C B 11 OK OK 3057 3075 3060 3061 3090 C3' G B 12 OK OK 3088 3109 3091 3092 3124 C3' A B 13 OK OK 3122 3142 3125 3126 3157 C3' G B 14 OK OK 3155 3176 3158 3159 3191 C3' U B 15 OK OK 3189 3207 3192 3193 3221 C3' G B 16 OK OK 3219 3240 3222 3223 3255 C3' C B 17 OK OK 3253 3271 3256 3257 3286 C3' A B 18 OK OK 3284 3304 3287 3288 3319 C3' U B 19 OK OK 3317 3335 3320 3321 3349 C3' C B 20 OK OK 3347 3365 3350 3351 3380 C3' C B 21 OK OK 3378 3396 3381 3382 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2737 C4' G B 1 OK OK 2739 2757 2736 2738 2772 C4' G B 2 OK OK 2774 2792 2771 2773 2806 C4' A B 3 OK OK 2808 2825 2805 2807 2839 C4' U B 4 OK OK 2841 2856 2838 2840 2869 C4' G B 5 OK OK 2871 2889 2868 2870 2903 C4' C B 6 OK OK 2905 2920 2902 2904 2934 C4' C B 7 OK OK 2936 2951 2933 2935 2965 C4' U B 8 OK OK 2967 2982 2964 2966 2995 C4' C B 9 OK OK 2997 3012 2994 2996 3026 C4' C B 10 OK OK 3028 3043 3025 3027 3057 C4' C B 11 OK OK 3059 3074 3056 3058 3088 C4' G B 12 OK OK 3090 3108 3087 3089 3122 C4' A B 13 OK OK 3124 3141 3121 3123 3155 C4' G B 14 OK OK 3157 3175 3154 3156 3189 C4' U B 15 OK OK 3191 3206 3188 3190 3219 C4' G B 16 OK OK 3221 3239 3218 3220 3253 C4' C B 17 OK OK 3255 3270 3252 3254 3284 C4' A B 18 OK OK 3286 3303 3283 3285 3317 C4' U B 19 OK OK 3319 3334 3316 3318 3347 C4' C B 20 OK OK 3349 3364 3346 3348 3378 C4' C B 21 OK OK 3380 3395 3377 3379 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2736 C5' G B 1 OK OK 2735 2755 2756 2737 2771 C5' G B 2 OK OK 2770 2790 2791 2772 2805 C5' A B 3 OK OK 2804 2823 2824 2806 2838 C5' U B 4 OK OK 2837 2854 2855 2839 2868 C5' G B 5 OK OK 2867 2887 2888 2869 2902 C5' C B 6 OK OK 2901 2918 2919 2903 2933 C5' C B 7 OK OK 2932 2949 2950 2934 2964 C5' U B 8 OK OK 2963 2980 2981 2965 2994 C5' C B 9 OK OK 2993 3010 3011 2995 3025 C5' C B 10 OK OK 3024 3041 3042 3026 3056 C5' C B 11 OK OK 3055 3072 3073 3057 3087 C5' G B 12 OK OK 3086 3106 3107 3088 3121 C5' A B 13 OK OK 3120 3139 3140 3122 3154 C5' G B 14 OK OK 3153 3173 3174 3155 3188 C5' U B 15 OK OK 3187 3204 3205 3189 3218 C5' G B 16 OK OK 3217 3237 3238 3219 3252 C5' C B 17 OK OK 3251 3268 3269 3253 3283 C5' A B 18 OK OK 3282 3301 3302 3284 3316 C5' U B 19 OK OK 3315 3332 3333 3317 3346 C5' C B 20 OK OK 3345 3362 3363 3347 3377 C5' C B 21 OK OK 3376 3393 3394 3378 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2767 P G B 2 distorted distorted 2740 2768 2769 2770 2801 P A B 3 distorted distorted 2775 2802 2803 2804 2834 P U B 4 distorted distorted 2809 2835 2836 2837 2864 P G B 5 distorted distorted 2842 2865 2866 2867 2898 P C B 6 distorted distorted 2872 2899 2900 2901 2929 P C B 7 distorted distorted 2906 2930 2931 2932 2960 P U B 8 distorted distorted 2937 2961 2962 2963 2990 P C B 9 distorted distorted 2968 2991 2992 2993 3021 P C B 10 distorted distorted 2998 3022 3023 3024 3052 P C B 11 distorted distorted 3029 3053 3054 3055 3083 P G B 12 distorted distorted 3060 3084 3085 3086 3117 P A B 13 distorted distorted 3091 3118 3119 3120 3150 P G B 14 distorted distorted 3125 3151 3152 3153 3184 P U B 15 distorted distorted 3158 3185 3186 3187 3214 P G B 16 distorted distorted 3192 3215 3216 3217 3248 P C B 17 distorted distorted 3222 3249 3250 3251 3279 P A B 18 distorted distorted 3256 3280 3281 3282 3312 P U B 19 distorted distorted 3287 3313 3314 3315 3342 P C B 20 distorted distorted 3320 3343 3344 3345 3373 P C B 21 distorted distorted 3350 3374 3375 3376 ---------------------------------------------------------------------------------