ID code: '2C50' 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' --------------------------------------------------------------------------------- 2907 C1' A R 3 beta 2902 2908 2905 2929 C1' U R 4 beta 2924 2930 2927 2949 C1' G R 5 beta 2944 2950 2947 2972 C1' A R 6 beta 2967 2973 2970 2994 C1' G R 7 beta 2989 2995 2992 3017 C1' G R 8 beta 3012 3018 3015 3040 C1' A R 9 beta 3035 3041 3038 3062 C1' U R 10 beta 3057 3063 3060 3082 C1' A R 11 beta 3077 3083 3080 3104 C1' A R 12 beta 3099 3105 3102 3126 C1' C R 13 beta 3121 3127 3124 3146 C1' C R 14 beta 3141 3147 3144 3166 C1' C R 15 beta 3161 3167 3164 3186 C1' A R 16 beta 3181 3187 3184 3206 C1' U S 4 beta 3201 3207 3204 3226 C1' G S 5 beta 3221 3227 3224 3249 C1' A S 6 beta 3244 3250 3247 3271 C1' G S 7 beta 3266 3272 3269 3294 C1' G S 8 beta 3289 3295 3292 3317 C1' A S 9 beta 3312 3318 3315 3339 C1' U S 10 beta 3334 3340 3337 3359 C1' A S 11 beta 3354 3360 3357 3381 C1' A S 12 beta 3376 3382 3379 3403 C1' C S 13 beta 3398 3404 3401 3423 C1' C S 14 beta 3418 3424 3421 3443 C1' C S 15 beta 3438 3444 3441 3463 C1' A S 16 beta 3458 3464 3461 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2905 C2' A R 3 OK 2907 2903 2906 2927 C2' U R 4 OK 2929 2925 2928 2947 C2' G R 5 OK 2949 2945 2948 2970 C2' A R 6 OK 2972 2968 2971 2992 C2' G R 7 OK 2994 2990 2993 3015 C2' G R 8 OK 3017 3013 3016 3038 C2' A R 9 OK 3040 3036 3039 3060 C2' U R 10 OK 3062 3058 3061 3080 C2' A R 11 OK 3082 3078 3081 3102 C2' A R 12 OK 3104 3100 3103 3124 C2' C R 13 OK 3126 3122 3125 3144 C2' C R 14 OK 3146 3142 3145 3164 C2' C R 15 OK 3166 3162 3165 3184 C2' A R 16 OK 3186 3182 3185 3204 C2' U S 4 OK 3206 3202 3205 3224 C2' G S 5 OK 3226 3222 3225 3247 C2' A S 6 OK 3249 3245 3248 3269 C2' G S 7 OK 3271 3267 3270 3292 C2' G S 8 OK 3294 3290 3293 3315 C2' A S 9 OK 3317 3313 3316 3337 C2' U S 10 OK 3339 3335 3338 3357 C2' A S 11 OK 3359 3355 3358 3379 C2' A S 12 OK 3381 3377 3380 3401 C2' C S 13 OK 3403 3399 3402 3421 C2' C S 14 OK 3423 3419 3422 3441 C2' C S 15 OK 3443 3439 3442 3461 C2' A S 16 OK 3463 3459 3462 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2903 C3' A R 3 OK 2901 2904 2905 2925 C3' U R 4 OK 2923 2926 2927 2945 C3' G R 5 OK 2943 2946 2947 2968 C3' A R 6 OK 2966 2969 2970 2990 C3' G R 7 OK 2988 2991 2992 3013 C3' G R 8 OK 3011 3014 3015 3036 C3' A R 9 OK 3034 3037 3038 3058 C3' U R 10 OK 3056 3059 3060 3078 C3' A R 11 OK 3076 3079 3080 3100 C3' A R 12 OK 3098 3101 3102 3122 C3' C R 13 OK 3120 3123 3124 3142 C3' C R 14 OK 3140 3143 3144 3162 C3' C R 15 OK 3160 3163 3164 3182 C3' A R 16 OK 3180 3183 3184 3202 C3' U S 4 OK 3200 3203 3204 3222 C3' G S 5 OK 3220 3223 3224 3245 C3' A S 6 OK 3243 3246 3247 3267 C3' G S 7 OK 3265 3268 3269 3290 C3' G S 8 OK 3288 3291 3292 3313 C3' A S 9 OK 3311 3314 3315 3335 C3' U S 10 OK 3333 3336 3337 3355 C3' A S 11 OK 3353 3356 3357 3377 C3' A S 12 OK 3375 3378 3379 3399 C3' C S 13 OK 3397 3400 3401 3419 C3' C S 14 OK 3417 3420 3421 3439 C3' C S 15 OK 3437 3440 3441 3459 C3' A S 16 OK 3457 3460 3461 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2901 C4' A R 3 OK 2903 2900 2902 2923 C4' U R 4 OK 2925 2922 2924 2943 C4' G R 5 OK 2945 2942 2944 2966 C4' A R 6 OK 2968 2965 2967 2988 C4' G R 7 OK 2990 2987 2989 3011 C4' G R 8 OK 3013 3010 3012 3034 C4' A R 9 OK 3036 3033 3035 3056 C4' U R 10 OK 3058 3055 3057 3076 C4' A R 11 OK 3078 3075 3077 3098 C4' A R 12 OK 3100 3097 3099 3120 C4' C R 13 OK 3122 3119 3121 3140 C4' C R 14 OK 3142 3139 3141 3160 C4' C R 15 OK 3162 3159 3161 3180 C4' A R 16 OK 3182 3179 3181 3200 C4' U S 4 OK 3202 3199 3201 3220 C4' G S 5 OK 3222 3219 3221 3243 C4' A S 6 OK 3245 3242 3244 3265 C4' G S 7 OK 3267 3264 3266 3288 C4' G S 8 OK 3290 3287 3289 3311 C4' A S 9 OK 3313 3310 3312 3333 C4' U S 10 OK 3335 3332 3334 3353 C4' A S 11 OK 3355 3352 3354 3375 C4' A S 12 OK 3377 3374 3376 3397 C4' C S 13 OK 3399 3396 3398 3417 C4' C S 14 OK 3419 3416 3418 3437 C4' C S 15 OK 3439 3436 3438 3457 C4' A S 16 OK 3459 3456 3458 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2900 C5' A R 3 2899 2901 2922 C5' U R 4 2921 2923 2942 C5' G R 5 2941 2943 2965 C5' A R 6 2964 2966 2987 C5' G R 7 2986 2988 3010 C5' G R 8 3009 3011 3033 C5' A R 9 3032 3034 3055 C5' U R 10 3054 3056 3075 C5' A R 11 3074 3076 3097 C5' A R 12 3096 3098 3119 C5' C R 13 3118 3120 3139 C5' C R 14 3138 3140 3159 C5' C R 15 3158 3160 3179 C5' A R 16 3178 3180 3199 C5' U S 4 3198 3200 3219 C5' G S 5 3218 3220 3242 C5' A S 6 3241 3243 3264 C5' G S 7 3263 3265 3287 C5' G S 8 3286 3288 3310 C5' A S 9 3309 3311 3332 C5' U S 10 3331 3333 3352 C5' A S 11 3351 3353 3374 C5' A S 12 3373 3375 3396 C5' C S 13 3395 3397 3416 C5' C S 14 3415 3417 3436 C5' C S 15 3435 3437 3456 C5' A S 16 3455 3457 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2918 P U R 4 distorted distorted 2904 2919 2920 2921 2938 P G R 5 distorted distorted 2926 2939 2940 2941 2961 P A R 6 distorted distorted 2946 2962 2963 2964 2983 P G R 7 distorted distorted 2969 2984 2985 2986 3006 P G R 8 distorted distorted 2991 3007 3008 3009 3029 P A R 9 distorted distorted 3014 3030 3031 3032 3051 P U R 10 distorted distorted 3037 3052 3053 3054 3071 P A R 11 distorted distorted 3059 3072 3073 3074 3093 P A R 12 distorted distorted 3079 3094 3095 3096 3115 P C R 13 distorted distorted 3101 3116 3117 3118 3135 P C R 14 distorted distorted 3123 3136 3137 3138 3155 P C R 15 distorted distorted 3143 3156 3157 3158 3175 P A R 16 distorted distorted 3163 3176 3177 3178 3215 P G S 5 distorted distorted 3203 3216 3217 3218 3238 P A S 6 distorted distorted 3223 3239 3240 3241 3260 P G S 7 distorted distorted 3246 3261 3262 3263 3283 P G S 8 distorted distorted 3268 3284 3285 3286 3306 P A S 9 distorted distorted 3291 3307 3308 3309 3328 P U S 10 distorted distorted 3314 3329 3330 3331 3348 P A S 11 distorted distorted 3336 3349 3350 3351 3370 P A S 12 distorted distorted 3356 3371 3372 3373 3392 P C S 13 distorted distorted 3378 3393 3394 3395 3412 P C S 14 distorted distorted 3400 3413 3414 3415 3432 P C S 15 distorted distorted 3420 3433 3434 3435 3452 P A S 16 distorted distorted 3440 3453 3454 3455 ---------------------------------------------------------------------------------