ID code: '2C51' 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' G R 11 beta 3077 3083 3080 3105 C1' A R 12 beta 3100 3106 3103 3127 C1' C R 13 beta 3122 3128 3125 3147 C1' C R 14 beta 3142 3148 3145 3167 C1' C R 15 beta 3162 3168 3165 3187 C1' A R 16 beta 3182 3188 3185 3209 C1' U R 17 beta 3204 3210 3207 3227 C1' U S 4 beta 3222 3228 3225 3247 C1' G S 5 beta 3242 3248 3245 3270 C1' A S 6 beta 3265 3271 3268 3292 C1' G S 7 beta 3287 3293 3290 3315 C1' G S 8 beta 3310 3316 3313 3338 C1' A S 9 beta 3333 3339 3336 3360 C1' U S 10 beta 3355 3361 3358 3380 C1' G S 11 beta 3375 3381 3378 3403 C1' A S 12 beta 3398 3404 3401 3425 C1' C S 13 beta 3420 3426 3423 3445 C1' C S 14 beta 3440 3446 3443 3465 C1' C S 15 beta 3460 3466 3463 3485 C1' A S 16 beta 3480 3486 3483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G R 11 OK 3082 3078 3081 3103 C2' A R 12 OK 3105 3101 3104 3125 C2' C R 13 OK 3127 3123 3126 3145 C2' C R 14 OK 3147 3143 3146 3165 C2' C R 15 OK 3167 3163 3166 3185 C2' A R 16 OK 3187 3183 3186 3207 C2' U R 17 OK 3209 3205 3208 3225 C2' U S 4 OK 3227 3223 3226 3245 C2' G S 5 OK 3247 3243 3246 3268 C2' A S 6 OK 3270 3266 3269 3290 C2' G S 7 OK 3292 3288 3291 3313 C2' G S 8 OK 3315 3311 3314 3336 C2' A S 9 OK 3338 3334 3337 3358 C2' U S 10 OK 3360 3356 3359 3378 C2' G S 11 OK 3380 3376 3379 3401 C2' A S 12 OK 3403 3399 3402 3423 C2' C S 13 OK 3425 3421 3424 3443 C2' C S 14 OK 3445 3441 3444 3463 C2' C S 15 OK 3465 3461 3464 3483 C2' A S 16 OK 3485 3481 3484 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G R 11 OK 3076 3079 3080 3101 C3' A R 12 OK 3099 3102 3103 3123 C3' C R 13 OK 3121 3124 3125 3143 C3' C R 14 OK 3141 3144 3145 3163 C3' C R 15 OK 3161 3164 3165 3183 C3' A R 16 OK 3181 3184 3185 3205 C3' U R 17 OK 3203 3206 3207 3223 C3' U S 4 OK 3221 3224 3225 3243 C3' G S 5 OK 3241 3244 3245 3266 C3' A S 6 OK 3264 3267 3268 3288 C3' G S 7 OK 3286 3289 3290 3311 C3' G S 8 OK 3309 3312 3313 3334 C3' A S 9 OK 3332 3335 3336 3356 C3' U S 10 OK 3354 3357 3358 3376 C3' G S 11 OK 3374 3377 3378 3399 C3' A S 12 OK 3397 3400 3401 3421 C3' C S 13 OK 3419 3422 3423 3441 C3' C S 14 OK 3439 3442 3443 3461 C3' C S 15 OK 3459 3462 3463 3481 C3' A S 16 OK 3479 3482 3483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G R 11 OK 3078 3075 3077 3099 C4' A R 12 OK 3101 3098 3100 3121 C4' C R 13 OK 3123 3120 3122 3141 C4' C R 14 OK 3143 3140 3142 3161 C4' C R 15 OK 3163 3160 3162 3181 C4' A R 16 OK 3183 3180 3182 3203 C4' U R 17 OK 3205 3202 3204 3221 C4' U S 4 OK 3223 3220 3222 3241 C4' G S 5 OK 3243 3240 3242 3264 C4' A S 6 OK 3266 3263 3265 3286 C4' G S 7 OK 3288 3285 3287 3309 C4' G S 8 OK 3311 3308 3310 3332 C4' A S 9 OK 3334 3331 3333 3354 C4' U S 10 OK 3356 3353 3355 3374 C4' G S 11 OK 3376 3373 3375 3397 C4' A S 12 OK 3399 3396 3398 3419 C4' C S 13 OK 3421 3418 3420 3439 C4' C S 14 OK 3441 3438 3440 3459 C4' C S 15 OK 3461 3458 3460 3479 C4' A S 16 OK 3481 3478 3480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G R 11 3074 3076 3098 C5' A R 12 3097 3099 3120 C5' C R 13 3119 3121 3140 C5' C R 14 3139 3141 3160 C5' C R 15 3159 3161 3180 C5' A R 16 3179 3181 3202 C5' U R 17 3201 3203 3220 C5' U S 4 3219 3221 3240 C5' G S 5 3239 3241 3263 C5' A S 6 3262 3264 3285 C5' G S 7 3284 3286 3308 C5' G S 8 3307 3309 3331 C5' A S 9 3330 3332 3353 C5' U S 10 3352 3354 3373 C5' G S 11 3372 3374 3396 C5' A S 12 3395 3397 3418 C5' C S 13 3417 3419 3438 C5' C S 14 3437 3439 3458 C5' C S 15 3457 3459 3478 C5' A S 16 3477 3479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G R 11 distorted distorted 3059 3072 3073 3074 3094 P A R 12 distorted distorted 3079 3095 3096 3097 3116 P C R 13 distorted distorted 3102 3117 3118 3119 3136 P C R 14 distorted distorted 3124 3137 3138 3139 3156 P C R 15 distorted distorted 3144 3157 3158 3159 3176 P A R 16 distorted distorted 3164 3177 3178 3179 3198 P U R 17 distorted distorted 3184 3199 3200 3201 3236 P G S 5 distorted distorted 3224 3237 3238 3239 3259 P A S 6 distorted distorted 3244 3260 3261 3262 3281 P G S 7 distorted distorted 3267 3282 3283 3284 3304 P G S 8 distorted distorted 3289 3305 3306 3307 3327 P A S 9 distorted distorted 3312 3328 3329 3330 3349 P U S 10 distorted distorted 3335 3350 3351 3352 3369 P G S 11 distorted distorted 3357 3370 3371 3372 3392 P A S 12 distorted distorted 3377 3393 3394 3395 3414 P C S 13 distorted distorted 3400 3415 3416 3417 3434 P C S 14 distorted distorted 3422 3435 3436 3437 3454 P C S 15 distorted distorted 3442 3455 3456 3457 3474 P A S 16 distorted distorted 3462 3475 3476 3477 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