ID code: '2IZ8' 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' C R 9 beta 3035 3041 3038 3060 C1' U R 10 beta 3055 3061 3058 3080 C1' C R 11 beta 3075 3081 3078 3100 C1' A R 12 beta 3095 3101 3098 3122 C1' C R 13 beta 3117 3123 3120 3142 C1' C R 14 beta 3137 3143 3140 3162 C1' C R 15 beta 3157 3163 3160 3182 C1' A R 16 beta 3177 3183 3180 3204 C1' U R 17 beta 3199 3205 3202 3224 C1' G R 18 beta 3219 3225 3222 3245 C1' U S 4 beta 3240 3246 3243 3265 C1' G S 5 beta 3260 3266 3263 3288 C1' A S 6 beta 3283 3289 3286 3310 C1' G S 7 beta 3305 3311 3308 3333 C1' G S 8 beta 3328 3334 3331 3356 C1' C S 9 beta 3351 3357 3354 3376 C1' U S 10 beta 3371 3377 3374 3396 C1' C S 11 beta 3391 3397 3394 3416 C1' A S 12 beta 3411 3417 3414 3438 C1' C S 13 beta 3433 3439 3436 3458 C1' C S 14 beta 3453 3459 3456 3478 C1' C S 15 beta 3473 3479 3476 3498 C1' A S 16 beta 3493 3499 3496 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C R 9 OK 3040 3036 3039 3058 C2' U R 10 OK 3060 3056 3059 3078 C2' C R 11 OK 3080 3076 3079 3098 C2' A R 12 OK 3100 3096 3099 3120 C2' C R 13 OK 3122 3118 3121 3140 C2' C R 14 OK 3142 3138 3141 3160 C2' C R 15 OK 3162 3158 3161 3180 C2' A R 16 OK 3182 3178 3181 3202 C2' U R 17 OK 3204 3200 3203 3222 C2' G R 18 OK 3224 3220 3223 3243 C2' U S 4 OK 3245 3241 3244 3263 C2' G S 5 OK 3265 3261 3264 3286 C2' A S 6 OK 3288 3284 3287 3308 C2' G S 7 OK 3310 3306 3309 3331 C2' G S 8 OK 3333 3329 3332 3354 C2' C S 9 OK 3356 3352 3355 3374 C2' U S 10 OK 3376 3372 3375 3394 C2' C S 11 OK 3396 3392 3395 3414 C2' A S 12 OK 3416 3412 3415 3436 C2' C S 13 OK 3438 3434 3437 3456 C2' C S 14 OK 3458 3454 3457 3476 C2' C S 15 OK 3478 3474 3477 3496 C2' A S 16 OK 3498 3494 3497 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C R 9 OK 3034 3037 3038 3056 C3' U R 10 OK 3054 3057 3058 3076 C3' C R 11 OK 3074 3077 3078 3096 C3' A R 12 OK 3094 3097 3098 3118 C3' C R 13 OK 3116 3119 3120 3138 C3' C R 14 OK 3136 3139 3140 3158 C3' C R 15 OK 3156 3159 3160 3178 C3' A R 16 OK 3176 3179 3180 3200 C3' U R 17 OK 3198 3201 3202 3220 C3' G R 18 OK 3218 3221 3222 3241 C3' U S 4 OK 3239 3242 3243 3261 C3' G S 5 OK 3259 3262 3263 3284 C3' A S 6 OK 3282 3285 3286 3306 C3' G S 7 OK 3304 3307 3308 3329 C3' G S 8 OK 3327 3330 3331 3352 C3' C S 9 OK 3350 3353 3354 3372 C3' U S 10 OK 3370 3373 3374 3392 C3' C S 11 OK 3390 3393 3394 3412 C3' A S 12 OK 3410 3413 3414 3434 C3' C S 13 OK 3432 3435 3436 3454 C3' C S 14 OK 3452 3455 3456 3474 C3' C S 15 OK 3472 3475 3476 3494 C3' A S 16 OK 3492 3495 3496 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C R 9 OK 3036 3033 3035 3054 C4' U R 10 OK 3056 3053 3055 3074 C4' C R 11 OK 3076 3073 3075 3094 C4' A R 12 OK 3096 3093 3095 3116 C4' C R 13 OK 3118 3115 3117 3136 C4' C R 14 OK 3138 3135 3137 3156 C4' C R 15 OK 3158 3155 3157 3176 C4' A R 16 OK 3178 3175 3177 3198 C4' U R 17 OK 3200 3197 3199 3218 C4' G R 18 OK 3220 3217 3219 3239 C4' U S 4 OK 3241 3238 3240 3259 C4' G S 5 OK 3261 3258 3260 3282 C4' A S 6 OK 3284 3281 3283 3304 C4' G S 7 OK 3306 3303 3305 3327 C4' G S 8 OK 3329 3326 3328 3350 C4' C S 9 OK 3352 3349 3351 3370 C4' U S 10 OK 3372 3369 3371 3390 C4' C S 11 OK 3392 3389 3391 3410 C4' A S 12 OK 3412 3409 3411 3432 C4' C S 13 OK 3434 3431 3433 3452 C4' C S 14 OK 3454 3451 3453 3472 C4' C S 15 OK 3474 3471 3473 3492 C4' A S 16 OK 3494 3491 3493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C R 9 3032 3034 3053 C5' U R 10 3052 3054 3073 C5' C R 11 3072 3074 3093 C5' A R 12 3092 3094 3115 C5' C R 13 3114 3116 3135 C5' C R 14 3134 3136 3155 C5' C R 15 3154 3156 3175 C5' A R 16 3174 3176 3197 C5' U R 17 3196 3198 3217 C5' G R 18 3216 3218 3238 C5' U S 4 3237 3239 3258 C5' G S 5 3257 3259 3281 C5' A S 6 3280 3282 3303 C5' G S 7 3302 3304 3326 C5' G S 8 3325 3327 3349 C5' C S 9 3348 3350 3369 C5' U S 10 3368 3370 3389 C5' C S 11 3388 3390 3409 C5' A S 12 3408 3410 3431 C5' C S 13 3430 3432 3451 C5' C S 14 3450 3452 3471 C5' C S 15 3470 3472 3491 C5' A S 16 3490 3492 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 C R 9 distorted distorted 3014 3030 3031 3032 3049 P U R 10 distorted distorted 3037 3050 3051 3052 3069 P C R 11 distorted distorted 3057 3070 3071 3072 3089 P A R 12 distorted distorted 3077 3090 3091 3092 3111 P C R 13 distorted distorted 3097 3112 3113 3114 3131 P C R 14 distorted distorted 3119 3132 3133 3134 3151 P C R 15 distorted distorted 3139 3152 3153 3154 3171 P A R 16 distorted distorted 3159 3172 3173 3174 3193 P U R 17 distorted distorted 3179 3194 3195 3196 3213 P G R 18 distorted distorted 3201 3214 3215 3216 3254 P G S 5 distorted distorted 3242 3255 3256 3257 3277 P A S 6 distorted distorted 3262 3278 3279 3280 3299 P G S 7 distorted distorted 3285 3300 3301 3302 3322 P G S 8 distorted distorted 3307 3323 3324 3325 3345 P C S 9 distorted distorted 3330 3346 3347 3348 3365 P U S 10 distorted distorted 3353 3366 3367 3368 3385 P C S 11 distorted distorted 3373 3386 3387 3388 3405 P A S 12 distorted distorted 3393 3406 3407 3408 3427 P C S 13 distorted distorted 3413 3428 3429 3430 3447 P C S 14 distorted distorted 3435 3448 3449 3450 3467 P C S 15 distorted distorted 3455 3468 3469 3470 3487 P A S 16 distorted distorted 3475 3488 3489 3490 ---------------------------------------------------------------------------------