ID code: '2C4Y' 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' C R 2 beta 2902 2908 2905 2927 C1' A R 3 beta 2922 2928 2925 2949 C1' U R 4 beta 2944 2950 2947 2969 C1' G R 5 beta 2964 2970 2967 2992 C1' A R 6 beta 2987 2993 2990 3014 C1' G R 7 beta 3009 3015 3012 3037 C1' G R 8 beta 3032 3038 3035 3060 C1' A R 9 beta 3055 3061 3058 3082 C1' U R 10 beta 3077 3083 3080 3099 C1' SUR R 11 beta 3097 3100 3101 3122 C1' A R 12 beta 3117 3123 3120 3144 C1' C R 13 beta 3139 3145 3142 3164 C1' C R 14 beta 3159 3165 3162 3184 C1' C R 15 beta 3179 3185 3182 3204 C1' A R 16 beta 3199 3205 3202 3226 C1' U R 17 beta 3221 3227 3224 3246 C1' G R 18 beta 3241 3247 3244 3267 C1' U S 4 beta 3262 3268 3265 3287 C1' G S 5 beta 3282 3288 3285 3310 C1' A S 6 beta 3305 3311 3308 3332 C1' G S 7 beta 3327 3333 3330 3355 C1' G S 8 beta 3350 3356 3353 3378 C1' A S 9 beta 3373 3379 3376 3400 C1' U S 10 beta 3395 3401 3398 3417 C1' SUR S 11 beta 3415 3418 3419 3440 C1' A S 12 beta 3435 3441 3438 3462 C1' C S 13 beta 3457 3463 3460 3482 C1' C S 14 beta 3477 3483 3480 3502 C1' C S 15 beta 3497 3503 3500 3522 C1' A S 16 beta 3517 3523 3520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2905 C2' C R 2 OK 2907 2903 2906 2925 C2' A R 3 OK 2927 2923 2926 2947 C2' U R 4 OK 2949 2945 2948 2967 C2' G R 5 OK 2969 2965 2968 2990 C2' A R 6 OK 2992 2988 2991 3012 C2' G R 7 OK 3014 3010 3013 3035 C2' G R 8 OK 3037 3033 3036 3058 C2' A R 9 OK 3060 3056 3059 3080 C2' U R 10 OK 3082 3078 3081 3101 C2' SUR R 11 OK 3099 3098 3109 3120 C2' A R 12 OK 3122 3118 3121 3142 C2' C R 13 OK 3144 3140 3143 3162 C2' C R 14 OK 3164 3160 3163 3182 C2' C R 15 OK 3184 3180 3183 3202 C2' A R 16 OK 3204 3200 3203 3224 C2' U R 17 OK 3226 3222 3225 3244 C2' G R 18 OK 3246 3242 3245 3265 C2' U S 4 OK 3267 3263 3266 3285 C2' G S 5 OK 3287 3283 3286 3308 C2' A S 6 OK 3310 3306 3309 3330 C2' G S 7 OK 3332 3328 3331 3353 C2' G S 8 OK 3355 3351 3354 3376 C2' A S 9 OK 3378 3374 3377 3398 C2' U S 10 OK 3400 3396 3399 3419 C2' SUR S 11 OK 3417 3416 3427 3438 C2' A S 12 OK 3440 3436 3439 3460 C2' C S 13 OK 3462 3458 3461 3480 C2' C S 14 OK 3482 3478 3481 3500 C2' C S 15 OK 3502 3498 3501 3520 C2' A S 16 OK 3522 3518 3521 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2903 C3' C R 2 OK 2901 2904 2905 2923 C3' A R 3 OK 2921 2924 2925 2945 C3' U R 4 OK 2943 2946 2947 2965 C3' G R 5 OK 2963 2966 2967 2988 C3' A R 6 OK 2986 2989 2990 3010 C3' G R 7 OK 3008 3011 3012 3033 C3' G R 8 OK 3031 3034 3035 3056 C3' A R 9 OK 3054 3057 3058 3078 C3' U R 10 OK 3076 3079 3080 3098 C3' SUR R 11 OK 3096 3110 3101 3118 C3' A R 12 OK 3116 3119 3120 3140 C3' C R 13 OK 3138 3141 3142 3160 C3' C R 14 OK 3158 3161 3162 3180 C3' C R 15 OK 3178 3181 3182 3200 C3' A R 16 OK 3198 3201 3202 3222 C3' U R 17 OK 3220 3223 3224 3242 C3' G R 18 OK 3240 3243 3244 3263 C3' U S 4 OK 3261 3264 3265 3283 C3' G S 5 OK 3281 3284 3285 3306 C3' A S 6 OK 3304 3307 3308 3328 C3' G S 7 OK 3326 3329 3330 3351 C3' G S 8 OK 3349 3352 3353 3374 C3' A S 9 OK 3372 3375 3376 3396 C3' U S 10 OK 3394 3397 3398 3416 C3' SUR S 11 OK 3414 3428 3419 3436 C3' A S 12 OK 3434 3437 3438 3458 C3' C S 13 OK 3456 3459 3460 3478 C3' C S 14 OK 3476 3479 3480 3498 C3' C S 15 OK 3496 3499 3500 3518 C3' A S 16 OK 3516 3519 3520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2901 C4' C R 2 OK 2903 2900 2902 2921 C4' A R 3 OK 2923 2920 2922 2943 C4' U R 4 OK 2945 2942 2944 2963 C4' G R 5 OK 2965 2962 2964 2986 C4' A R 6 OK 2988 2985 2987 3008 C4' G R 7 OK 3010 3007 3009 3031 C4' G R 8 OK 3033 3030 3032 3054 C4' A R 9 OK 3056 3053 3055 3076 C4' U R 10 OK 3078 3075 3077 3096 C4' SUR R 11 OK 3098 3095 3097 3116 C4' A R 12 OK 3118 3115 3117 3138 C4' C R 13 OK 3140 3137 3139 3158 C4' C R 14 OK 3160 3157 3159 3178 C4' C R 15 OK 3180 3177 3179 3198 C4' A R 16 OK 3200 3197 3199 3220 C4' U R 17 OK 3222 3219 3221 3240 C4' G R 18 OK 3242 3239 3241 3261 C4' U S 4 OK 3263 3260 3262 3281 C4' G S 5 OK 3283 3280 3282 3304 C4' A S 6 OK 3306 3303 3305 3326 C4' G S 7 OK 3328 3325 3327 3349 C4' G S 8 OK 3351 3348 3350 3372 C4' A S 9 OK 3374 3371 3373 3394 C4' U S 10 OK 3396 3393 3395 3414 C4' SUR S 11 OK 3416 3413 3415 3434 C4' A S 12 OK 3436 3433 3435 3456 C4' C S 13 OK 3458 3455 3457 3476 C4' C S 14 OK 3478 3475 3477 3496 C4' C S 15 OK 3498 3495 3497 3516 C4' A S 16 OK 3518 3515 3517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2900 C5' C R 2 2899 2901 2920 C5' A R 3 2919 2921 2942 C5' U R 4 2941 2943 2962 C5' G R 5 2961 2963 2985 C5' A R 6 2984 2986 3007 C5' G R 7 3006 3008 3030 C5' G R 8 3029 3031 3053 C5' A R 9 3052 3054 3075 C5' U R 10 3074 3076 3095 C5' SUR R 11 3094 3096 3115 C5' A R 12 3114 3116 3137 C5' C R 13 3136 3138 3157 C5' C R 14 3156 3158 3177 C5' C R 15 3176 3178 3197 C5' A R 16 3196 3198 3219 C5' U R 17 3218 3220 3239 C5' G R 18 3238 3240 3260 C5' U S 4 3259 3261 3280 C5' G S 5 3279 3281 3303 C5' A S 6 3302 3304 3325 C5' G S 7 3324 3326 3348 C5' G S 8 3347 3349 3371 C5' A S 9 3370 3372 3393 C5' U S 10 3392 3394 3413 C5' SUR S 11 3412 3414 3433 C5' A S 12 3432 3434 3455 C5' C S 13 3454 3456 3475 C5' C S 14 3474 3476 3495 C5' C S 15 3494 3496 3515 C5' A S 16 3514 3516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2916 P A R 3 distorted distorted 2904 2917 2918 2919 2938 P U R 4 distorted distorted 2924 2939 2940 2941 2958 P G R 5 distorted distorted 2946 2959 2960 2961 2981 P A R 6 distorted distorted 2966 2982 2983 2984 3003 P G R 7 distorted distorted 2989 3004 3005 3006 3026 P G R 8 distorted distorted 3011 3027 3028 3029 3049 P A R 9 distorted distorted 3034 3050 3051 3052 3071 P U R 10 distorted distorted 3057 3072 3073 3074 3091 P SUR R 11 distorted distorted 3079 3092 3093 3094 3111 P A R 12 distorted distorted 3110 3112 3113 3114 3133 P C R 13 distorted distorted 3119 3134 3135 3136 3153 P C R 14 distorted distorted 3141 3154 3155 3156 3173 P C R 15 distorted distorted 3161 3174 3175 3176 3193 P A R 16 distorted distorted 3181 3194 3195 3196 3215 P U R 17 distorted distorted 3201 3216 3217 3218 3235 P G R 18 distorted distorted 3223 3236 3237 3238 3276 P G S 5 distorted distorted 3264 3277 3278 3279 3299 P A S 6 distorted distorted 3284 3300 3301 3302 3321 P G S 7 distorted distorted 3307 3322 3323 3324 3344 P G S 8 distorted distorted 3329 3345 3346 3347 3367 P A S 9 distorted distorted 3352 3368 3369 3370 3389 P U S 10 distorted distorted 3375 3390 3391 3392 3409 P SUR S 11 distorted distorted 3397 3410 3411 3412 3429 P A S 12 distorted distorted 3428 3430 3431 3432 3451 P C S 13 distorted distorted 3437 3452 3453 3454 3471 P C S 14 distorted distorted 3459 3472 3473 3474 3491 P C S 15 distorted distorted 3479 3492 3493 3494 3511 P A S 16 distorted distorted 3499 3512 3513 3514 ---------------------------------------------------------------------------------