ID code: '2IZ9' 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' ONE R 11 beta 3077 3083 3079 3101 C1' A R 12 beta 3096 3102 3099 3123 C1' C R 13 beta 3118 3124 3121 3143 C1' C R 14 beta 3138 3144 3141 3163 C1' C R 15 beta 3158 3164 3161 3183 C1' A R 16 beta 3178 3184 3181 3205 C1' U R 17 beta 3200 3206 3203 3223 C1' A S 3 beta 3218 3224 3221 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' A S 9 beta 3351 3357 3354 3378 C1' U S 10 beta 3373 3379 3376 3398 C1' ONE S 11 beta 3393 3399 3395 3417 C1' A S 12 beta 3412 3418 3415 3439 C1' C S 13 beta 3434 3440 3437 3459 C1' C S 14 beta 3454 3460 3457 3479 C1' C S 15 beta 3474 3480 3477 3499 C1' A S 16 beta 3494 3500 3497 3521 C1' U S 17 beta 3516 3522 3519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 3079 C2' ONE R 11 OK 3082 3078 3080 3099 C2' A R 12 OK 3101 3097 3100 3121 C2' C R 13 OK 3123 3119 3122 3141 C2' C R 14 OK 3143 3139 3142 3161 C2' C R 15 OK 3163 3159 3162 3181 C2' A R 16 OK 3183 3179 3182 3203 C2' U R 17 OK 3205 3201 3204 3221 C2' A S 3 OK 3223 3219 3222 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' A S 9 OK 3356 3352 3355 3376 C2' U S 10 OK 3378 3374 3377 3395 C2' ONE S 11 OK 3398 3394 3396 3415 C2' A S 12 OK 3417 3413 3416 3437 C2' C S 13 OK 3439 3435 3438 3457 C2' C S 14 OK 3459 3455 3458 3477 C2' C S 15 OK 3479 3475 3478 3497 C2' A S 16 OK 3499 3495 3498 3519 C2' U S 17 OK 3521 3517 3520 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' ONE R 11 OK 3076 3081 3079 3097 C3' A R 12 OK 3095 3098 3099 3119 C3' C R 13 OK 3117 3120 3121 3139 C3' C R 14 OK 3137 3140 3141 3159 C3' C R 15 OK 3157 3160 3161 3179 C3' A R 16 OK 3177 3180 3181 3201 C3' U R 17 OK 3199 3202 3203 3219 C3' A S 3 OK 3217 3220 3221 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' A S 9 OK 3350 3353 3354 3374 C3' U S 10 OK 3372 3375 3376 3394 C3' ONE S 11 OK 3392 3397 3395 3413 C3' A S 12 OK 3411 3414 3415 3435 C3' C S 13 OK 3433 3436 3437 3455 C3' C S 14 OK 3453 3456 3457 3475 C3' C S 15 OK 3473 3476 3477 3495 C3' A S 16 OK 3493 3496 3497 3517 C3' U S 17 OK 3515 3518 3519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' ONE R 11 OK 3078 3075 3077 3095 C4' A R 12 OK 3097 3094 3096 3117 C4' C R 13 OK 3119 3116 3118 3137 C4' C R 14 OK 3139 3136 3138 3157 C4' C R 15 OK 3159 3156 3158 3177 C4' A R 16 OK 3179 3176 3178 3199 C4' U R 17 OK 3201 3198 3200 3217 C4' A S 3 OK 3219 3216 3218 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' A S 9 OK 3352 3349 3351 3372 C4' U S 10 OK 3374 3371 3373 3392 C4' ONE S 11 OK 3394 3391 3393 3411 C4' A S 12 OK 3413 3410 3412 3433 C4' C S 13 OK 3435 3432 3434 3453 C4' C S 14 OK 3455 3452 3454 3473 C4' C S 15 OK 3475 3472 3474 3493 C4' A S 16 OK 3495 3492 3494 3515 C4' U S 17 OK 3517 3514 3516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' ONE R 11 3074 3076 3094 C5' A R 12 3093 3095 3116 C5' C R 13 3115 3117 3136 C5' C R 14 3135 3137 3156 C5' C R 15 3155 3157 3176 C5' A R 16 3175 3177 3198 C5' U R 17 3197 3199 3216 C5' A S 3 3215 3217 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' A S 9 3348 3350 3371 C5' U S 10 3370 3372 3391 C5' ONE S 11 3390 3392 3410 C5' A S 12 3409 3411 3432 C5' C S 13 3431 3433 3452 C5' C S 14 3451 3453 3472 C5' C S 15 3471 3473 3492 C5' A S 16 3491 3493 3514 C5' U S 17 3513 3515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 ONE R 11 distorted distorted 3059 3072 3073 3074 3090 P A R 12 distorted distorted 3081 3091 3092 3093 3112 P C R 13 distorted distorted 3098 3113 3114 3115 3132 P C R 14 distorted distorted 3120 3133 3134 3135 3152 P C R 15 distorted distorted 3140 3153 3154 3155 3172 P A R 16 distorted distorted 3160 3173 3174 3175 3194 P U R 17 distorted distorted 3180 3195 3196 3197 3234 P U S 4 distorted distorted 3220 3235 3236 3237 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 A S 9 distorted distorted 3330 3346 3347 3348 3367 P U S 10 distorted distorted 3353 3368 3369 3370 3387 P ONE S 11 distorted distorted 3375 3388 3389 3390 3406 P A S 12 distorted distorted 3397 3407 3408 3409 3428 P C S 13 distorted distorted 3414 3429 3430 3431 3448 P C S 14 distorted distorted 3436 3449 3450 3451 3468 P C S 15 distorted distorted 3456 3469 3470 3471 3488 P A S 16 distorted distorted 3476 3489 3490 3491 3510 P U S 17 distorted distorted 3496 3511 3512 3513 ---------------------------------------------------------------------------------