ID code: '2B2E' 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' --------------------------------------------------------------------------------- 2901 C1' A R 302 beta 2896 2902 2899 2923 C1' U R 303 beta 2918 2924 2921 2943 C1' G R 304 beta 2938 2944 2941 2966 C1' A R 305 beta 2961 2967 2964 2988 C1' G R 306 beta 2983 2989 2986 3011 C1' G R 307 beta 3006 3012 3009 3034 C1' A R 308 beta 3029 3035 3032 3056 C1' U R 309 beta 3051 3057 3054 3076 C1' U R 310 beta 3071 3077 3074 3096 C1' A R 311 beta 3091 3097 3094 3118 C1' C R 312 beta 3113 3119 3116 3138 C1' C R 313 beta 3133 3139 3136 3158 C1' C R 314 beta 3153 3159 3156 3178 C1' A R 315 beta 3173 3179 3176 3200 C1' U R 316 beta 3195 3201 3198 3220 C1' G R 317 beta 3215 3221 3218 3244 C1' U S 403 beta 3239 3245 3242 3264 C1' G S 404 beta 3259 3265 3262 3287 C1' A S 405 beta 3282 3288 3285 3309 C1' G S 406 beta 3304 3310 3307 3332 C1' G S 407 beta 3327 3333 3330 3355 C1' A S 408 beta 3350 3356 3353 3377 C1' U S 409 beta 3372 3378 3375 3397 C1' U S 410 beta 3392 3398 3395 3417 C1' A S 411 beta 3412 3418 3415 3439 C1' C S 412 beta 3434 3440 3437 3459 C1' C S 413 beta 3454 3460 3457 3479 C1' C S 414 beta 3474 3480 3477 3499 C1' A S 415 beta 3494 3500 3497 3521 C1' U S 416 beta 3516 3522 3519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2899 C2' A R 302 OK 2901 2897 2900 2921 C2' U R 303 OK 2923 2919 2922 2941 C2' G R 304 OK 2943 2939 2942 2964 C2' A R 305 OK 2966 2962 2965 2986 C2' G R 306 OK 2988 2984 2987 3009 C2' G R 307 OK 3011 3007 3010 3032 C2' A R 308 OK 3034 3030 3033 3054 C2' U R 309 OK 3056 3052 3055 3074 C2' U R 310 OK 3076 3072 3075 3094 C2' A R 311 OK 3096 3092 3095 3116 C2' C R 312 OK 3118 3114 3117 3136 C2' C R 313 OK 3138 3134 3137 3156 C2' C R 314 OK 3158 3154 3157 3176 C2' A R 315 OK 3178 3174 3177 3198 C2' U R 316 OK 3200 3196 3199 3218 C2' G R 317 OK 3220 3216 3219 3242 C2' U S 403 OK 3244 3240 3243 3262 C2' G S 404 OK 3264 3260 3263 3285 C2' A S 405 OK 3287 3283 3286 3307 C2' G S 406 OK 3309 3305 3308 3330 C2' G S 407 OK 3332 3328 3331 3353 C2' A S 408 OK 3355 3351 3354 3375 C2' U S 409 OK 3377 3373 3376 3395 C2' U S 410 OK 3397 3393 3396 3415 C2' A S 411 OK 3417 3413 3416 3437 C2' C S 412 OK 3439 3435 3438 3457 C2' C S 413 OK 3459 3455 3458 3477 C2' C S 414 OK 3479 3475 3478 3497 C2' A S 415 OK 3499 3495 3498 3519 C2' U S 416 OK 3521 3517 3520 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2897 C3' A R 302 OK 2895 2898 2899 2919 C3' U R 303 OK 2917 2920 2921 2939 C3' G R 304 OK 2937 2940 2941 2962 C3' A R 305 OK 2960 2963 2964 2984 C3' G R 306 OK 2982 2985 2986 3007 C3' G R 307 OK 3005 3008 3009 3030 C3' A R 308 OK 3028 3031 3032 3052 C3' U R 309 OK 3050 3053 3054 3072 C3' U R 310 OK 3070 3073 3074 3092 C3' A R 311 OK 3090 3093 3094 3114 C3' C R 312 OK 3112 3115 3116 3134 C3' C R 313 OK 3132 3135 3136 3154 C3' C R 314 OK 3152 3155 3156 3174 C3' A R 315 OK 3172 3175 3176 3196 C3' U R 316 OK 3194 3197 3198 3216 C3' G R 317 OK 3214 3217 3218 3240 C3' U S 403 OK 3238 3241 3242 3260 C3' G S 404 OK 3258 3261 3262 3283 C3' A S 405 OK 3281 3284 3285 3305 C3' G S 406 OK 3303 3306 3307 3328 C3' G S 407 OK 3326 3329 3330 3351 C3' A S 408 OK 3349 3352 3353 3373 C3' U S 409 OK 3371 3374 3375 3393 C3' U S 410 OK 3391 3394 3395 3413 C3' A S 411 OK 3411 3414 3415 3435 C3' C S 412 OK 3433 3436 3437 3455 C3' C S 413 OK 3453 3456 3457 3475 C3' C S 414 OK 3473 3476 3477 3495 C3' A S 415 OK 3493 3496 3497 3517 C3' U S 416 OK 3515 3518 3519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2895 C4' A R 302 OK 2897 2894 2896 2917 C4' U R 303 OK 2919 2916 2918 2937 C4' G R 304 OK 2939 2936 2938 2960 C4' A R 305 OK 2962 2959 2961 2982 C4' G R 306 OK 2984 2981 2983 3005 C4' G R 307 OK 3007 3004 3006 3028 C4' A R 308 OK 3030 3027 3029 3050 C4' U R 309 OK 3052 3049 3051 3070 C4' U R 310 OK 3072 3069 3071 3090 C4' A R 311 OK 3092 3089 3091 3112 C4' C R 312 OK 3114 3111 3113 3132 C4' C R 313 OK 3134 3131 3133 3152 C4' C R 314 OK 3154 3151 3153 3172 C4' A R 315 OK 3174 3171 3173 3194 C4' U R 316 OK 3196 3193 3195 3214 C4' G R 317 OK 3216 3213 3215 3238 C4' U S 403 OK 3240 3237 3239 3258 C4' G S 404 OK 3260 3257 3259 3281 C4' A S 405 OK 3283 3280 3282 3303 C4' G S 406 OK 3305 3302 3304 3326 C4' G S 407 OK 3328 3325 3327 3349 C4' A S 408 OK 3351 3348 3350 3371 C4' U S 409 OK 3373 3370 3372 3391 C4' U S 410 OK 3393 3390 3392 3411 C4' A S 411 OK 3413 3410 3412 3433 C4' C S 412 OK 3435 3432 3434 3453 C4' C S 413 OK 3455 3452 3454 3473 C4' C S 414 OK 3475 3472 3474 3493 C4' A S 415 OK 3495 3492 3494 3515 C4' U S 416 OK 3517 3514 3516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2894 C5' A R 302 2893 2895 2916 C5' U R 303 2915 2917 2936 C5' G R 304 2935 2937 2959 C5' A R 305 2958 2960 2981 C5' G R 306 2980 2982 3004 C5' G R 307 3003 3005 3027 C5' A R 308 3026 3028 3049 C5' U R 309 3048 3050 3069 C5' U R 310 3068 3070 3089 C5' A R 311 3088 3090 3111 C5' C R 312 3110 3112 3131 C5' C R 313 3130 3132 3151 C5' C R 314 3150 3152 3171 C5' A R 315 3170 3172 3193 C5' U R 316 3192 3194 3213 C5' G R 317 3212 3214 3237 C5' U S 403 3236 3238 3257 C5' G S 404 3256 3258 3280 C5' A S 405 3279 3281 3302 C5' G S 406 3301 3303 3325 C5' G S 407 3324 3326 3348 C5' A S 408 3347 3349 3370 C5' U S 409 3369 3371 3390 C5' U S 410 3389 3391 3410 C5' A S 411 3409 3411 3432 C5' C S 412 3431 3433 3452 C5' C S 413 3451 3453 3472 C5' C S 414 3471 3473 3492 C5' A S 415 3491 3493 3514 C5' U S 416 3513 3515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2890 P A R 302 OK OK 2891 2892 2893 2912 P U R 303 distorted distorted 2898 2913 2914 2915 2932 P G R 304 distorted distorted 2920 2933 2934 2935 2955 P A R 305 distorted distorted 2940 2956 2957 2958 2977 P G R 306 distorted distorted 2963 2978 2979 2980 3000 P G R 307 distorted distorted 2985 3001 3002 3003 3023 P A R 308 distorted distorted 3008 3024 3025 3026 3045 P U R 309 distorted distorted 3031 3046 3047 3048 3065 P U R 310 distorted distorted 3053 3066 3067 3068 3085 P A R 311 distorted distorted 3073 3086 3087 3088 3107 P C R 312 distorted distorted 3093 3108 3109 3110 3127 P C R 313 distorted distorted 3115 3128 3129 3130 3147 P C R 314 distorted distorted 3135 3148 3149 3150 3167 P A R 315 distorted distorted 3155 3168 3169 3170 3189 P U R 316 distorted distorted 3175 3190 3191 3192 3209 P G R 317 distorted distorted 3197 3210 3211 3212 3233 P U S 403 OK OK 3234 3235 3236 3253 P G S 404 distorted distorted 3241 3254 3255 3256 3276 P A S 405 distorted distorted 3261 3277 3278 3279 3298 P G S 406 distorted distorted 3284 3299 3300 3301 3321 P G S 407 distorted distorted 3306 3322 3323 3324 3344 P A S 408 distorted distorted 3329 3345 3346 3347 3366 P U S 409 distorted distorted 3352 3367 3368 3369 3386 P U S 410 distorted distorted 3374 3387 3388 3389 3406 P A S 411 distorted distorted 3394 3407 3408 3409 3428 P C S 412 distorted distorted 3414 3429 3430 3431 3448 P C S 413 distorted distorted 3436 3449 3450 3451 3468 P C S 414 distorted distorted 3456 3469 3470 3471 3488 P A S 415 distorted distorted 3476 3489 3490 3491 3510 P U S 416 distorted distorted 3496 3511 3512 3513 ---------------------------------------------------------------------------------