ID code: '1U1Y' 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' --------------------------------------------------------------------------------- 2904 C1' C R 1 beta 2899 2905 2902 2924 C1' C R 2 beta 2919 2925 2922 2944 C1' G R 3 beta 2939 2945 2942 2967 C1' G R 4 beta 2962 2968 2965 2989 C1' 2PR R 5 beta 2985 2990 2988 3011 C1' G R 6 beta 3006 3012 3009 3034 C1' G R 7 beta 3029 3035 3032 3057 C1' A R 8 beta 3052 3058 3055 3079 C1' U R 9 beta 3074 3080 3077 3099 C1' C R 10 beta 3094 3100 3097 3119 C1' A R 11 beta 3114 3120 3117 3141 C1' C R 12 beta 3136 3142 3139 3161 C1' C R 13 beta 3156 3162 3159 3181 C1' A R 14 beta 3176 3182 3179 3203 C1' C R 15 beta 3198 3204 3201 3223 C1' G R 16 beta 3218 3224 3221 3243 C1' G R 17 beta 3241 3244 3242 3267 C1' C S 102 beta 3262 3268 3265 3287 C1' G S 103 beta 3282 3288 3285 3310 C1' G S 104 beta 3305 3311 3308 3332 C1' 2PR S 105 beta 3328 3333 3331 3354 C1' G S 106 beta 3349 3355 3352 3377 C1' G S 107 beta 3372 3378 3375 3400 C1' A S 108 beta 3395 3401 3398 3422 C1' U S 109 beta 3417 3423 3420 3442 C1' C S 110 beta 3437 3443 3440 3462 C1' A S 111 beta 3457 3463 3460 3484 C1' C S 112 beta 3479 3485 3482 3504 C1' C S 113 beta 3499 3505 3502 3524 C1' A S 114 beta 3519 3525 3522 3546 C1' C S 115 beta 3541 3547 3544 3566 C1' G S 116 beta 3561 3567 3564 3589 C1' G S 117 beta 3584 3590 3587 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2902 C2' C R 1 OK 2904 2900 2903 2922 C2' C R 2 OK 2924 2920 2923 2942 C2' G R 3 OK 2944 2940 2943 2965 C2' G R 4 OK 2967 2963 2966 2988 C2' 2PR R 5 2989 2986 3009 C2' G R 6 OK 3011 3007 3010 3032 C2' G R 7 OK 3034 3030 3033 3055 C2' A R 8 OK 3057 3053 3056 3077 C2' U R 9 OK 3079 3075 3078 3097 C2' C R 10 OK 3099 3095 3098 3117 C2' A R 11 OK 3119 3115 3118 3139 C2' C R 12 OK 3141 3137 3140 3159 C2' C R 13 OK 3161 3157 3160 3179 C2' A R 14 OK 3181 3177 3180 3201 C2' C R 15 OK 3203 3199 3202 3221 C2' G R 16 OK 3223 3219 3222 3242 C2' G R 17 3243 3265 C2' C S 102 OK 3267 3263 3266 3285 C2' G S 103 OK 3287 3283 3286 3308 C2' G S 104 OK 3310 3306 3309 3331 C2' 2PR S 105 3332 3329 3352 C2' G S 106 OK 3354 3350 3353 3375 C2' G S 107 OK 3377 3373 3376 3398 C2' A S 108 OK 3400 3396 3399 3420 C2' U S 109 OK 3422 3418 3421 3440 C2' C S 110 OK 3442 3438 3441 3460 C2' A S 111 OK 3462 3458 3461 3482 C2' C S 112 OK 3484 3480 3483 3502 C2' C S 113 OK 3504 3500 3503 3522 C2' A S 114 OK 3524 3520 3523 3544 C2' C S 115 OK 3546 3542 3545 3564 C2' G S 116 OK 3566 3562 3565 3587 C2' G S 117 OK 3589 3585 3588 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2900 C3' C R 1 OK 2898 2901 2902 2920 C3' C R 2 OK 2918 2921 2922 2940 C3' G R 3 OK 2938 2941 2942 2963 C3' G R 4 OK 2961 2964 2965 2986 C3' 2PR R 5 OK 2984 2987 2988 3007 C3' G R 6 OK 3005 3008 3009 3030 C3' G R 7 OK 3028 3031 3032 3053 C3' A R 8 OK 3051 3054 3055 3075 C3' U R 9 OK 3073 3076 3077 3095 C3' C R 10 OK 3093 3096 3097 3115 C3' A R 11 OK 3113 3116 3117 3137 C3' C R 12 OK 3135 3138 3139 3157 C3' C R 13 OK 3155 3158 3159 3177 C3' A R 14 OK 3175 3178 3179 3199 C3' C R 15 OK 3197 3200 3201 3219 C3' G R 16 OK 3217 3220 3221 3263 C3' C S 102 OK 3261 3264 3265 3283 C3' G S 103 OK 3281 3284 3285 3306 C3' G S 104 OK 3304 3307 3308 3329 C3' 2PR S 105 OK 3327 3330 3331 3350 C3' G S 106 OK 3348 3351 3352 3373 C3' G S 107 OK 3371 3374 3375 3396 C3' A S 108 OK 3394 3397 3398 3418 C3' U S 109 OK 3416 3419 3420 3438 C3' C S 110 OK 3436 3439 3440 3458 C3' A S 111 OK 3456 3459 3460 3480 C3' C S 112 OK 3478 3481 3482 3500 C3' C S 113 OK 3498 3501 3502 3520 C3' A S 114 OK 3518 3521 3522 3542 C3' C S 115 OK 3540 3543 3544 3562 C3' G S 116 OK 3560 3563 3564 3585 C3' G S 117 OK 3583 3586 3587 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2898 C4' C R 1 OK 2900 2897 2899 2918 C4' C R 2 OK 2920 2917 2919 2938 C4' G R 3 OK 2940 2937 2939 2961 C4' G R 4 OK 2963 2960 2962 2984 C4' 2PR R 5 OK 2986 2983 2985 3005 C4' G R 6 OK 3007 3004 3006 3028 C4' G R 7 OK 3030 3027 3029 3051 C4' A R 8 OK 3053 3050 3052 3073 C4' U R 9 OK 3075 3072 3074 3093 C4' C R 10 OK 3095 3092 3094 3113 C4' A R 11 OK 3115 3112 3114 3135 C4' C R 12 OK 3137 3134 3136 3155 C4' C R 13 OK 3157 3154 3156 3175 C4' A R 14 OK 3177 3174 3176 3197 C4' C R 15 OK 3199 3196 3198 3217 C4' G R 16 OK 3219 3216 3218 3240 C4' G R 17 3239 3241 3261 C4' C S 102 OK 3263 3260 3262 3281 C4' G S 103 OK 3283 3280 3282 3304 C4' G S 104 OK 3306 3303 3305 3327 C4' 2PR S 105 OK 3329 3326 3328 3348 C4' G S 106 OK 3350 3347 3349 3371 C4' G S 107 OK 3373 3370 3372 3394 C4' A S 108 OK 3396 3393 3395 3416 C4' U S 109 OK 3418 3415 3417 3436 C4' C S 110 OK 3438 3435 3437 3456 C4' A S 111 OK 3458 3455 3457 3478 C4' C S 112 OK 3480 3477 3479 3498 C4' C S 113 OK 3500 3497 3499 3518 C4' A S 114 OK 3520 3517 3519 3540 C4' C S 115 OK 3542 3539 3541 3560 C4' G S 116 OK 3562 3559 3561 3583 C4' G S 117 OK 3585 3582 3584 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2897 C5' C R 1 2896 2898 2917 C5' C R 2 2916 2918 2937 C5' G R 3 2936 2938 2960 C5' G R 4 2959 2961 2983 C5' 2PR R 5 2982 2984 3004 C5' G R 6 3003 3005 3027 C5' G R 7 3026 3028 3050 C5' A R 8 3049 3051 3072 C5' U R 9 3071 3073 3092 C5' C R 10 3091 3093 3112 C5' A R 11 3111 3113 3134 C5' C R 12 3133 3135 3154 C5' C R 13 3153 3155 3174 C5' A R 14 3173 3175 3196 C5' C R 15 3195 3197 3216 C5' G R 16 3215 3217 3239 C5' G R 17 3238 3240 3260 C5' C S 102 3259 3261 3280 C5' G S 103 3279 3281 3303 C5' G S 104 3302 3304 3326 C5' 2PR S 105 3325 3327 3347 C5' G S 106 3346 3348 3370 C5' G S 107 3369 3371 3393 C5' A S 108 3392 3394 3415 C5' U S 109 3414 3416 3435 C5' C S 110 3434 3436 3455 C5' A S 111 3454 3456 3477 C5' C S 112 3476 3478 3497 C5' C S 113 3496 3498 3517 C5' A S 114 3516 3518 3539 C5' C S 115 3538 3540 3559 C5' G S 116 3558 3560 3582 C5' G S 117 3581 3583 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2913 P C R 2 distorted distorted 2901 2914 2915 2916 2933 P G R 3 distorted distorted 2921 2934 2935 2936 2956 P G R 4 distorted distorted 2941 2957 2958 2959 2979 P 2PR R 5 distorted distorted 2964 2980 2981 2982 3000 P G R 6 distorted distorted 2987 3001 3002 3003 3023 P G R 7 distorted distorted 3008 3024 3025 3026 3046 P A R 8 distorted distorted 3031 3047 3048 3049 3068 P U R 9 distorted distorted 3054 3069 3070 3071 3088 P C R 10 distorted distorted 3076 3089 3090 3091 3108 P A R 11 distorted distorted 3096 3109 3110 3111 3130 P C R 12 distorted distorted 3116 3131 3132 3133 3150 P C R 13 distorted distorted 3138 3151 3152 3153 3170 P A R 14 distorted distorted 3158 3171 3172 3173 3192 P C R 15 distorted distorted 3178 3193 3194 3195 3212 P G R 16 distorted distorted 3200 3213 3214 3215 3235 P G R 17 distorted distorted 3220 3236 3237 3238 3256 P C S 102 distorted distorted 3257 3258 3259 3276 P G S 103 distorted distorted 3264 3277 3278 3279 3299 P G S 104 distorted distorted 3284 3300 3301 3302 3322 P 2PR S 105 distorted distorted 3307 3323 3324 3325 3343 P G S 106 distorted distorted 3330 3344 3345 3346 3366 P G S 107 distorted distorted 3351 3367 3368 3369 3389 P A S 108 distorted distorted 3374 3390 3391 3392 3411 P U S 109 distorted distorted 3397 3412 3413 3414 3431 P C S 110 distorted distorted 3419 3432 3433 3434 3451 P A S 111 distorted distorted 3439 3452 3453 3454 3473 P C S 112 distorted distorted 3459 3474 3475 3476 3493 P C S 113 distorted distorted 3481 3494 3495 3496 3513 P A S 114 distorted distorted 3501 3514 3515 3516 3535 P C S 115 distorted distorted 3521 3536 3537 3538 3555 P G S 116 distorted distorted 3543 3556 3557 3558 3578 P G S 117 distorted distorted 3563 3579 3580 3581 ---------------------------------------------------------------------------------