ID code: '2BU1' 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' --------------------------------------------------------------------------------- 2911 C1' C R 2 beta 2906 2912 2909 2931 C1' A R 3 beta 2926 2932 2929 2953 C1' U R 4 beta 2948 2954 2951 2973 C1' G R 5 beta 2968 2974 2971 2996 C1' A R 6 beta 2991 2997 2994 3018 C1' G R 7 beta 3013 3019 3016 3041 C1' G R 8 beta 3036 3042 3039 3064 C1' A R 9 beta 3059 3065 3062 3086 C1' U R 10 beta 3081 3087 3084 3106 C1' 5BU R 11 beta 3101 3107 3104 3127 C1' A R 12 beta 3122 3128 3125 3149 C1' C R 13 beta 3144 3150 3147 3169 C1' C R 14 beta 3164 3170 3167 3189 C1' C R 15 beta 3184 3190 3187 3209 C1' A R 16 beta 3204 3210 3207 3231 C1' U R 17 beta 3226 3232 3229 3251 C1' G R 18 beta 3246 3252 3249 3276 C1' C S 2 beta 3271 3277 3274 3296 C1' A S 3 beta 3291 3297 3294 3318 C1' U S 4 beta 3313 3319 3316 3338 C1' G S 5 beta 3333 3339 3336 3361 C1' A S 6 beta 3356 3362 3359 3383 C1' G S 7 beta 3378 3384 3381 3406 C1' G S 8 beta 3401 3407 3404 3429 C1' A S 9 beta 3424 3430 3427 3451 C1' U S 10 beta 3446 3452 3449 3471 C1' 5BU S 11 beta 3466 3472 3469 3492 C1' A S 12 beta 3487 3493 3490 3514 C1' C S 13 beta 3509 3515 3512 3534 C1' C S 14 beta 3529 3535 3532 3554 C1' C S 15 beta 3549 3555 3552 3574 C1' A S 16 beta 3569 3575 3572 3596 C1' U S 17 beta 3591 3597 3594 3616 C1' G S 18 beta 3611 3617 3614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2909 C2' C R 2 OK 2911 2907 2910 2929 C2' A R 3 OK 2931 2927 2930 2951 C2' U R 4 OK 2953 2949 2952 2971 C2' G R 5 OK 2973 2969 2972 2994 C2' A R 6 OK 2996 2992 2995 3016 C2' G R 7 OK 3018 3014 3017 3039 C2' G R 8 OK 3041 3037 3040 3062 C2' A R 9 OK 3064 3060 3063 3084 C2' U R 10 OK 3086 3082 3085 3104 C2' 5BU R 11 OK 3106 3102 3105 3125 C2' A R 12 OK 3127 3123 3126 3147 C2' C R 13 OK 3149 3145 3148 3167 C2' C R 14 OK 3169 3165 3168 3187 C2' C R 15 OK 3189 3185 3188 3207 C2' A R 16 OK 3209 3205 3208 3229 C2' U R 17 OK 3231 3227 3230 3249 C2' G R 18 OK 3251 3247 3250 3274 C2' C S 2 OK 3276 3272 3275 3294 C2' A S 3 OK 3296 3292 3295 3316 C2' U S 4 OK 3318 3314 3317 3336 C2' G S 5 OK 3338 3334 3337 3359 C2' A S 6 OK 3361 3357 3360 3381 C2' G S 7 OK 3383 3379 3382 3404 C2' G S 8 OK 3406 3402 3405 3427 C2' A S 9 OK 3429 3425 3428 3449 C2' U S 10 OK 3451 3447 3450 3469 C2' 5BU S 11 OK 3471 3467 3470 3490 C2' A S 12 OK 3492 3488 3491 3512 C2' C S 13 OK 3514 3510 3513 3532 C2' C S 14 OK 3534 3530 3533 3552 C2' C S 15 OK 3554 3550 3553 3572 C2' A S 16 OK 3574 3570 3573 3594 C2' U S 17 OK 3596 3592 3595 3614 C2' G S 18 OK 3616 3612 3615 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2907 C3' C R 2 distorted 2905 2908 2909 2927 C3' A R 3 OK 2925 2928 2929 2949 C3' U R 4 OK 2947 2950 2951 2969 C3' G R 5 OK 2967 2970 2971 2992 C3' A R 6 OK 2990 2993 2994 3014 C3' G R 7 OK 3012 3015 3016 3037 C3' G R 8 OK 3035 3038 3039 3060 C3' A R 9 OK 3058 3061 3062 3082 C3' U R 10 OK 3080 3083 3084 3102 C3' 5BU R 11 OK 3100 3103 3104 3123 C3' A R 12 OK 3121 3124 3125 3145 C3' C R 13 OK 3143 3146 3147 3165 C3' C R 14 OK 3163 3166 3167 3185 C3' C R 15 OK 3183 3186 3187 3205 C3' A R 16 OK 3203 3206 3207 3227 C3' U R 17 OK 3225 3228 3229 3247 C3' G R 18 OK 3245 3248 3249 3272 C3' C S 2 distorted 3270 3273 3274 3292 C3' A S 3 OK 3290 3293 3294 3314 C3' U S 4 OK 3312 3315 3316 3334 C3' G S 5 OK 3332 3335 3336 3357 C3' A S 6 OK 3355 3358 3359 3379 C3' G S 7 OK 3377 3380 3381 3402 C3' G S 8 OK 3400 3403 3404 3425 C3' A S 9 OK 3423 3426 3427 3447 C3' U S 10 OK 3445 3448 3449 3467 C3' 5BU S 11 OK 3465 3468 3469 3488 C3' A S 12 OK 3486 3489 3490 3510 C3' C S 13 OK 3508 3511 3512 3530 C3' C S 14 OK 3528 3531 3532 3550 C3' C S 15 OK 3548 3551 3552 3570 C3' A S 16 OK 3568 3571 3572 3592 C3' U S 17 OK 3590 3593 3594 3612 C3' G S 18 OK 3610 3613 3614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2905 C4' C R 2 OK 2907 2904 2906 2925 C4' A R 3 OK 2927 2924 2926 2947 C4' U R 4 OK 2949 2946 2948 2967 C4' G R 5 OK 2969 2966 2968 2990 C4' A R 6 OK 2992 2989 2991 3012 C4' G R 7 OK 3014 3011 3013 3035 C4' G R 8 OK 3037 3034 3036 3058 C4' A R 9 OK 3060 3057 3059 3080 C4' U R 10 OK 3082 3079 3081 3100 C4' 5BU R 11 OK 3102 3099 3101 3121 C4' A R 12 OK 3123 3120 3122 3143 C4' C R 13 OK 3145 3142 3144 3163 C4' C R 14 OK 3165 3162 3164 3183 C4' C R 15 OK 3185 3182 3184 3203 C4' A R 16 OK 3205 3202 3204 3225 C4' U R 17 OK 3227 3224 3226 3245 C4' G R 18 OK 3247 3244 3246 3270 C4' C S 2 OK 3272 3269 3271 3290 C4' A S 3 OK 3292 3289 3291 3312 C4' U S 4 OK 3314 3311 3313 3332 C4' G S 5 OK 3334 3331 3333 3355 C4' A S 6 OK 3357 3354 3356 3377 C4' G S 7 OK 3379 3376 3378 3400 C4' G S 8 OK 3402 3399 3401 3423 C4' A S 9 OK 3425 3422 3424 3445 C4' U S 10 OK 3447 3444 3446 3465 C4' 5BU S 11 OK 3467 3464 3466 3486 C4' A S 12 OK 3488 3485 3487 3508 C4' C S 13 OK 3510 3507 3509 3528 C4' C S 14 OK 3530 3527 3529 3548 C4' C S 15 OK 3550 3547 3549 3568 C4' A S 16 OK 3570 3567 3569 3590 C4' U S 17 OK 3592 3589 3591 3610 C4' G S 18 OK 3612 3609 3611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2904 C5' C R 2 2903 2905 2924 C5' A R 3 2923 2925 2946 C5' U R 4 2945 2947 2966 C5' G R 5 2965 2967 2989 C5' A R 6 2988 2990 3011 C5' G R 7 3010 3012 3034 C5' G R 8 3033 3035 3057 C5' A R 9 3056 3058 3079 C5' U R 10 3078 3080 3099 C5' 5BU R 11 3098 3100 3120 C5' A R 12 3119 3121 3142 C5' C R 13 3141 3143 3162 C5' C R 14 3161 3163 3182 C5' C R 15 3181 3183 3202 C5' A R 16 3201 3203 3224 C5' U R 17 3223 3225 3244 C5' G R 18 3243 3245 3269 C5' C S 2 3268 3270 3289 C5' A S 3 3288 3290 3311 C5' U S 4 3310 3312 3331 C5' G S 5 3330 3332 3354 C5' A S 6 3353 3355 3376 C5' G S 7 3375 3377 3399 C5' G S 8 3398 3400 3422 C5' A S 9 3421 3423 3444 C5' U S 10 3443 3445 3464 C5' 5BU S 11 3463 3465 3485 C5' A S 12 3484 3486 3507 C5' C S 13 3506 3508 3527 C5' C S 14 3526 3528 3547 C5' C S 15 3546 3548 3567 C5' A S 16 3566 3568 3589 C5' U S 17 3588 3590 3609 C5' G S 18 3608 3610 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2900 P C R 2 distorted distorted 2901 2902 2903 2920 P A R 3 distorted distorted 2908 2921 2922 2923 2942 P U R 4 distorted distorted 2928 2943 2944 2945 2962 P G R 5 distorted distorted 2950 2963 2964 2965 2985 P A R 6 distorted distorted 2970 2986 2987 2988 3007 P G R 7 distorted distorted 2993 3008 3009 3010 3030 P G R 8 distorted distorted 3015 3031 3032 3033 3053 P A R 9 distorted distorted 3038 3054 3055 3056 3075 P U R 10 distorted distorted 3061 3076 3077 3078 3095 P 5BU R 11 distorted distorted 3083 3096 3097 3098 3116 P A R 12 distorted distorted 3103 3117 3118 3119 3138 P C R 13 distorted distorted 3124 3139 3140 3141 3158 P C R 14 distorted distorted 3146 3159 3160 3161 3178 P C R 15 distorted distorted 3166 3179 3180 3181 3198 P A R 16 distorted distorted 3186 3199 3200 3201 3220 P U R 17 distorted distorted 3206 3221 3222 3223 3240 P G R 18 distorted distorted 3228 3241 3242 3243 3265 P C S 2 distorted distorted 3266 3267 3268 3285 P A S 3 distorted distorted 3273 3286 3287 3288 3307 P U S 4 distorted distorted 3293 3308 3309 3310 3327 P G S 5 distorted distorted 3315 3328 3329 3330 3350 P A S 6 distorted distorted 3335 3351 3352 3353 3372 P G S 7 distorted distorted 3358 3373 3374 3375 3395 P G S 8 distorted distorted 3380 3396 3397 3398 3418 P A S 9 distorted distorted 3403 3419 3420 3421 3440 P U S 10 distorted distorted 3426 3441 3442 3443 3460 P 5BU S 11 distorted distorted 3448 3461 3462 3463 3481 P A S 12 distorted distorted 3468 3482 3483 3484 3503 P C S 13 distorted distorted 3489 3504 3505 3506 3523 P C S 14 distorted distorted 3511 3524 3525 3526 3543 P C S 15 distorted distorted 3531 3544 3545 3546 3563 P A S 16 distorted distorted 3551 3564 3565 3566 3585 P U S 17 distorted distorted 3571 3586 3587 3588 3605 P G S 18 distorted distorted 3593 3606 3607 3608 ---------------------------------------------------------------------------------