ID code: '2BQ5' 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' --------------------------------------------------------------------------------- 2898 C1' A R 1 beta 2893 2899 2896 2920 C1' C R 2 beta 2915 2921 2918 2940 C1' A R 3 beta 2935 2941 2938 2962 C1' U R 4 beta 2957 2963 2960 2982 C1' G R 5 beta 2977 2983 2980 3005 C1' A R 6 beta 3000 3006 3003 3027 C1' G R 7 beta 3022 3028 3025 3050 C1' G R 8 beta 3045 3051 3048 3073 C1' A R 9 beta 3068 3074 3071 3095 C1' U R 10 beta 3090 3096 3093 3115 C1' U R 11 beta 3110 3116 3113 3135 C1' A R 12 beta 3130 3136 3133 3157 C1' C R 13 beta 3152 3158 3155 3177 C1' C R 14 beta 3172 3178 3175 3197 C1' C R 15 beta 3192 3198 3195 3217 C1' A R 16 beta 3212 3218 3215 3239 C1' U R 17 beta 3234 3240 3237 3259 C1' G R 18 beta 3254 3260 3257 3282 C1' U R 19 beta 3277 3283 3280 3300 C1' C S 2 beta 3295 3301 3298 3320 C1' A S 3 beta 3315 3321 3318 3342 C1' U S 4 beta 3337 3343 3340 3362 C1' G S 5 beta 3357 3363 3360 3385 C1' A S 6 beta 3380 3386 3383 3407 C1' G S 7 beta 3402 3408 3405 3430 C1' G S 8 beta 3425 3431 3428 3453 C1' A S 9 beta 3448 3454 3451 3475 C1' U S 10 beta 3470 3476 3473 3495 C1' U S 11 beta 3490 3496 3493 3515 C1' A S 12 beta 3510 3516 3513 3537 C1' C S 13 beta 3532 3538 3535 3557 C1' C S 14 beta 3552 3558 3555 3577 C1' C S 15 beta 3572 3578 3575 3597 C1' A S 16 beta 3592 3598 3595 3619 C1' U S 17 beta 3614 3620 3617 3639 C1' G S 18 beta 3634 3640 3637 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2896 C2' A R 1 OK 2898 2894 2897 2918 C2' C R 2 OK 2920 2916 2919 2938 C2' A R 3 OK 2940 2936 2939 2960 C2' U R 4 OK 2962 2958 2961 2980 C2' G R 5 OK 2982 2978 2981 3003 C2' A R 6 OK 3005 3001 3004 3025 C2' G R 7 OK 3027 3023 3026 3048 C2' G R 8 OK 3050 3046 3049 3071 C2' A R 9 OK 3073 3069 3072 3093 C2' U R 10 OK 3095 3091 3094 3113 C2' U R 11 OK 3115 3111 3114 3133 C2' A R 12 OK 3135 3131 3134 3155 C2' C R 13 OK 3157 3153 3156 3175 C2' C R 14 OK 3177 3173 3176 3195 C2' C R 15 OK 3197 3193 3196 3215 C2' A R 16 OK 3217 3213 3216 3237 C2' U R 17 OK 3239 3235 3238 3257 C2' G R 18 OK 3259 3255 3258 3280 C2' U R 19 OK 3282 3278 3281 3298 C2' C S 2 OK 3300 3296 3299 3318 C2' A S 3 OK 3320 3316 3319 3340 C2' U S 4 OK 3342 3338 3341 3360 C2' G S 5 OK 3362 3358 3361 3383 C2' A S 6 OK 3385 3381 3384 3405 C2' G S 7 OK 3407 3403 3406 3428 C2' G S 8 OK 3430 3426 3429 3451 C2' A S 9 OK 3453 3449 3452 3473 C2' U S 10 OK 3475 3471 3474 3493 C2' U S 11 OK 3495 3491 3494 3513 C2' A S 12 OK 3515 3511 3514 3535 C2' C S 13 OK 3537 3533 3536 3555 C2' C S 14 OK 3557 3553 3556 3575 C2' C S 15 OK 3577 3573 3576 3595 C2' A S 16 OK 3597 3593 3596 3617 C2' U S 17 OK 3619 3615 3618 3637 C2' G S 18 OK 3639 3635 3638 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2894 C3' A R 1 OK 2892 2895 2896 2916 C3' C R 2 OK 2914 2917 2918 2936 C3' A R 3 OK 2934 2937 2938 2958 C3' U R 4 OK 2956 2959 2960 2978 C3' G R 5 OK 2976 2979 2980 3001 C3' A R 6 OK 2999 3002 3003 3023 C3' G R 7 OK 3021 3024 3025 3046 C3' G R 8 OK 3044 3047 3048 3069 C3' A R 9 OK 3067 3070 3071 3091 C3' U R 10 OK 3089 3092 3093 3111 C3' U R 11 OK 3109 3112 3113 3131 C3' A R 12 OK 3129 3132 3133 3153 C3' C R 13 OK 3151 3154 3155 3173 C3' C R 14 OK 3171 3174 3175 3193 C3' C R 15 OK 3191 3194 3195 3213 C3' A R 16 OK 3211 3214 3215 3235 C3' U R 17 OK 3233 3236 3237 3255 C3' G R 18 OK 3253 3256 3257 3278 C3' U R 19 OK 3276 3279 3280 3296 C3' C S 2 OK 3294 3297 3298 3316 C3' A S 3 OK 3314 3317 3318 3338 C3' U S 4 OK 3336 3339 3340 3358 C3' G S 5 OK 3356 3359 3360 3381 C3' A S 6 OK 3379 3382 3383 3403 C3' G S 7 OK 3401 3404 3405 3426 C3' G S 8 OK 3424 3427 3428 3449 C3' A S 9 OK 3447 3450 3451 3471 C3' U S 10 OK 3469 3472 3473 3491 C3' U S 11 OK 3489 3492 3493 3511 C3' A S 12 OK 3509 3512 3513 3533 C3' C S 13 OK 3531 3534 3535 3553 C3' C S 14 OK 3551 3554 3555 3573 C3' C S 15 OK 3571 3574 3575 3593 C3' A S 16 OK 3591 3594 3595 3615 C3' U S 17 OK 3613 3616 3617 3635 C3' G S 18 OK 3633 3636 3637 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2892 C4' A R 1 OK 2894 2891 2893 2914 C4' C R 2 OK 2916 2913 2915 2934 C4' A R 3 OK 2936 2933 2935 2956 C4' U R 4 OK 2958 2955 2957 2976 C4' G R 5 OK 2978 2975 2977 2999 C4' A R 6 OK 3001 2998 3000 3021 C4' G R 7 OK 3023 3020 3022 3044 C4' G R 8 OK 3046 3043 3045 3067 C4' A R 9 OK 3069 3066 3068 3089 C4' U R 10 OK 3091 3088 3090 3109 C4' U R 11 OK 3111 3108 3110 3129 C4' A R 12 OK 3131 3128 3130 3151 C4' C R 13 OK 3153 3150 3152 3171 C4' C R 14 OK 3173 3170 3172 3191 C4' C R 15 OK 3193 3190 3192 3211 C4' A R 16 OK 3213 3210 3212 3233 C4' U R 17 OK 3235 3232 3234 3253 C4' G R 18 OK 3255 3252 3254 3276 C4' U R 19 OK 3278 3275 3277 3294 C4' C S 2 OK 3296 3293 3295 3314 C4' A S 3 OK 3316 3313 3315 3336 C4' U S 4 OK 3338 3335 3337 3356 C4' G S 5 OK 3358 3355 3357 3379 C4' A S 6 OK 3381 3378 3380 3401 C4' G S 7 OK 3403 3400 3402 3424 C4' G S 8 OK 3426 3423 3425 3447 C4' A S 9 OK 3449 3446 3448 3469 C4' U S 10 OK 3471 3468 3470 3489 C4' U S 11 OK 3491 3488 3490 3509 C4' A S 12 OK 3511 3508 3510 3531 C4' C S 13 OK 3533 3530 3532 3551 C4' C S 14 OK 3553 3550 3552 3571 C4' C S 15 OK 3573 3570 3572 3591 C4' A S 16 OK 3593 3590 3592 3613 C4' U S 17 OK 3615 3612 3614 3633 C4' G S 18 OK 3635 3632 3634 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2891 C5' A R 1 2890 2892 2913 C5' C R 2 2912 2914 2933 C5' A R 3 2932 2934 2955 C5' U R 4 2954 2956 2975 C5' G R 5 2974 2976 2998 C5' A R 6 2997 2999 3020 C5' G R 7 3019 3021 3043 C5' G R 8 3042 3044 3066 C5' A R 9 3065 3067 3088 C5' U R 10 3087 3089 3108 C5' U R 11 3107 3109 3128 C5' A R 12 3127 3129 3150 C5' C R 13 3149 3151 3170 C5' C R 14 3169 3171 3190 C5' C R 15 3189 3191 3210 C5' A R 16 3209 3211 3232 C5' U R 17 3231 3233 3252 C5' G R 18 3251 3253 3275 C5' U R 19 3274 3276 3293 C5' C S 2 3292 3294 3313 C5' A S 3 3312 3314 3335 C5' U S 4 3334 3336 3355 C5' G S 5 3354 3356 3378 C5' A S 6 3377 3379 3400 C5' G S 7 3399 3401 3423 C5' G S 8 3422 3424 3446 C5' A S 9 3445 3447 3468 C5' U S 10 3467 3469 3488 C5' U S 11 3487 3489 3508 C5' A S 12 3507 3509 3530 C5' C S 13 3529 3531 3550 C5' C S 14 3549 3551 3570 C5' C S 15 3569 3571 3590 C5' A S 16 3589 3591 3612 C5' U S 17 3611 3613 3632 C5' G S 18 3631 3633 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2909 P C R 2 distorted distorted 2895 2910 2911 2912 2929 P A R 3 distorted distorted 2917 2930 2931 2932 2951 P U R 4 distorted distorted 2937 2952 2953 2954 2971 P G R 5 distorted distorted 2959 2972 2973 2974 2994 P A R 6 distorted distorted 2979 2995 2996 2997 3016 P G R 7 distorted distorted 3002 3017 3018 3019 3039 P G R 8 distorted distorted 3024 3040 3041 3042 3062 P A R 9 distorted distorted 3047 3063 3064 3065 3084 P U R 10 distorted distorted 3070 3085 3086 3087 3104 P U R 11 distorted distorted 3092 3105 3106 3107 3124 P A R 12 distorted distorted 3112 3125 3126 3127 3146 P C R 13 distorted distorted 3132 3147 3148 3149 3166 P C R 14 distorted distorted 3154 3167 3168 3169 3186 P C R 15 distorted distorted 3174 3187 3188 3189 3206 P A R 16 distorted distorted 3194 3207 3208 3209 3228 P U R 17 distorted distorted 3214 3229 3230 3231 3248 P G R 18 distorted distorted 3236 3249 3250 3251 3271 P U R 19 distorted distorted 3256 3272 3273 3274 3309 P A S 3 distorted distorted 3297 3310 3311 3312 3331 P U S 4 distorted distorted 3317 3332 3333 3334 3351 P G S 5 distorted distorted 3339 3352 3353 3354 3374 P A S 6 distorted distorted 3359 3375 3376 3377 3396 P G S 7 distorted distorted 3382 3397 3398 3399 3419 P G S 8 distorted distorted 3404 3420 3421 3422 3442 P A S 9 distorted distorted 3427 3443 3444 3445 3464 P U S 10 distorted distorted 3450 3465 3466 3467 3484 P U S 11 distorted distorted 3472 3485 3486 3487 3504 P A S 12 distorted distorted 3492 3505 3506 3507 3526 P C S 13 distorted distorted 3512 3527 3528 3529 3546 P C S 14 distorted distorted 3534 3547 3548 3549 3566 P C S 15 distorted distorted 3554 3567 3568 3569 3586 P A S 16 distorted distorted 3574 3587 3588 3589 3608 P U S 17 distorted distorted 3594 3609 3610 3611 3628 P G S 18 distorted distorted 3616 3629 3630 3631 ---------------------------------------------------------------------------------