ID code: '4K9B' 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' --------------------------------------------------------------------------------- 2938 C1' DA D 1 beta 2934 2939 2937 2959 C1' DA D 2 beta 2955 2960 2958 2980 C1' DA D 3 beta 2976 2981 2979 3001 C1' DT D 4 beta 2997 3002 3000 3021 C1' DT D 5 beta 3017 3022 3020 3041 C1' DG D 6 beta 3037 3042 3040 3063 C1' DC D 7 beta 3059 3064 3062 3082 C1' DC D 8 beta 3078 3083 3081 3101 C1' DG D 9 beta 3097 3102 3100 3123 C1' DA D 10 beta 3119 3124 3122 3144 C1' DA D 11 beta 3140 3145 3143 3165 C1' DG D 12 beta 3161 3166 3164 3187 C1' DA D 13 beta 3183 3188 3186 3208 C1' DC D 14 beta 3204 3209 3207 3227 C1' DG D 15 beta 3223 3228 3226 3247 C1' DC E 4 beta 3243 3248 3246 3266 C1' DG E 5 beta 3262 3267 3265 3288 C1' DT E 6 beta 3284 3289 3287 3308 C1' DC E 7 beta 3304 3309 3307 3327 C1' DT E 8 beta 3323 3328 3326 3347 C1' DT E 9 beta 3343 3348 3346 3367 C1' DC E 10 beta 3363 3368 3366 3386 C1' DG E 11 beta 3382 3387 3385 3408 C1' DG E 12 beta 3404 3409 3407 3430 C1' DC E 13 beta 3426 3431 3429 3449 C1' DA E 14 beta 3445 3450 3448 3470 C1' DA E 15 beta 3466 3471 3469 3491 C1' DT E 16 beta 3487 3492 3490 3511 C1' DT E 17 beta 3507 3512 3510 3539 C1' G A 603 beta 3534 3540 3537 3562 C1' A A 604 beta 3557 3563 3560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2937 C2' DA D 1 2938 2935 2958 C2' DA D 2 2959 2956 2979 C2' DA D 3 2980 2977 3000 C2' DT D 4 3001 2998 3020 C2' DT D 5 3021 3018 3040 C2' DG D 6 3041 3038 3062 C2' DC D 7 3063 3060 3081 C2' DC D 8 3082 3079 3100 C2' DG D 9 3101 3098 3122 C2' DA D 10 3123 3120 3143 C2' DA D 11 3144 3141 3164 C2' DG D 12 3165 3162 3186 C2' DA D 13 3187 3184 3207 C2' DC D 14 3208 3205 3226 C2' DG D 15 3227 3224 3246 C2' DC E 4 3247 3244 3265 C2' DG E 5 3266 3263 3287 C2' DT E 6 3288 3285 3307 C2' DC E 7 3308 3305 3326 C2' DT E 8 3327 3324 3346 C2' DT E 9 3347 3344 3366 C2' DC E 10 3367 3364 3385 C2' DG E 11 3386 3383 3407 C2' DG E 12 3408 3405 3429 C2' DC E 13 3430 3427 3448 C2' DA E 14 3449 3446 3469 C2' DA E 15 3470 3467 3490 C2' DT E 16 3491 3488 3510 C2' DT E 17 3511 3508 3537 C2' G A 603 OK 3539 3535 3538 3560 C2' A A 604 OK 3562 3558 3561 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2935 C3' DA D 1 OK 2933 2936 2937 2956 C3' DA D 2 OK 2954 2957 2958 2977 C3' DA D 3 OK 2975 2978 2979 2998 C3' DT D 4 OK 2996 2999 3000 3018 C3' DT D 5 OK 3016 3019 3020 3038 C3' DG D 6 OK 3036 3039 3040 3060 C3' DC D 7 OK 3058 3061 3062 3079 C3' DC D 8 OK 3077 3080 3081 3098 C3' DG D 9 OK 3096 3099 3100 3120 C3' DA D 10 OK 3118 3121 3122 3141 C3' DA D 11 OK 3139 3142 3143 3162 C3' DG D 12 OK 3160 3163 3164 3184 C3' DA D 13 OK 3182 3185 3186 3205 C3' DC D 14 OK 3203 3206 3207 3224 C3' DG D 15 OK 3222 3225 3226 3244 C3' DC E 4 OK 3242 3245 3246 3263 C3' DG E 5 OK 3261 3264 3265 3285 C3' DT E 6 OK 3283 3286 3287 3305 C3' DC E 7 OK 3303 3306 3307 3324 C3' DT E 8 OK 3322 3325 3326 3344 C3' DT E 9 OK 3342 3345 3346 3364 C3' DC E 10 OK 3362 3365 3366 3383 C3' DG E 11 OK 3381 3384 3385 3405 C3' DG E 12 OK 3403 3406 3407 3427 C3' DC E 13 OK 3425 3428 3429 3446 C3' DA E 14 OK 3444 3447 3448 3467 C3' DA E 15 OK 3465 3468 3469 3488 C3' DT E 16 OK 3486 3489 3490 3508 C3' DT E 17 OK 3506 3509 3510 3535 C3' G A 603 OK 3533 3536 3537 3558 C3' A A 604 OK 3556 3559 3560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2933 C4' DA D 1 OK 2935 2932 2934 2954 C4' DA D 2 OK 2956 2953 2955 2975 C4' DA D 3 OK 2977 2974 2976 2996 C4' DT D 4 OK 2998 2995 2997 3016 C4' DT D 5 OK 3018 3015 3017 3036 C4' DG D 6 OK 3038 3035 3037 3058 C4' DC D 7 OK 3060 3057 3059 3077 C4' DC D 8 OK 3079 3076 3078 3096 C4' DG D 9 OK 3098 3095 3097 3118 C4' DA D 10 OK 3120 3117 3119 3139 C4' DA D 11 OK 3141 3138 3140 3160 C4' DG D 12 OK 3162 3159 3161 3182 C4' DA D 13 OK 3184 3181 3183 3203 C4' DC D 14 OK 3205 3202 3204 3222 C4' DG D 15 OK 3224 3221 3223 3242 C4' DC E 4 OK 3244 3241 3243 3261 C4' DG E 5 OK 3263 3260 3262 3283 C4' DT E 6 OK 3285 3282 3284 3303 C4' DC E 7 OK 3305 3302 3304 3322 C4' DT E 8 OK 3324 3321 3323 3342 C4' DT E 9 OK 3344 3341 3343 3362 C4' DC E 10 OK 3364 3361 3363 3381 C4' DG E 11 OK 3383 3380 3382 3403 C4' DG E 12 OK 3405 3402 3404 3425 C4' DC E 13 OK 3427 3424 3426 3444 C4' DA E 14 OK 3446 3443 3445 3465 C4' DA E 15 OK 3467 3464 3466 3486 C4' DT E 16 OK 3488 3485 3487 3506 C4' DT E 17 OK 3508 3505 3507 3533 C4' G A 603 OK 3535 3532 3534 3556 C4' A A 604 OK 3558 3555 3557 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2932 C5' DA D 1 2931 2933 2953 C5' DA D 2 2952 2954 2974 C5' DA D 3 2973 2975 2995 C5' DT D 4 2994 2996 3015 C5' DT D 5 3014 3016 3035 C5' DG D 6 3034 3036 3057 C5' DC D 7 3056 3058 3076 C5' DC D 8 3075 3077 3095 C5' DG D 9 3094 3096 3117 C5' DA D 10 3116 3118 3138 C5' DA D 11 3137 3139 3159 C5' DG D 12 3158 3160 3181 C5' DA D 13 3180 3182 3202 C5' DC D 14 3201 3203 3221 C5' DG D 15 3220 3222 3241 C5' DC E 4 3240 3242 3260 C5' DG E 5 3259 3261 3282 C5' DT E 6 3281 3283 3302 C5' DC E 7 3301 3303 3321 C5' DT E 8 3320 3322 3341 C5' DT E 9 3340 3342 3361 C5' DC E 10 3360 3362 3380 C5' DG E 11 3379 3381 3402 C5' DG E 12 3401 3403 3424 C5' DC E 13 3423 3425 3443 C5' DA E 14 3442 3444 3464 C5' DA E 15 3463 3465 3485 C5' DT E 16 3484 3486 3505 C5' DT E 17 3504 3506 3532 C5' G A 603 3531 3533 3555 C5' A A 604 3554 3556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2949 P DA D 2 distorted distorted 2936 2950 2951 2952 2970 P DA D 3 distorted distorted 2957 2971 2972 2973 2991 P DT D 4 distorted distorted 2978 2992 2993 2994 3011 P DT D 5 distorted distorted 2999 3012 3013 3014 3031 P DG D 6 distorted distorted 3019 3032 3033 3034 3053 P DC D 7 distorted distorted 3039 3054 3055 3056 3072 P DC D 8 distorted distorted 3061 3073 3074 3075 3091 P DG D 9 distorted distorted 3080 3092 3093 3094 3113 P DA D 10 distorted distorted 3099 3114 3115 3116 3134 P DA D 11 distorted distorted 3121 3135 3136 3137 3155 P DG D 12 distorted distorted 3142 3156 3157 3158 3177 P DA D 13 distorted distorted 3163 3178 3179 3180 3198 P DC D 14 distorted distorted 3185 3199 3200 3201 3217 P DG D 15 distorted distorted 3206 3218 3219 3220 3256 P DG E 5 distorted distorted 3245 3257 3258 3259 3278 P DT E 6 distorted distorted 3264 3279 3280 3281 3298 P DC E 7 distorted distorted 3286 3299 3300 3301 3317 P DT E 8 distorted distorted 3306 3318 3319 3320 3337 P DT E 9 distorted distorted 3325 3338 3339 3340 3357 P DC E 10 distorted distorted 3345 3358 3359 3360 3376 P DG E 11 distorted distorted 3365 3377 3378 3379 3398 P DG E 12 distorted distorted 3384 3399 3400 3401 3420 P DC E 13 distorted distorted 3406 3421 3422 3423 3439 P DA E 14 distorted distorted 3428 3440 3441 3442 3460 P DA E 15 distorted distorted 3447 3461 3462 3463 3481 P DT E 16 distorted distorted 3468 3482 3483 3484 3501 P DT E 17 distorted distorted 3489 3502 3503 3504 3523 P PO4 A 602 3528 P G A 603 OK OK 3559 3529 3530 3531 3551 P A A 604 distorted distorted 3552 3553 3554 ---------------------------------------------------------------------------------