ID code: '4K98' 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' --------------------------------------------------------------------------------- 2933 C1' DA D 1 beta 2929 2934 2932 2954 C1' DA D 2 beta 2950 2955 2953 2975 C1' DA D 3 beta 2971 2976 2974 2996 C1' DT D 4 beta 2992 2997 2995 3016 C1' DT D 5 beta 3012 3017 3015 3036 C1' DG D 6 beta 3032 3037 3035 3058 C1' DC D 7 beta 3054 3059 3057 3077 C1' DC D 8 beta 3073 3078 3076 3096 C1' DG D 9 beta 3092 3097 3095 3118 C1' DA D 10 beta 3114 3119 3117 3139 C1' DA D 11 beta 3135 3140 3138 3160 C1' DG D 12 beta 3156 3161 3159 3182 C1' DA D 13 beta 3178 3183 3181 3203 C1' DC D 14 beta 3199 3204 3202 3222 C1' DG D 15 beta 3218 3223 3221 3245 C1' DC E 4 beta 3241 3246 3244 3264 C1' DG E 5 beta 3260 3265 3263 3286 C1' DT E 6 beta 3282 3287 3285 3306 C1' DC E 7 beta 3302 3307 3305 3325 C1' DT E 8 beta 3321 3326 3324 3345 C1' DT E 9 beta 3341 3346 3344 3365 C1' DC E 10 beta 3361 3366 3364 3384 C1' DG E 11 beta 3380 3385 3383 3406 C1' DG E 12 beta 3402 3407 3405 3428 C1' DC E 13 beta 3424 3429 3427 3447 C1' DA E 14 beta 3443 3448 3446 3468 C1' DA E 15 beta 3464 3469 3467 3489 C1' DT E 16 beta 3485 3490 3488 3509 C1' DT E 17 beta 3505 3510 3508 3543 C1' GTP A 604 beta 3538 3544 3541 3566 C1' G A 605 beta 3561 3567 3564 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2932 C2' DA D 1 2933 2930 2953 C2' DA D 2 2954 2951 2974 C2' DA D 3 2975 2972 2995 C2' DT D 4 2996 2993 3015 C2' DT D 5 3016 3013 3035 C2' DG D 6 3036 3033 3057 C2' DC D 7 3058 3055 3076 C2' DC D 8 3077 3074 3095 C2' DG D 9 3096 3093 3117 C2' DA D 10 3118 3115 3138 C2' DA D 11 3139 3136 3159 C2' DG D 12 3160 3157 3181 C2' DA D 13 3182 3179 3202 C2' DC D 14 3203 3200 3221 C2' DG D 15 3222 3219 3244 C2' DC E 4 3245 3242 3263 C2' DG E 5 3264 3261 3285 C2' DT E 6 3286 3283 3305 C2' DC E 7 3306 3303 3324 C2' DT E 8 3325 3322 3344 C2' DT E 9 3345 3342 3364 C2' DC E 10 3365 3362 3383 C2' DG E 11 3384 3381 3405 C2' DG E 12 3406 3403 3427 C2' DC E 13 3428 3425 3446 C2' DA E 14 3447 3444 3467 C2' DA E 15 3468 3465 3488 C2' DT E 16 3489 3486 3508 C2' DT E 17 3509 3506 3541 C2' GTP A 604 OK 3543 3539 3542 3564 C2' G A 605 OK 3566 3562 3565 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2930 C3' DA D 1 OK 2928 2931 2932 2951 C3' DA D 2 OK 2949 2952 2953 2972 C3' DA D 3 OK 2970 2973 2974 2993 C3' DT D 4 OK 2991 2994 2995 3013 C3' DT D 5 OK 3011 3014 3015 3033 C3' DG D 6 OK 3031 3034 3035 3055 C3' DC D 7 OK 3053 3056 3057 3074 C3' DC D 8 OK 3072 3075 3076 3093 C3' DG D 9 OK 3091 3094 3095 3115 C3' DA D 10 OK 3113 3116 3117 3136 C3' DA D 11 OK 3134 3137 3138 3157 C3' DG D 12 OK 3155 3158 3159 3179 C3' DA D 13 OK 3177 3180 3181 3200 C3' DC D 14 OK 3198 3201 3202 3219 C3' DG D 15 OK 3217 3220 3221 3242 C3' DC E 4 OK 3240 3243 3244 3261 C3' DG E 5 OK 3259 3262 3263 3283 C3' DT E 6 OK 3281 3284 3285 3303 C3' DC E 7 OK 3301 3304 3305 3322 C3' DT E 8 OK 3320 3323 3324 3342 C3' DT E 9 OK 3340 3343 3344 3362 C3' DC E 10 OK 3360 3363 3364 3381 C3' DG E 11 OK 3379 3382 3383 3403 C3' DG E 12 OK 3401 3404 3405 3425 C3' DC E 13 OK 3423 3426 3427 3444 C3' DA E 14 OK 3442 3445 3446 3465 C3' DA E 15 OK 3463 3466 3467 3486 C3' DT E 16 OK 3484 3487 3488 3506 C3' DT E 17 OK 3504 3507 3508 3539 C3' GTP A 604 OK 3537 3540 3541 3562 C3' G A 605 OK 3560 3563 3564 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2928 C4' DA D 1 OK 2930 2927 2929 2949 C4' DA D 2 OK 2951 2948 2950 2970 C4' DA D 3 OK 2972 2969 2971 2991 C4' DT D 4 OK 2993 2990 2992 3011 C4' DT D 5 OK 3013 3010 3012 3031 C4' DG D 6 OK 3033 3030 3032 3053 C4' DC D 7 OK 3055 3052 3054 3072 C4' DC D 8 OK 3074 3071 3073 3091 C4' DG D 9 OK 3093 3090 3092 3113 C4' DA D 10 OK 3115 3112 3114 3134 C4' DA D 11 OK 3136 3133 3135 3155 C4' DG D 12 OK 3157 3154 3156 3177 C4' DA D 13 OK 3179 3176 3178 3198 C4' DC D 14 OK 3200 3197 3199 3217 C4' DG D 15 OK 3219 3216 3218 3240 C4' DC E 4 OK 3242 3239 3241 3259 C4' DG E 5 OK 3261 3258 3260 3281 C4' DT E 6 OK 3283 3280 3282 3301 C4' DC E 7 OK 3303 3300 3302 3320 C4' DT E 8 OK 3322 3319 3321 3340 C4' DT E 9 OK 3342 3339 3341 3360 C4' DC E 10 OK 3362 3359 3361 3379 C4' DG E 11 OK 3381 3378 3380 3401 C4' DG E 12 OK 3403 3400 3402 3423 C4' DC E 13 OK 3425 3422 3424 3442 C4' DA E 14 OK 3444 3441 3443 3463 C4' DA E 15 OK 3465 3462 3464 3484 C4' DT E 16 OK 3486 3483 3485 3504 C4' DT E 17 OK 3506 3503 3505 3537 C4' GTP A 604 OK 3539 3536 3538 3560 C4' G A 605 OK 3562 3559 3561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2927 C5' DA D 1 2926 2928 2948 C5' DA D 2 2947 2949 2969 C5' DA D 3 2968 2970 2990 C5' DT D 4 2989 2991 3010 C5' DT D 5 3009 3011 3030 C5' DG D 6 3029 3031 3052 C5' DC D 7 3051 3053 3071 C5' DC D 8 3070 3072 3090 C5' DG D 9 3089 3091 3112 C5' DA D 10 3111 3113 3133 C5' DA D 11 3132 3134 3154 C5' DG D 12 3153 3155 3176 C5' DA D 13 3175 3177 3197 C5' DC D 14 3196 3198 3216 C5' DG D 15 3215 3217 3239 C5' DC E 4 3238 3240 3258 C5' DG E 5 3257 3259 3280 C5' DT E 6 3279 3281 3300 C5' DC E 7 3299 3301 3319 C5' DT E 8 3318 3320 3339 C5' DT E 9 3338 3340 3359 C5' DC E 10 3358 3360 3378 C5' DG E 11 3377 3379 3400 C5' DG E 12 3399 3401 3422 C5' DC E 13 3421 3423 3441 C5' DA E 14 3440 3442 3462 C5' DA E 15 3461 3463 3483 C5' DT E 16 3482 3484 3503 C5' DT E 17 3502 3504 3536 C5' GTP A 604 3535 3537 3559 C5' G A 605 3558 3560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2944 P DA D 2 distorted distorted 2931 2945 2946 2947 2965 P DA D 3 distorted distorted 2952 2966 2967 2968 2986 P DT D 4 distorted distorted 2973 2987 2988 2989 3006 P DT D 5 distorted distorted 2994 3007 3008 3009 3026 P DG D 6 distorted distorted 3014 3027 3028 3029 3048 P DC D 7 distorted distorted 3034 3049 3050 3051 3067 P DC D 8 distorted distorted 3056 3068 3069 3070 3086 P DG D 9 distorted distorted 3075 3087 3088 3089 3108 P DA D 10 distorted distorted 3094 3109 3110 3111 3129 P DA D 11 distorted distorted 3116 3130 3131 3132 3150 P DG D 12 distorted distorted 3137 3151 3152 3153 3172 P DA D 13 distorted distorted 3158 3173 3174 3175 3193 P DC D 14 distorted distorted 3180 3194 3195 3196 3212 P DG D 15 distorted distorted 3201 3213 3214 3215 3235 P DC E 4 OK OK 3236 3237 3238 3254 P DG E 5 distorted distorted 3243 3255 3256 3257 3276 P DT E 6 distorted distorted 3262 3277 3278 3279 3296 P DC E 7 distorted distorted 3284 3297 3298 3299 3315 P DT E 8 distorted distorted 3304 3316 3317 3318 3335 P DT E 9 distorted distorted 3323 3336 3337 3338 3355 P DC E 10 distorted distorted 3343 3356 3357 3358 3374 P DG E 11 distorted distorted 3363 3375 3376 3377 3396 P DG E 12 distorted distorted 3382 3397 3398 3399 3418 P DC E 13 distorted distorted 3404 3419 3420 3421 3437 P DA E 14 distorted distorted 3426 3438 3439 3440 3458 P DA E 15 distorted distorted 3445 3459 3460 3461 3479 P DT E 16 distorted distorted 3466 3480 3481 3482 3499 P DT E 17 distorted distorted 3487 3500 3501 3502 3555 P G A 605 distorted distorted 3556 3557 3558 ---------------------------------------------------------------------------------