ID code: '2XLK' 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' --------------------------------------------------------------------------------- 3006 C1' C C 6 beta 3001 3007 3004 3026 C1' U C 7 beta 3021 3027 3024 3046 C1' G C 8 beta 3041 3047 3044 3069 C1' C C 9 beta 3064 3070 3067 3089 C1' C C 10 beta 3084 3090 3087 3109 C1' G C 11 beta 3104 3110 3107 3132 C1' U C 12 beta 3127 3133 3130 3152 C1' A C 13 beta 3147 3153 3150 3174 C1' U C 14 beta 3169 3175 3172 3194 C1' A C 15 beta 3189 3195 3192 3216 C1' G C 16 beta 3211 3217 3214 3239 C1' G C 17 beta 3234 3240 3237 3262 C1' C C 18 beta 3257 3263 3260 3282 C1' A C 19 beta 3277 3283 3280 3303 C1' DG C 20 beta 3299 3304 3302 3328 C1' C D 6 beta 3323 3329 3326 3348 C1' U D 7 beta 3343 3349 3346 3368 C1' G D 8 beta 3363 3369 3366 3391 C1' C D 9 beta 3386 3392 3389 3411 C1' C D 10 beta 3406 3412 3409 3431 C1' G D 11 beta 3426 3432 3429 3454 C1' U D 12 beta 3449 3455 3452 3474 C1' A D 13 beta 3469 3475 3472 3496 C1' U D 14 beta 3491 3497 3494 3516 C1' A D 15 beta 3511 3517 3514 3538 C1' G D 16 beta 3533 3539 3536 3561 C1' G D 17 beta 3556 3562 3559 3584 C1' C D 18 beta 3579 3585 3582 3604 C1' A D 19 beta 3599 3605 3602 3625 C1' DG D 20 beta 3621 3626 3624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3004 C2' C C 6 OK 3006 3002 3005 3024 C2' U C 7 OK 3026 3022 3025 3044 C2' G C 8 OK 3046 3042 3045 3067 C2' C C 9 OK 3069 3065 3068 3087 C2' C C 10 OK 3089 3085 3088 3107 C2' G C 11 OK 3109 3105 3108 3130 C2' U C 12 OK 3132 3128 3131 3150 C2' A C 13 OK 3152 3148 3151 3172 C2' U C 14 OK 3174 3170 3173 3192 C2' A C 15 OK 3194 3190 3193 3214 C2' G C 16 OK 3216 3212 3215 3237 C2' G C 17 OK 3239 3235 3238 3260 C2' C C 18 OK 3262 3258 3261 3280 C2' A C 19 OK 3282 3278 3281 3302 C2' DG C 20 3303 3300 3326 C2' C D 6 OK 3328 3324 3327 3346 C2' U D 7 OK 3348 3344 3347 3366 C2' G D 8 OK 3368 3364 3367 3389 C2' C D 9 OK 3391 3387 3390 3409 C2' C D 10 OK 3411 3407 3410 3429 C2' G D 11 OK 3431 3427 3430 3452 C2' U D 12 OK 3454 3450 3453 3472 C2' A D 13 OK 3474 3470 3473 3494 C2' U D 14 OK 3496 3492 3495 3514 C2' A D 15 OK 3516 3512 3515 3536 C2' G D 16 OK 3538 3534 3537 3559 C2' G D 17 OK 3561 3557 3560 3582 C2' C D 18 OK 3584 3580 3583 3602 C2' A D 19 OK 3604 3600 3603 3624 C2' DG D 20 3625 3622 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3002 C3' C C 6 OK 3000 3003 3004 3022 C3' U C 7 OK 3020 3023 3024 3042 C3' G C 8 OK 3040 3043 3044 3065 C3' C C 9 OK 3063 3066 3067 3085 C3' C C 10 OK 3083 3086 3087 3105 C3' G C 11 OK 3103 3106 3107 3128 C3' U C 12 OK 3126 3129 3130 3148 C3' A C 13 OK 3146 3149 3150 3170 C3' U C 14 OK 3168 3171 3172 3190 C3' A C 15 OK 3188 3191 3192 3212 C3' G C 16 OK 3210 3213 3214 3235 C3' G C 17 OK 3233 3236 3237 3258 C3' C C 18 OK 3256 3259 3260 3278 C3' A C 19 OK 3276 3279 3280 3300 C3' DG C 20 OK 3298 3301 3302 3324 C3' C D 6 OK 3322 3325 3326 3344 C3' U D 7 OK 3342 3345 3346 3364 C3' G D 8 OK 3362 3365 3366 3387 C3' C D 9 OK 3385 3388 3389 3407 C3' C D 10 OK 3405 3408 3409 3427 C3' G D 11 OK 3425 3428 3429 3450 C3' U D 12 OK 3448 3451 3452 3470 C3' A D 13 OK 3468 3471 3472 3492 C3' U D 14 OK 3490 3493 3494 3512 C3' A D 15 OK 3510 3513 3514 3534 C3' G D 16 OK 3532 3535 3536 3557 C3' G D 17 OK 3555 3558 3559 3580 C3' C D 18 OK 3578 3581 3582 3600 C3' A D 19 OK 3598 3601 3602 3622 C3' DG D 20 OK 3620 3623 3624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3000 C4' C C 6 OK 3002 2999 3001 3020 C4' U C 7 OK 3022 3019 3021 3040 C4' G C 8 OK 3042 3039 3041 3063 C4' C C 9 OK 3065 3062 3064 3083 C4' C C 10 OK 3085 3082 3084 3103 C4' G C 11 OK 3105 3102 3104 3126 C4' U C 12 OK 3128 3125 3127 3146 C4' A C 13 OK 3148 3145 3147 3168 C4' U C 14 OK 3170 3167 3169 3188 C4' A C 15 OK 3190 3187 3189 3210 C4' G C 16 OK 3212 3209 3211 3233 C4' G C 17 OK 3235 3232 3234 3256 C4' C C 18 OK 3258 3255 3257 3276 C4' A C 19 OK 3278 3275 3277 3298 C4' DG C 20 OK 3300 3297 3299 3322 C4' C D 6 OK 3324 3321 3323 3342 C4' U D 7 OK 3344 3341 3343 3362 C4' G D 8 OK 3364 3361 3363 3385 C4' C D 9 OK 3387 3384 3386 3405 C4' C D 10 OK 3407 3404 3406 3425 C4' G D 11 OK 3427 3424 3426 3448 C4' U D 12 OK 3450 3447 3449 3468 C4' A D 13 OK 3470 3467 3469 3490 C4' U D 14 OK 3492 3489 3491 3510 C4' A D 15 OK 3512 3509 3511 3532 C4' G D 16 OK 3534 3531 3533 3555 C4' G D 17 OK 3557 3554 3556 3578 C4' C D 18 OK 3580 3577 3579 3598 C4' A D 19 OK 3600 3597 3599 3620 C4' DG D 20 OK 3622 3619 3621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2999 C5' C C 6 2998 3000 3019 C5' U C 7 3018 3020 3039 C5' G C 8 3038 3040 3062 C5' C C 9 3061 3063 3082 C5' C C 10 3081 3083 3102 C5' G C 11 3101 3103 3125 C5' U C 12 3124 3126 3145 C5' A C 13 3144 3146 3167 C5' U C 14 3166 3168 3187 C5' A C 15 3186 3188 3209 C5' G C 16 3208 3210 3232 C5' G C 17 3231 3233 3255 C5' C C 18 3254 3256 3275 C5' A C 19 3274 3276 3297 C5' DG C 20 3296 3298 3321 C5' C D 6 3320 3322 3341 C5' U D 7 3340 3342 3361 C5' G D 8 3360 3362 3384 C5' C D 9 3383 3385 3404 C5' C D 10 3403 3405 3424 C5' G D 11 3423 3425 3447 C5' U D 12 3446 3448 3467 C5' A D 13 3466 3468 3489 C5' U D 14 3488 3490 3509 C5' A D 15 3508 3510 3531 C5' G D 16 3530 3532 3554 C5' G D 17 3553 3555 3577 C5' C D 18 3576 3578 3597 C5' A D 19 3596 3598 3619 C5' DG D 20 3618 3620 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3015 P U C 7 distorted distorted 3003 3016 3017 3018 3035 P G C 8 distorted distorted 3023 3036 3037 3038 3058 P C C 9 distorted distorted 3043 3059 3060 3061 3078 P C C 10 distorted distorted 3066 3079 3080 3081 3098 P G C 11 distorted distorted 3086 3099 3100 3101 3121 P U C 12 OK OK 3106 3122 3123 3124 3141 P A C 13 distorted distorted 3129 3142 3143 3144 3163 P U C 14 distorted distorted 3149 3164 3165 3166 3183 P A C 15 OK OK 3171 3184 3185 3186 3205 P G C 16 distorted distorted 3191 3206 3207 3208 3228 P G C 17 OK OK 3213 3229 3230 3231 3251 P C C 18 distorted distorted 3236 3252 3253 3254 3271 P A C 19 distorted distorted 3259 3272 3273 3274 3293 P DG C 20 distorted distorted 3279 3294 3295 3296 3315 P C C 21 distorted distorted 3301 3316 3317 3318 3337 P U D 7 distorted distorted 3325 3338 3339 3340 3357 P G D 8 distorted distorted 3345 3358 3359 3360 3380 P C D 9 distorted distorted 3365 3381 3382 3383 3400 P C D 10 distorted distorted 3388 3401 3402 3403 3420 P G D 11 distorted distorted 3408 3421 3422 3423 3443 P U D 12 OK OK 3428 3444 3445 3446 3463 P A D 13 distorted distorted 3451 3464 3465 3466 3485 P U D 14 distorted distorted 3471 3486 3487 3488 3505 P A D 15 distorted distorted 3493 3506 3507 3508 3527 P G D 16 distorted distorted 3513 3528 3529 3530 3550 P G D 17 distorted distorted 3535 3551 3552 3553 3573 P C D 18 distorted distorted 3558 3574 3575 3576 3593 P A D 19 distorted distorted 3581 3594 3595 3596 3615 P DG D 20 OK OK 3601 3616 3617 3618 3637 P C D 21 distorted distorted 3623 3638 3639 3640 ---------------------------------------------------------------------------------