ID code: '1VOL' 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' --------------------------------------------------------------------------------- 3076 C1' G C 1 beta 3072 3077 3075 3098 C1' G C 2 beta 3094 3099 3097 3120 C1' C C 3 beta 3116 3121 3119 3139 C1' T C 4 beta 3135 3140 3138 3159 C1' A C 5 beta 3155 3160 3158 3180 C1' T C 6 beta 3176 3181 3179 3200 C1' A C 7 beta 3196 3201 3199 3221 C1' A C 8 beta 3217 3222 3220 3242 C1' A C 9 beta 3238 3243 3241 3263 C1' A C 10 beta 3259 3264 3262 3284 C1' G C 11 beta 3280 3285 3283 3306 C1' G C 12 beta 3302 3307 3305 3328 C1' G C 13 beta 3324 3329 3327 3350 C1' C C 14 beta 3346 3351 3349 3369 C1' T C 15 beta 3365 3370 3368 3389 C1' G C 16 beta 3385 3390 3388 3409 C1' C D 101 beta 3405 3410 3408 3428 C1' A D 102 beta 3424 3429 3427 3449 C1' G D 103 beta 3445 3450 3448 3471 C1' C D 104 beta 3467 3472 3470 3490 C1' C D 105 beta 3486 3491 3489 3509 C1' C D 106 beta 3505 3510 3508 3528 C1' T D 107 beta 3524 3529 3527 3548 C1' T D 108 beta 3544 3549 3547 3568 C1' T D 109 beta 3564 3569 3567 3588 C1' T D 110 beta 3584 3589 3587 3608 C1' A D 111 beta 3604 3609 3607 3629 C1' T D 112 beta 3625 3630 3628 3649 C1' A D 113 beta 3645 3650 3648 3670 C1' G D 114 beta 3666 3671 3669 3692 C1' C D 115 beta 3688 3693 3691 3711 C1' C D 116 beta 3707 3712 3710 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3075 C2' G C 1 3076 3073 3097 C2' G C 2 3098 3095 3119 C2' C C 3 3120 3117 3138 C2' T C 4 3139 3136 3158 C2' A C 5 3159 3156 3179 C2' T C 6 3180 3177 3199 C2' A C 7 3200 3197 3220 C2' A C 8 3221 3218 3241 C2' A C 9 3242 3239 3262 C2' A C 10 3263 3260 3283 C2' G C 11 3284 3281 3305 C2' G C 12 3306 3303 3327 C2' G C 13 3328 3325 3349 C2' C C 14 3350 3347 3368 C2' T C 15 3369 3366 3388 C2' G C 16 3389 3386 3408 C2' C D 101 3409 3406 3427 C2' A D 102 3428 3425 3448 C2' G D 103 3449 3446 3470 C2' C D 104 3471 3468 3489 C2' C D 105 3490 3487 3508 C2' C D 106 3509 3506 3527 C2' T D 107 3528 3525 3547 C2' T D 108 3548 3545 3567 C2' T D 109 3568 3565 3587 C2' T D 110 3588 3585 3607 C2' A D 111 3608 3605 3628 C2' T D 112 3629 3626 3648 C2' A D 113 3649 3646 3669 C2' G D 114 3670 3667 3691 C2' C D 115 3692 3689 3710 C2' C D 116 3711 3708 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3073 C3' G C 1 OK 3071 3074 3075 3095 C3' G C 2 OK 3093 3096 3097 3117 C3' C C 3 OK 3115 3118 3119 3136 C3' T C 4 OK 3134 3137 3138 3156 C3' A C 5 OK 3154 3157 3158 3177 C3' T C 6 OK 3175 3178 3179 3197 C3' A C 7 OK 3195 3198 3199 3218 C3' A C 8 OK 3216 3219 3220 3239 C3' A C 9 OK 3237 3240 3241 3260 C3' A C 10 OK 3258 3261 3262 3281 C3' G C 11 OK 3279 3282 3283 3303 C3' G C 12 OK 3301 3304 3305 3325 C3' G C 13 OK 3323 3326 3327 3347 C3' C C 14 OK 3345 3348 3349 3366 C3' T C 15 OK 3364 3367 3368 3386 C3' G C 16 OK 3384 3387 3388 3406 C3' C D 101 OK 3404 3407 3408 3425 C3' A D 102 OK 3423 3426 3427 3446 C3' G D 103 OK 3444 3447 3448 3468 C3' C D 104 OK 3466 3469 3470 3487 C3' C D 105 OK 3485 3488 3489 3506 C3' C D 106 OK 3504 3507 3508 3525 C3' T D 107 OK 3523 3526 3527 3545 C3' T D 108 OK 3543 3546 3547 3565 C3' T D 109 OK 3563 3566 3567 3585 C3' T D 110 OK 3583 3586 3587 3605 C3' A D 111 OK 3603 3606 3607 3626 C3' T D 112 OK 3624 3627 3628 3646 C3' A D 113 OK 3644 3647 3648 3667 C3' G D 114 OK 3665 3668 3669 3689 C3' C D 115 OK 3687 3690 3691 3708 C3' C D 116 OK 3706 3709 3710 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3071 C4' G C 1 OK 3073 3070 3072 3093 C4' G C 2 OK 3095 3092 3094 3115 C4' C C 3 OK 3117 3114 3116 3134 C4' T C 4 OK 3136 3133 3135 3154 C4' A C 5 OK 3156 3153 3155 3175 C4' T C 6 OK 3177 3174 3176 3195 C4' A C 7 OK 3197 3194 3196 3216 C4' A C 8 OK 3218 3215 3217 3237 C4' A C 9 OK 3239 3236 3238 3258 C4' A C 10 OK 3260 3257 3259 3279 C4' G C 11 OK 3281 3278 3280 3301 C4' G C 12 OK 3303 3300 3302 3323 C4' G C 13 OK 3325 3322 3324 3345 C4' C C 14 OK 3347 3344 3346 3364 C4' T C 15 OK 3366 3363 3365 3384 C4' G C 16 OK 3386 3383 3385 3404 C4' C D 101 OK 3406 3403 3405 3423 C4' A D 102 OK 3425 3422 3424 3444 C4' G D 103 OK 3446 3443 3445 3466 C4' C D 104 OK 3468 3465 3467 3485 C4' C D 105 OK 3487 3484 3486 3504 C4' C D 106 OK 3506 3503 3505 3523 C4' T D 107 OK 3525 3522 3524 3543 C4' T D 108 OK 3545 3542 3544 3563 C4' T D 109 OK 3565 3562 3564 3583 C4' T D 110 OK 3585 3582 3584 3603 C4' A D 111 OK 3605 3602 3604 3624 C4' T D 112 OK 3626 3623 3625 3644 C4' A D 113 OK 3646 3643 3645 3665 C4' G D 114 OK 3667 3664 3666 3687 C4' C D 115 OK 3689 3686 3688 3706 C4' C D 116 OK 3708 3705 3707 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3070 C5' G C 1 3069 3071 3092 C5' G C 2 3091 3093 3114 C5' C C 3 3113 3115 3133 C5' T C 4 3132 3134 3153 C5' A C 5 3152 3154 3174 C5' T C 6 3173 3175 3194 C5' A C 7 3193 3195 3215 C5' A C 8 3214 3216 3236 C5' A C 9 3235 3237 3257 C5' A C 10 3256 3258 3278 C5' G C 11 3277 3279 3300 C5' G C 12 3299 3301 3322 C5' G C 13 3321 3323 3344 C5' C C 14 3343 3345 3363 C5' T C 15 3362 3364 3383 C5' G C 16 3382 3384 3403 C5' C D 101 3402 3404 3422 C5' A D 102 3421 3423 3443 C5' G D 103 3442 3444 3465 C5' C D 104 3464 3466 3484 C5' C D 105 3483 3485 3503 C5' C D 106 3502 3504 3522 C5' T D 107 3521 3523 3542 C5' T D 108 3541 3543 3562 C5' T D 109 3561 3563 3582 C5' T D 110 3581 3583 3602 C5' A D 111 3601 3603 3623 C5' T D 112 3622 3624 3643 C5' A D 113 3642 3644 3664 C5' G D 114 3663 3665 3686 C5' C D 115 3685 3687 3705 C5' C D 116 3704 3706 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3088 P G C 2 OK OK 3074 3089 3090 3091 3110 P C C 3 OK OK 3096 3111 3112 3113 3129 P T C 4 distorted distorted 3118 3130 3131 3132 3149 P A C 5 OK OK 3137 3150 3151 3152 3170 P T C 6 OK OK 3157 3171 3172 3173 3190 P A C 7 OK OK 3178 3191 3192 3193 3211 P A C 8 OK OK 3198 3212 3213 3214 3232 P A C 9 OK OK 3219 3233 3234 3235 3253 P A C 10 OK OK 3240 3254 3255 3256 3274 P G C 11 OK OK 3261 3275 3276 3277 3296 P G C 12 OK OK 3282 3297 3298 3299 3318 P G C 13 OK OK 3304 3319 3320 3321 3340 P C C 14 OK OK 3326 3341 3342 3343 3359 P T C 15 OK OK 3348 3360 3361 3362 3379 P G C 16 OK OK 3367 3380 3381 3382 3418 P A D 102 OK OK 3407 3419 3420 3421 3439 P G D 103 OK OK 3426 3440 3441 3442 3461 P C D 104 OK OK 3447 3462 3463 3464 3480 P C D 105 OK OK 3469 3481 3482 3483 3499 P C D 106 OK OK 3488 3500 3501 3502 3518 P T D 107 OK OK 3507 3519 3520 3521 3538 P T D 108 OK OK 3526 3539 3540 3541 3558 P T D 109 OK OK 3546 3559 3560 3561 3578 P T D 110 OK OK 3566 3579 3580 3581 3598 P A D 111 OK OK 3586 3599 3600 3601 3619 P T D 112 OK OK 3606 3620 3621 3622 3639 P A D 113 OK OK 3627 3640 3641 3642 3660 P G D 114 OK OK 3647 3661 3662 3663 3682 P C D 115 OK OK 3668 3683 3684 3685 3701 P C D 116 OK OK 3690 3702 3703 3704 ---------------------------------------------------------------------------------