ID code: '1Z0L' 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' --------------------------------------------------------------------------------- 3032 C1' T C 21 beta 3028 3033 3031 3052 C1' A C 22 beta 3048 3053 3051 3073 C1' T C 23 beta 3069 3074 3072 3093 C1' A C 24 beta 3089 3094 3092 3114 C1' G C 25 beta 3110 3115 3113 3136 C1' G C 26 beta 3132 3137 3135 3158 C1' T C 27 beta 3154 3159 3157 3178 C1' G C 28 beta 3174 3179 3177 3200 C1' G C 29 beta 3196 3201 3199 3222 C1' C C 30 beta 3218 3223 3221 3241 C1' T C 31 beta 3237 3242 3240 3261 C1' G C 32 beta 3257 3262 3260 3283 C1' T C 33 beta 3279 3284 3282 3303 C1' C C 34 beta 3299 3304 3302 3322 C1' A C 35 beta 3318 3323 3321 3343 C1' A C 36 beta 3339 3344 3342 3364 C1' G C 37 beta 3360 3365 3363 3386 C1' T C 38 beta 3382 3387 3385 3406 C1' A C 39 beta 3402 3407 3405 3427 C1' T C 40 beta 3423 3428 3426 3445 C1' A D 1 beta 3441 3446 3444 3466 C1' A D 2 beta 3462 3467 3465 3487 C1' T D 3 beta 3483 3488 3486 3507 C1' A D 4 beta 3503 3508 3506 3528 C1' C D 5 beta 3524 3529 3527 3547 C1' T D 6 beta 3543 3548 3546 3567 C1' T D 7 beta 3563 3568 3566 3587 C1' G D 8 beta 3583 3588 3586 3609 C1' A D 9 beta 3605 3610 3608 3630 C1' C D 10 beta 3626 3631 3629 3649 C1' A D 11 beta 3645 3650 3648 3670 C1' G D 12 beta 3666 3671 3669 3692 C1' C D 13 beta 3688 3693 3691 3711 C1' C D 14 beta 3707 3712 3710 3730 C1' A D 15 beta 3726 3731 3729 3751 C1' C D 16 beta 3747 3752 3750 3770 C1' C D 17 beta 3766 3771 3769 3789 C1' T D 18 beta 3785 3790 3788 3809 C1' A D 19 beta 3805 3810 3808 3830 C1' T D 20 beta 3826 3831 3829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3031 C2' T C 21 3032 3029 3051 C2' A C 22 3052 3049 3072 C2' T C 23 3073 3070 3092 C2' A C 24 3093 3090 3113 C2' G C 25 3114 3111 3135 C2' G C 26 3136 3133 3157 C2' T C 27 3158 3155 3177 C2' G C 28 3178 3175 3199 C2' G C 29 3200 3197 3221 C2' C C 30 3222 3219 3240 C2' T C 31 3241 3238 3260 C2' G C 32 3261 3258 3282 C2' T C 33 3283 3280 3302 C2' C C 34 3303 3300 3321 C2' A C 35 3322 3319 3342 C2' A C 36 3343 3340 3363 C2' G C 37 3364 3361 3385 C2' T C 38 3386 3383 3405 C2' A C 39 3406 3403 3426 C2' T C 40 3427 3424 3444 C2' A D 1 3445 3442 3465 C2' A D 2 3466 3463 3486 C2' T D 3 3487 3484 3506 C2' A D 4 3507 3504 3527 C2' C D 5 3528 3525 3546 C2' T D 6 3547 3544 3566 C2' T D 7 3567 3564 3586 C2' G D 8 3587 3584 3608 C2' A D 9 3609 3606 3629 C2' C D 10 3630 3627 3648 C2' A D 11 3649 3646 3669 C2' G D 12 3670 3667 3691 C2' C D 13 3692 3689 3710 C2' C D 14 3711 3708 3729 C2' A D 15 3730 3727 3750 C2' C D 16 3751 3748 3769 C2' C D 17 3770 3767 3788 C2' T D 18 3789 3786 3808 C2' A D 19 3809 3806 3829 C2' T D 20 3830 3827 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3029 C3' T C 21 OK 3027 3030 3031 3049 C3' A C 22 OK 3047 3050 3051 3070 C3' T C 23 OK 3068 3071 3072 3090 C3' A C 24 OK 3088 3091 3092 3111 C3' G C 25 OK 3109 3112 3113 3133 C3' G C 26 OK 3131 3134 3135 3155 C3' T C 27 OK 3153 3156 3157 3175 C3' G C 28 OK 3173 3176 3177 3197 C3' G C 29 OK 3195 3198 3199 3219 C3' C C 30 OK 3217 3220 3221 3238 C3' T C 31 OK 3236 3239 3240 3258 C3' G C 32 OK 3256 3259 3260 3280 C3' T C 33 OK 3278 3281 3282 3300 C3' C C 34 OK 3298 3301 3302 3319 C3' A C 35 OK 3317 3320 3321 3340 C3' A C 36 OK 3338 3341 3342 3361 C3' G C 37 OK 3359 3362 3363 3383 C3' T C 38 OK 3381 3384 3385 3403 C3' A C 39 OK 3401 3404 3405 3424 C3' T C 40 OK 3422 3425 3426 3442 C3' A D 1 OK 3440 3443 3444 3463 C3' A D 2 OK 3461 3464 3465 3484 C3' T D 3 OK 3482 3485 3486 3504 C3' A D 4 OK 3502 3505 3506 3525 C3' C D 5 OK 3523 3526 3527 3544 C3' T D 6 OK 3542 3545 3546 3564 C3' T D 7 OK 3562 3565 3566 3584 C3' G D 8 OK 3582 3585 3586 3606 C3' A D 9 OK 3604 3607 3608 3627 C3' C D 10 OK 3625 3628 3629 3646 C3' A D 11 OK 3644 3647 3648 3667 C3' G D 12 OK 3665 3668 3669 3689 C3' C D 13 OK 3687 3690 3691 3708 C3' C D 14 OK 3706 3709 3710 3727 C3' A D 15 OK 3725 3728 3729 3748 C3' C D 16 OK 3746 3749 3750 3767 C3' C D 17 OK 3765 3768 3769 3786 C3' T D 18 OK 3784 3787 3788 3806 C3' A D 19 OK 3804 3807 3808 3827 C3' T D 20 OK 3825 3828 3829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3027 C4' T C 21 OK 3029 3026 3028 3047 C4' A C 22 OK 3049 3046 3048 3068 C4' T C 23 OK 3070 3067 3069 3088 C4' A C 24 OK 3090 3087 3089 3109 C4' G C 25 OK 3111 3108 3110 3131 C4' G C 26 OK 3133 3130 3132 3153 C4' T C 27 OK 3155 3152 3154 3173 C4' G C 28 OK 3175 3172 3174 3195 C4' G C 29 OK 3197 3194 3196 3217 C4' C C 30 OK 3219 3216 3218 3236 C4' T C 31 OK 3238 3235 3237 3256 C4' G C 32 OK 3258 3255 3257 3278 C4' T C 33 OK 3280 3277 3279 3298 C4' C C 34 OK 3300 3297 3299 3317 C4' A C 35 OK 3319 3316 3318 3338 C4' A C 36 OK 3340 3337 3339 3359 C4' G C 37 OK 3361 3358 3360 3381 C4' T C 38 OK 3383 3380 3382 3401 C4' A C 39 OK 3403 3400 3402 3422 C4' T C 40 OK 3424 3421 3423 3440 C4' A D 1 OK 3442 3439 3441 3461 C4' A D 2 OK 3463 3460 3462 3482 C4' T D 3 OK 3484 3481 3483 3502 C4' A D 4 OK 3504 3501 3503 3523 C4' C D 5 OK 3525 3522 3524 3542 C4' T D 6 OK 3544 3541 3543 3562 C4' T D 7 OK 3564 3561 3563 3582 C4' G D 8 OK 3584 3581 3583 3604 C4' A D 9 OK 3606 3603 3605 3625 C4' C D 10 OK 3627 3624 3626 3644 C4' A D 11 OK 3646 3643 3645 3665 C4' G D 12 OK 3667 3664 3666 3687 C4' C D 13 OK 3689 3686 3688 3706 C4' C D 14 OK 3708 3705 3707 3725 C4' A D 15 OK 3727 3724 3726 3746 C4' C D 16 OK 3748 3745 3747 3765 C4' C D 17 OK 3767 3764 3766 3784 C4' T D 18 OK 3786 3783 3785 3804 C4' A D 19 OK 3806 3803 3805 3825 C4' T D 20 OK 3827 3824 3826 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3026 C5' T C 21 3025 3027 3046 C5' A C 22 3045 3047 3067 C5' T C 23 3066 3068 3087 C5' A C 24 3086 3088 3108 C5' G C 25 3107 3109 3130 C5' G C 26 3129 3131 3152 C5' T C 27 3151 3153 3172 C5' G C 28 3171 3173 3194 C5' G C 29 3193 3195 3216 C5' C C 30 3215 3217 3235 C5' T C 31 3234 3236 3255 C5' G C 32 3254 3256 3277 C5' T C 33 3276 3278 3297 C5' C C 34 3296 3298 3316 C5' A C 35 3315 3317 3337 C5' A C 36 3336 3338 3358 C5' G C 37 3357 3359 3380 C5' T C 38 3379 3381 3400 C5' A C 39 3399 3401 3421 C5' T C 40 3420 3422 3439 C5' A D 1 3438 3440 3460 C5' A D 2 3459 3461 3481 C5' T D 3 3480 3482 3501 C5' A D 4 3500 3502 3522 C5' C D 5 3521 3523 3541 C5' T D 6 3540 3542 3561 C5' T D 7 3560 3562 3581 C5' G D 8 3580 3582 3603 C5' A D 9 3602 3604 3624 C5' C D 10 3623 3625 3643 C5' A D 11 3642 3644 3664 C5' G D 12 3663 3665 3686 C5' C D 13 3685 3687 3705 C5' C D 14 3704 3706 3724 C5' A D 15 3723 3725 3745 C5' C D 16 3744 3746 3764 C5' C D 17 3763 3765 3783 C5' T D 18 3782 3784 3803 C5' A D 19 3802 3804 3824 C5' T D 20 3823 3825 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3042 P A C 22 distorted distorted 3030 3043 3044 3045 3063 P T C 23 distorted distorted 3050 3064 3065 3066 3083 P A C 24 distorted distorted 3071 3084 3085 3086 3104 P G C 25 distorted distorted 3091 3105 3106 3107 3126 P G C 26 distorted distorted 3112 3127 3128 3129 3148 P T C 27 distorted distorted 3134 3149 3150 3151 3168 P G C 28 distorted distorted 3156 3169 3170 3171 3190 P G C 29 distorted distorted 3176 3191 3192 3193 3212 P C C 30 distorted distorted 3198 3213 3214 3215 3231 P T C 31 distorted distorted 3220 3232 3233 3234 3251 P G C 32 distorted distorted 3239 3252 3253 3254 3273 P T C 33 distorted distorted 3259 3274 3275 3276 3293 P C C 34 distorted distorted 3281 3294 3295 3296 3312 P A C 35 distorted distorted 3301 3313 3314 3315 3333 P A C 36 distorted distorted 3320 3334 3335 3336 3354 P G C 37 distorted distorted 3341 3355 3356 3357 3376 P T C 38 distorted distorted 3362 3377 3378 3379 3396 P A C 39 distorted distorted 3384 3397 3398 3399 3417 P T C 40 distorted distorted 3404 3418 3419 3420 3456 P A D 2 distorted distorted 3443 3457 3458 3459 3477 P T D 3 distorted distorted 3464 3478 3479 3480 3497 P A D 4 distorted distorted 3485 3498 3499 3500 3518 P C D 5 distorted distorted 3505 3519 3520 3521 3537 P T D 6 distorted distorted 3526 3538 3539 3540 3557 P T D 7 distorted distorted 3545 3558 3559 3560 3577 P G D 8 distorted distorted 3565 3578 3579 3580 3599 P A D 9 distorted distorted 3585 3600 3601 3602 3620 P C D 10 distorted distorted 3607 3621 3622 3623 3639 P A D 11 distorted distorted 3628 3640 3641 3642 3660 P G D 12 distorted distorted 3647 3661 3662 3663 3682 P C D 13 distorted distorted 3668 3683 3684 3685 3701 P C D 14 distorted distorted 3690 3702 3703 3704 3720 P A D 15 distorted distorted 3709 3721 3722 3723 3741 P C D 16 distorted distorted 3728 3742 3743 3744 3760 P C D 17 distorted distorted 3749 3761 3762 3763 3779 P T D 18 distorted distorted 3768 3780 3781 3782 3799 P A D 19 distorted distorted 3787 3800 3801 3802 3820 P T D 20 distorted distorted 3807 3821 3822 3823 ---------------------------------------------------------------------------------