ID code: '4NDI' 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' --------------------------------------------------------------------------------- 3066 C1' G D 1 beta 3061 3067 3064 3088 C1' DT D 2 beta 3084 3089 3087 3190 C1' DT D 5 beta 3186 3191 3189 3210 C1' DG D 6 beta 3206 3211 3209 3232 C1' DA D 7 beta 3228 3233 3231 3253 C1' DT D 8 beta 3249 3254 3252 3273 C1' DT D 9 beta 3269 3274 3272 3293 C1' DC D 10 beta 3289 3294 3292 3310 C1' DG E 1 beta 3306 3311 3309 3332 C1' DA E 2 beta 3328 3333 3331 3353 C1' DA E 3 beta 3349 3354 3352 3374 C1' DT E 4 beta 3370 3375 3373 3394 C1' DC E 5 beta 3390 3395 3393 3413 C1' DA E 6 beta 3409 3414 3412 3434 C1' DT E 7 beta 3430 3435 3433 3454 C1' DA E 8 beta 3450 3455 3453 3475 C1' DA E 9 beta 3471 3476 3474 3496 C1' DC E 10 beta 3492 3497 3495 3518 C1' G G 1 beta 3513 3519 3516 3540 C1' DT G 2 beta 3536 3541 3539 3560 C1' DT G 3 beta 3556 3561 3559 3580 C1' DA G 4 beta 3576 3581 3579 3601 C1' DT G 5 beta 3597 3602 3600 3621 C1' DG G 6 beta 3617 3622 3620 3643 C1' DA G 7 beta 3639 3644 3642 3664 C1' DT G 8 beta 3660 3665 3663 3684 C1' DT G 9 beta 3680 3685 3683 3704 C1' DC G 10 beta 3700 3705 3703 3721 C1' DG H 1 beta 3717 3722 3720 3743 C1' DA H 2 beta 3739 3744 3742 3764 C1' DA H 3 beta 3760 3765 3763 3785 C1' DT H 4 beta 3781 3786 3784 3805 C1' DC H 5 beta 3801 3806 3804 3824 C1' DA H 6 beta 3820 3825 3823 3845 C1' DT H 7 beta 3841 3846 3844 3865 C1' DA H 8 beta 3861 3866 3864 3886 C1' DA H 9 beta 3882 3887 3885 3907 C1' DC H 10 beta 3903 3908 3906 3929 C1' AMP A 401 beta 3924 3930 3927 3964 C1' AMP B 401 beta 3959 3965 3962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3064 C2' G D 1 OK 3066 3062 3065 3087 C2' DT D 2 3088 3085 3189 C2' DT D 5 3190 3187 3209 C2' DG D 6 3210 3207 3231 C2' DA D 7 3232 3229 3252 C2' DT D 8 3253 3250 3272 C2' DT D 9 3273 3270 3292 C2' DC D 10 3293 3290 3309 C2' DG E 1 3310 3307 3331 C2' DA E 2 3332 3329 3352 C2' DA E 3 3353 3350 3373 C2' DT E 4 3374 3371 3393 C2' DC E 5 3394 3391 3412 C2' DA E 6 3413 3410 3433 C2' DT E 7 3434 3431 3453 C2' DA E 8 3454 3451 3474 C2' DA E 9 3475 3472 3495 C2' DC E 10 3496 3493 3516 C2' G G 1 OK 3518 3514 3517 3539 C2' DT G 2 3540 3537 3559 C2' DT G 3 3560 3557 3579 C2' DA G 4 3580 3577 3600 C2' DT G 5 3601 3598 3620 C2' DG G 6 3621 3618 3642 C2' DA G 7 3643 3640 3663 C2' DT G 8 3664 3661 3683 C2' DT G 9 3684 3681 3703 C2' DC G 10 3704 3701 3720 C2' DG H 1 3721 3718 3742 C2' DA H 2 3743 3740 3763 C2' DA H 3 3764 3761 3784 C2' DT H 4 3785 3782 3804 C2' DC H 5 3805 3802 3823 C2' DA H 6 3824 3821 3844 C2' DT H 7 3845 3842 3864 C2' DA H 8 3865 3862 3885 C2' DA H 9 3886 3883 3906 C2' DC H 10 3907 3904 3927 C2' AMP A 401 OK 3929 3925 3928 3962 C2' AMP B 401 OK 3964 3960 3963 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3062 C3' G D 1 OK 3060 3063 3064 3085 C3' DT D 2 OK 3083 3086 3087 3187 C3' DT D 5 OK 3185 3188 3189 3207 C3' DG D 6 OK 3205 3208 3209 3229 C3' DA D 7 OK 3227 3230 3231 3250 C3' DT D 8 OK 3248 3251 3252 3270 C3' DT D 9 OK 3268 3271 3272 3290 C3' DC D 10 OK 3288 3291 3292 3307 C3' DG E 1 OK 3305 3308 3309 3329 C3' DA E 2 OK 3327 3330 3331 3350 C3' DA E 3 OK 3348 3351 3352 3371 C3' DT E 4 OK 3369 3372 3373 3391 C3' DC E 5 OK 3389 3392 3393 3410 C3' DA E 6 OK 3408 3411 3412 3431 C3' DT E 7 OK 3429 3432 3433 3451 C3' DA E 8 OK 3449 3452 3453 3472 C3' DA E 9 OK 3470 3473 3474 3493 C3' DC E 10 OK 3491 3494 3495 3514 C3' G G 1 OK 3512 3515 3516 3537 C3' DT G 2 OK 3535 3538 3539 3557 C3' DT G 3 OK 3555 3558 3559 3577 C3' DA G 4 OK 3575 3578 3579 3598 C3' DT G 5 OK 3596 3599 3600 3618 C3' DG G 6 OK 3616 3619 3620 3640 C3' DA G 7 OK 3638 3641 3642 3661 C3' DT G 8 OK 3659 3662 3663 3681 C3' DT G 9 OK 3679 3682 3683 3701 C3' DC G 10 OK 3699 3702 3703 3718 C3' DG H 1 OK 3716 3719 3720 3740 C3' DA H 2 OK 3738 3741 3742 3761 C3' DA H 3 OK 3759 3762 3763 3782 C3' DT H 4 OK 3780 3783 3784 3802 C3' DC H 5 OK 3800 3803 3804 3821 C3' DA H 6 OK 3819 3822 3823 3842 C3' DT H 7 OK 3840 3843 3844 3862 C3' DA H 8 OK 3860 3863 3864 3883 C3' DA H 9 OK 3881 3884 3885 3904 C3' DC H 10 OK 3902 3905 3906 3925 C3' AMP A 401 OK 3923 3926 3927 3960 C3' AMP B 401 OK 3958 3961 3962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3060 C4' G D 1 OK 3062 3059 3061 3083 C4' DT D 2 OK 3085 3082 3084 3185 C4' DT D 5 OK 3187 3184 3186 3205 C4' DG D 6 OK 3207 3204 3206 3227 C4' DA D 7 OK 3229 3226 3228 3248 C4' DT D 8 OK 3250 3247 3249 3268 C4' DT D 9 OK 3270 3267 3269 3288 C4' DC D 10 OK 3290 3287 3289 3305 C4' DG E 1 OK 3307 3304 3306 3327 C4' DA E 2 OK 3329 3326 3328 3348 C4' DA E 3 OK 3350 3347 3349 3369 C4' DT E 4 OK 3371 3368 3370 3389 C4' DC E 5 OK 3391 3388 3390 3408 C4' DA E 6 OK 3410 3407 3409 3429 C4' DT E 7 OK 3431 3428 3430 3449 C4' DA E 8 OK 3451 3448 3450 3470 C4' DA E 9 OK 3472 3469 3471 3491 C4' DC E 10 OK 3493 3490 3492 3512 C4' G G 1 OK 3514 3511 3513 3535 C4' DT G 2 OK 3537 3534 3536 3555 C4' DT G 3 OK 3557 3554 3556 3575 C4' DA G 4 OK 3577 3574 3576 3596 C4' DT G 5 OK 3598 3595 3597 3616 C4' DG G 6 OK 3618 3615 3617 3638 C4' DA G 7 OK 3640 3637 3639 3659 C4' DT G 8 OK 3661 3658 3660 3679 C4' DT G 9 OK 3681 3678 3680 3699 C4' DC G 10 OK 3701 3698 3700 3716 C4' DG H 1 OK 3718 3715 3717 3738 C4' DA H 2 OK 3740 3737 3739 3759 C4' DA H 3 OK 3761 3758 3760 3780 C4' DT H 4 OK 3782 3779 3781 3800 C4' DC H 5 OK 3802 3799 3801 3819 C4' DA H 6 OK 3821 3818 3820 3840 C4' DT H 7 OK 3842 3839 3841 3860 C4' DA H 8 OK 3862 3859 3861 3881 C4' DA H 9 OK 3883 3880 3882 3902 C4' DC H 10 OK 3904 3901 3903 3923 C4' AMP A 401 OK 3925 3922 3924 3958 C4' AMP B 401 OK 3960 3957 3959 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3059 C5' G D 1 3058 3060 3082 C5' DT D 2 3081 3083 3184 C5' DT D 5 3183 3185 3204 C5' DG D 6 3203 3205 3226 C5' DA D 7 3225 3227 3247 C5' DT D 8 3246 3248 3267 C5' DT D 9 3266 3268 3287 C5' DC D 10 3286 3288 3304 C5' DG E 1 3303 3305 3326 C5' DA E 2 3325 3327 3347 C5' DA E 3 3346 3348 3368 C5' DT E 4 3367 3369 3388 C5' DC E 5 3387 3389 3407 C5' DA E 6 3406 3408 3428 C5' DT E 7 3427 3429 3448 C5' DA E 8 3447 3449 3469 C5' DA E 9 3468 3470 3490 C5' DC E 10 3489 3491 3511 C5' G G 1 3510 3512 3534 C5' DT G 2 3533 3535 3554 C5' DT G 3 3553 3555 3574 C5' DA G 4 3573 3575 3595 C5' DT G 5 3594 3596 3615 C5' DG G 6 3614 3616 3637 C5' DA G 7 3636 3638 3658 C5' DT G 8 3657 3659 3678 C5' DT G 9 3677 3679 3698 C5' DC G 10 3697 3699 3715 C5' DG H 1 3714 3716 3737 C5' DA H 2 3736 3738 3758 C5' DA H 3 3757 3759 3779 C5' DT H 4 3778 3780 3799 C5' DC H 5 3798 3800 3818 C5' DA H 6 3817 3819 3839 C5' DT H 7 3838 3840 3859 C5' DA H 8 3858 3860 3880 C5' DA H 9 3879 3881 3901 C5' DC H 10 3900 3902 3922 C5' AMP A 401 3921 3923 3957 C5' AMP B 401 3956 3958 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3055 P G D 1 distorted distorted 3056 3057 3058 3078 P DT D 2 distorted distorted 3063 3079 3080 3081 3098 P DT D 3 3086 3099 P DT D 3 3086 3138 P DA D 4 3139 P DA D 4 3180 P DT D 5 distorted distorted 3181 3182 3183 3200 P DG D 6 distorted distorted 3188 3201 3202 3203 3222 P DA D 7 distorted distorted 3208 3223 3224 3225 3243 P DT D 8 distorted distorted 3230 3244 3245 3246 3263 P DT D 9 distorted distorted 3251 3264 3265 3266 3283 P DC D 10 distorted distorted 3271 3284 3285 3286 3322 P DA E 2 distorted distorted 3308 3323 3324 3325 3343 P DA E 3 distorted distorted 3330 3344 3345 3346 3364 P DT E 4 distorted distorted 3351 3365 3366 3367 3384 P DC E 5 distorted distorted 3372 3385 3386 3387 3403 P DA E 6 distorted distorted 3392 3404 3405 3406 3424 P DT E 7 distorted distorted 3411 3425 3426 3427 3444 P DA E 8 distorted distorted 3432 3445 3446 3447 3465 P DA E 9 distorted distorted 3452 3466 3467 3468 3486 P DC E 10 distorted distorted 3473 3487 3488 3489 3507 P G G 1 OK OK 3508 3509 3510 3530 P DT G 2 distorted distorted 3515 3531 3532 3533 3550 P DT G 3 distorted distorted 3538 3551 3552 3553 3570 P DA G 4 distorted distorted 3558 3571 3572 3573 3591 P DT G 5 distorted distorted 3578 3592 3593 3594 3611 P DG G 6 distorted distorted 3599 3612 3613 3614 3633 P DA G 7 distorted distorted 3619 3634 3635 3636 3654 P DT G 8 distorted distorted 3641 3655 3656 3657 3674 P DT G 9 distorted distorted 3662 3675 3676 3677 3694 P DC G 10 distorted distorted 3682 3695 3696 3697 3733 P DA H 2 distorted distorted 3719 3734 3735 3736 3754 P DA H 3 distorted distorted 3741 3755 3756 3757 3775 P DT H 4 distorted distorted 3762 3776 3777 3778 3795 P DC H 5 distorted distorted 3783 3796 3797 3798 3814 P DA H 6 distorted distorted 3803 3815 3816 3817 3835 P DT H 7 distorted distorted 3822 3836 3837 3838 3855 P DA H 8 distorted distorted 3843 3856 3857 3858 3876 P DA H 9 distorted distorted 3863 3877 3878 3879 3897 P DC H 10 distorted distorted 3884 3898 3899 3900 3917 P AMP A 401 distorted distorted 3918 3919 3921 3952 P AMP B 401 OK OK 3953 3954 3956 ---------------------------------------------------------------------------------