ID code: '4Z7K' 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' --------------------------------------------------------------------------------- 3403 C1' G C 7 beta 3398 3404 3401 3426 C1' A C 8 beta 3421 3427 3424 3448 C1' A C 9 beta 3443 3449 3446 3470 C1' U C 10 beta 3465 3471 3468 3490 C1' A C 11 beta 3485 3491 3488 3512 C1' A C 12 beta 3507 3513 3510 3534 C1' C C 13 beta 3529 3535 3532 3554 C1' U C 14 beta 3549 3555 3552 3574 C1' U C 15 beta 3569 3575 3572 3594 C1' G C 16 beta 3589 3595 3592 3617 C1' C C 17 beta 3612 3618 3615 3637 C1' A C 18 beta 3632 3638 3635 3659 C1' A C 19 beta 3654 3660 3657 3681 C1' A C 20 beta 3676 3682 3679 3703 C1' A C 21 beta 3698 3704 3701 3725 C1' U C 22 beta 3720 3726 3723 3745 C1' A C 23 beta 3740 3746 3743 3767 C1' A C 24 beta 3762 3768 3765 3789 C1' C C 25 beta 3784 3790 3787 3809 C1' A C 26 beta 3804 3810 3807 3831 C1' A C 27 beta 3826 3832 3829 3853 C1' G C 28 beta 3848 3854 3851 3875 C1' DC C 29 beta 3871 3876 3874 3895 C1' A C 30 beta 3890 3896 3893 3917 C1' U C 31 beta 3912 3918 3915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3401 C2' G C 7 OK 3403 3399 3402 3424 C2' A C 8 OK 3426 3422 3425 3446 C2' A C 9 OK 3448 3444 3447 3468 C2' U C 10 OK 3470 3466 3469 3488 C2' A C 11 OK 3490 3486 3489 3510 C2' A C 12 OK 3512 3508 3511 3532 C2' C C 13 OK 3534 3530 3533 3552 C2' U C 14 OK 3554 3550 3553 3572 C2' U C 15 OK 3574 3570 3573 3592 C2' G C 16 OK 3594 3590 3593 3615 C2' C C 17 OK 3617 3613 3616 3635 C2' A C 18 OK 3637 3633 3636 3657 C2' A C 19 OK 3659 3655 3658 3679 C2' A C 20 OK 3681 3677 3680 3701 C2' A C 21 OK 3703 3699 3702 3723 C2' U C 22 OK 3725 3721 3724 3743 C2' A C 23 OK 3745 3741 3744 3765 C2' A C 24 OK 3767 3763 3766 3787 C2' C C 25 OK 3789 3785 3788 3807 C2' A C 26 OK 3809 3805 3808 3829 C2' A C 27 OK 3831 3827 3830 3851 C2' G C 28 OK 3853 3849 3852 3874 C2' DC C 29 3875 3872 3893 C2' A C 30 OK 3895 3891 3894 3915 C2' U C 31 OK 3917 3913 3916 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3399 C3' G C 7 OK 3397 3400 3401 3422 C3' A C 8 OK 3420 3423 3424 3444 C3' A C 9 OK 3442 3445 3446 3466 C3' U C 10 OK 3464 3467 3468 3486 C3' A C 11 OK 3484 3487 3488 3508 C3' A C 12 OK 3506 3509 3510 3530 C3' C C 13 OK 3528 3531 3532 3550 C3' U C 14 OK 3548 3551 3552 3570 C3' U C 15 OK 3568 3571 3572 3590 C3' G C 16 OK 3588 3591 3592 3613 C3' C C 17 OK 3611 3614 3615 3633 C3' A C 18 OK 3631 3634 3635 3655 C3' A C 19 OK 3653 3656 3657 3677 C3' A C 20 OK 3675 3678 3679 3699 C3' A C 21 OK 3697 3700 3701 3721 C3' U C 22 OK 3719 3722 3723 3741 C3' A C 23 OK 3739 3742 3743 3763 C3' A C 24 OK 3761 3764 3765 3785 C3' C C 25 OK 3783 3786 3787 3805 C3' A C 26 OK 3803 3806 3807 3827 C3' A C 27 OK 3825 3828 3829 3849 C3' G C 28 OK 3847 3850 3851 3872 C3' DC C 29 OK 3870 3873 3874 3891 C3' A C 30 OK 3889 3892 3893 3913 C3' U C 31 OK 3911 3914 3915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3397 C4' G C 7 OK 3399 3396 3398 3420 C4' A C 8 OK 3422 3419 3421 3442 C4' A C 9 OK 3444 3441 3443 3464 C4' U C 10 OK 3466 3463 3465 3484 C4' A C 11 OK 3486 3483 3485 3506 C4' A C 12 OK 3508 3505 3507 3528 C4' C C 13 OK 3530 3527 3529 3548 C4' U C 14 OK 3550 3547 3549 3568 C4' U C 15 OK 3570 3567 3569 3588 C4' G C 16 OK 3590 3587 3589 3611 C4' C C 17 OK 3613 3610 3612 3631 C4' A C 18 OK 3633 3630 3632 3653 C4' A C 19 OK 3655 3652 3654 3675 C4' A C 20 OK 3677 3674 3676 3697 C4' A C 21 OK 3699 3696 3698 3719 C4' U C 22 OK 3721 3718 3720 3739 C4' A C 23 OK 3741 3738 3740 3761 C4' A C 24 OK 3763 3760 3762 3783 C4' C C 25 OK 3785 3782 3784 3803 C4' A C 26 OK 3805 3802 3804 3825 C4' A C 27 OK 3827 3824 3826 3847 C4' G C 28 OK 3849 3846 3848 3870 C4' DC C 29 OK 3872 3869 3871 3889 C4' A C 30 OK 3891 3888 3890 3911 C4' U C 31 OK 3913 3910 3912 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3396 C5' G C 7 3395 3397 3419 C5' A C 8 3418 3420 3441 C5' A C 9 3440 3442 3463 C5' U C 10 3462 3464 3483 C5' A C 11 3482 3484 3505 C5' A C 12 3504 3506 3527 C5' C C 13 3526 3528 3547 C5' U C 14 3546 3548 3567 C5' U C 15 3566 3568 3587 C5' G C 16 3586 3588 3610 C5' C C 17 3609 3611 3630 C5' A C 18 3629 3631 3652 C5' A C 19 3651 3653 3674 C5' A C 20 3673 3675 3696 C5' A C 21 3695 3697 3718 C5' U C 22 3717 3719 3738 C5' A C 23 3737 3739 3760 C5' A C 24 3759 3761 3782 C5' C C 25 3781 3783 3802 C5' A C 26 3801 3803 3824 C5' A C 27 3823 3825 3846 C5' G C 28 3845 3847 3869 C5' DC C 29 3868 3870 3888 C5' A C 30 3887 3889 3910 C5' U C 31 3909 3911 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3415 P A C 8 distorted distorted 3400 3416 3417 3418 3437 P A C 9 distorted distorted 3423 3438 3439 3440 3459 P U C 10 distorted distorted 3445 3460 3461 3462 3479 P A C 11 distorted distorted 3467 3480 3481 3482 3501 P A C 12 distorted distorted 3487 3502 3503 3504 3523 P C C 13 distorted distorted 3509 3524 3525 3526 3543 P U C 14 distorted distorted 3531 3544 3545 3546 3563 P U C 15 distorted distorted 3551 3564 3565 3566 3583 P G C 16 distorted distorted 3571 3584 3585 3586 3606 P C C 17 distorted distorted 3591 3607 3608 3609 3626 P A C 18 distorted distorted 3614 3627 3628 3629 3648 P A C 19 distorted distorted 3634 3649 3650 3651 3670 P A C 20 distorted distorted 3656 3671 3672 3673 3692 P A C 21 distorted distorted 3678 3693 3694 3695 3714 P U C 22 distorted distorted 3700 3715 3716 3717 3734 P A C 23 distorted distorted 3722 3735 3736 3737 3756 P A C 24 distorted distorted 3742 3757 3758 3759 3778 P C C 25 distorted distorted 3764 3779 3780 3781 3798 P A C 26 distorted distorted 3786 3799 3800 3801 3820 P A C 27 distorted distorted 3806 3821 3822 3823 3842 P G C 28 distorted distorted 3828 3843 3844 3845 3865 P DC C 29 distorted distorted 3850 3866 3867 3868 3884 P A C 30 distorted distorted 3873 3885 3886 3887 3906 P U C 31 distorted distorted 3892 3907 3908 3909 ---------------------------------------------------------------------------------