ID code: '3BJY' 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' --------------------------------------------------------------------------------- 3379 C1' DT T 1 beta 3375 3380 3378 3399 C1' DA T 2 beta 3395 3400 3398 3420 C1' DA T 3 beta 3416 3421 3419 3441 C1' P T 4 beta 3437 3442 3440 3466 C1' DG T 5 beta 3462 3467 3465 3488 C1' DT T 6 beta 3484 3489 3487 3508 C1' DA T 7 beta 3504 3509 3507 3529 C1' DG T 8 beta 3525 3530 3528 3551 C1' DG T 9 beta 3547 3552 3550 3573 C1' DG T 10 beta 3569 3574 3572 3595 C1' DG T 11 beta 3591 3596 3594 3617 C1' DA T 12 beta 3613 3618 3616 3638 C1' DG T 13 beta 3634 3639 3637 3660 C1' DG T 14 beta 3656 3661 3659 3682 C1' DA T 15 beta 3678 3683 3681 3703 C1' DT T 16 beta 3699 3704 3702 3721 C1' DA P 1 beta 3717 3722 3720 3742 C1' DT P 2 beta 3738 3743 3741 3762 C1' DC P 3 beta 3758 3763 3761 3781 C1' DC P 4 beta 3777 3782 3780 3800 C1' DT P 5 beta 3796 3801 3799 3820 C1' DC P 6 beta 3816 3821 3819 3839 C1' DC P 7 beta 3835 3840 3838 3858 C1' DC P 8 beta 3854 3859 3857 3877 C1' DC P 9 beta 3873 3878 3876 3896 C1' DT P 10 beta 3892 3897 3895 3916 C1' DA P 11 beta 3912 3917 3915 3935 C1' DOC P 12 beta 3939 3927 3936 3954 C1' DCP A 739 beta 3958 3946 3955 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3378 C2' DT T 1 3379 3376 3398 C2' DA T 2 3399 3396 3419 C2' DA T 3 3420 3417 3440 C2' P T 4 3441 3438 3465 C2' DG T 5 3466 3463 3487 C2' DT T 6 3488 3485 3507 C2' DA T 7 3508 3505 3528 C2' DG T 8 3529 3526 3550 C2' DG T 9 3551 3548 3572 C2' DG T 10 3573 3570 3594 C2' DG T 11 3595 3592 3616 C2' DA T 12 3617 3614 3637 C2' DG T 13 3638 3635 3659 C2' DG T 14 3660 3657 3681 C2' DA T 15 3682 3679 3702 C2' DT T 16 3703 3700 3720 C2' DA P 1 3721 3718 3741 C2' DT P 2 3742 3739 3761 C2' DC P 3 3762 3759 3780 C2' DC P 4 3781 3778 3799 C2' DT P 5 3800 3797 3819 C2' DC P 6 3820 3817 3838 C2' DC P 7 3839 3836 3857 C2' DC P 8 3858 3855 3876 C2' DC P 9 3877 3874 3895 C2' DT P 10 3896 3893 3915 C2' DA P 11 3916 3913 3936 C2' DOC P 12 3935 3937 3955 C2' DCP A 739 3954 3956 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3376 C3' DT T 1 OK 3374 3377 3378 3396 C3' DA T 2 OK 3394 3397 3398 3417 C3' DA T 3 OK 3415 3418 3419 3438 C3' P T 4 OK 3436 3439 3440 3463 C3' DG T 5 OK 3461 3464 3465 3485 C3' DT T 6 OK 3483 3486 3487 3505 C3' DA T 7 OK 3503 3506 3507 3526 C3' DG T 8 OK 3524 3527 3528 3548 C3' DG T 9 OK 3546 3549 3550 3570 C3' DG T 10 OK 3568 3571 3572 3592 C3' DG T 11 OK 3590 3593 3594 3614 C3' DA T 12 OK 3612 3615 3616 3635 C3' DG T 13 OK 3633 3636 3637 3657 C3' DG T 14 OK 3655 3658 3659 3679 C3' DA T 15 OK 3677 3680 3681 3700 C3' DT T 16 OK 3698 3701 3702 3718 C3' DA P 1 OK 3716 3719 3720 3739 C3' DT P 2 OK 3737 3740 3741 3759 C3' DC P 3 OK 3757 3760 3761 3778 C3' DC P 4 OK 3776 3779 3780 3797 C3' DT P 5 OK 3795 3798 3799 3817 C3' DC P 6 OK 3815 3818 3819 3836 C3' DC P 7 OK 3834 3837 3838 3855 C3' DC P 8 OK 3853 3856 3857 3874 C3' DC P 9 OK 3872 3875 3876 3893 C3' DT P 10 OK 3891 3894 3895 3913 C3' DA P 11 OK 3911 3914 3915 3937 C3' DOC P 12 3938 3936 3956 C3' DCP A 739 OK 3957 3959 3955 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3374 C4' DT T 1 OK 3376 3373 3375 3394 C4' DA T 2 OK 3396 3393 3395 3415 C4' DA T 3 OK 3417 3414 3416 3436 C4' P T 4 OK 3438 3435 3437 3461 C4' DG T 5 OK 3463 3460 3462 3483 C4' DT T 6 OK 3485 3482 3484 3503 C4' DA T 7 OK 3505 3502 3504 3524 C4' DG T 8 OK 3526 3523 3525 3546 C4' DG T 9 OK 3548 3545 3547 3568 C4' DG T 10 OK 3570 3567 3569 3590 C4' DG T 11 OK 3592 3589 3591 3612 C4' DA T 12 OK 3614 3611 3613 3633 C4' DG T 13 OK 3635 3632 3634 3655 C4' DG T 14 OK 3657 3654 3656 3677 C4' DA T 15 OK 3679 3676 3678 3698 C4' DT T 16 OK 3700 3697 3699 3716 C4' DA P 1 OK 3718 3715 3717 3737 C4' DT P 2 OK 3739 3736 3738 3757 C4' DC P 3 OK 3759 3756 3758 3776 C4' DC P 4 OK 3778 3775 3777 3795 C4' DT P 5 OK 3797 3794 3796 3815 C4' DC P 6 OK 3817 3814 3816 3834 C4' DC P 7 OK 3836 3833 3835 3853 C4' DC P 8 OK 3855 3852 3854 3872 C4' DC P 9 OK 3874 3871 3873 3891 C4' DT P 10 OK 3893 3890 3892 3911 C4' DA P 11 OK 3913 3910 3912 3938 C4' DOC P 12 OK 3937 3940 3939 3957 C4' DCP A 739 OK 3956 3960 3958 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3373 C5' DT T 1 3372 3374 3393 C5' DA T 2 3392 3394 3414 C5' DA T 3 3413 3415 3435 C5' P T 4 3434 3436 3460 C5' DG T 5 3459 3461 3482 C5' DT T 6 3481 3483 3502 C5' DA T 7 3501 3503 3523 C5' DG T 8 3522 3524 3545 C5' DG T 9 3544 3546 3567 C5' DG T 10 3566 3568 3589 C5' DG T 11 3588 3590 3611 C5' DA T 12 3610 3612 3632 C5' DG T 13 3631 3633 3654 C5' DG T 14 3653 3655 3676 C5' DA T 15 3675 3677 3697 C5' DT T 16 3696 3698 3715 C5' DA P 1 3714 3716 3736 C5' DT P 2 3735 3737 3756 C5' DC P 3 3755 3757 3775 C5' DC P 4 3774 3776 3794 C5' DT P 5 3793 3795 3814 C5' DC P 6 3813 3815 3833 C5' DC P 7 3832 3834 3852 C5' DC P 8 3851 3853 3871 C5' DC P 9 3870 3872 3890 C5' DT P 10 3889 3891 3910 C5' DA P 11 3909 3911 3940 C5' DOC P 12 3941 3938 3960 C5' DCP A 739 3961 3957 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3389 P DA T 2 distorted distorted 3377 3390 3391 3392 3410 P DA T 3 distorted distorted 3397 3411 3412 3413 3431 P P T 4 distorted distorted 3418 3432 3433 3434 3456 P DG T 5 distorted distorted 3439 3457 3458 3459 3478 P DT T 6 distorted distorted 3464 3479 3480 3481 3498 P DA T 7 distorted distorted 3486 3499 3500 3501 3519 P DG T 8 distorted distorted 3506 3520 3521 3522 3541 P DG T 9 distorted distorted 3527 3542 3543 3544 3563 P DG T 10 distorted distorted 3549 3564 3565 3566 3585 P DG T 11 distorted distorted 3571 3586 3587 3588 3607 P DA T 12 distorted distorted 3593 3608 3609 3610 3628 P DG T 13 distorted distorted 3615 3629 3630 3631 3650 P DG T 14 distorted distorted 3636 3651 3652 3653 3672 P DA T 15 distorted distorted 3658 3673 3674 3675 3693 P DT T 16 distorted distorted 3680 3694 3695 3696 3732 P DT P 2 distorted distorted 3719 3733 3734 3735 3752 P DC P 3 distorted distorted 3740 3753 3754 3755 3771 P DC P 4 distorted distorted 3760 3772 3773 3774 3790 P DT P 5 distorted distorted 3779 3791 3792 3793 3810 P DC P 6 distorted distorted 3798 3811 3812 3813 3829 P DC P 7 distorted distorted 3818 3830 3831 3832 3848 P DC P 8 distorted distorted 3837 3849 3850 3851 3867 P DC P 9 distorted distorted 3856 3868 3869 3870 3886 P DT P 10 distorted distorted 3875 3887 3888 3889 3906 P DA P 11 distorted distorted 3894 3907 3908 3909 3942 P DOC P 12 distorted distorted 3914 3943 3944 3941 ---------------------------------------------------------------------------------