ID code: '2C0B' 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' --------------------------------------------------------------------------------- 3569 C1' U R 1 beta 3564 3570 3567 3589 C1' U R 2 beta 3584 3590 3587 3609 C1' U R 3 beta 3604 3610 3607 3629 C1' A R 4 beta 3624 3630 3627 3651 C1' C R 5 beta 3646 3652 3649 3671 C1' A R 6 beta 3666 3672 3669 3693 C1' G R 7 beta 3688 3694 3691 3716 C1' U R 8 beta 3711 3717 3714 3736 C1' A R 9 beta 3731 3737 3734 3758 C1' U R 10 beta 3753 3759 3756 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3567 C2' U R 1 OK 3569 3565 3568 3587 C2' U R 2 OK 3589 3585 3588 3607 C2' U R 3 OK 3609 3605 3608 3627 C2' A R 4 OK 3629 3625 3628 3649 C2' C R 5 OK 3651 3647 3650 3669 C2' A R 6 OK 3671 3667 3670 3691 C2' G R 7 OK 3693 3689 3692 3714 C2' U R 8 OK 3716 3712 3715 3734 C2' A R 9 OK 3736 3732 3735 3756 C2' U R 10 OK 3758 3754 3757 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3565 C3' U R 1 OK 3563 3566 3567 3585 C3' U R 2 OK 3583 3586 3587 3605 C3' U R 3 OK 3603 3606 3607 3625 C3' A R 4 OK 3623 3626 3627 3647 C3' C R 5 OK 3645 3648 3649 3667 C3' A R 6 OK 3665 3668 3669 3689 C3' G R 7 OK 3687 3690 3691 3712 C3' U R 8 OK 3710 3713 3714 3732 C3' A R 9 OK 3730 3733 3734 3754 C3' U R 10 OK 3752 3755 3756 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3563 C4' U R 1 OK 3565 3562 3564 3583 C4' U R 2 OK 3585 3582 3584 3603 C4' U R 3 OK 3605 3602 3604 3623 C4' A R 4 OK 3625 3622 3624 3645 C4' C R 5 OK 3647 3644 3646 3665 C4' A R 6 OK 3667 3664 3666 3687 C4' G R 7 OK 3689 3686 3688 3710 C4' U R 8 OK 3712 3709 3711 3730 C4' A R 9 OK 3732 3729 3731 3752 C4' U R 10 OK 3754 3751 3753 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3562 C5' U R 1 3561 3563 3582 C5' U R 2 3581 3583 3602 C5' U R 3 3601 3603 3622 C5' A R 4 3621 3623 3644 C5' C R 5 3643 3645 3664 C5' A R 6 3663 3665 3686 C5' G R 7 3685 3687 3709 C5' U R 8 3708 3710 3729 C5' A R 9 3728 3730 3751 C5' U R 10 3750 3752 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3558 P U R 1 distorted distorted 3559 3560 3561 3578 P U R 2 distorted distorted 3566 3579 3580 3581 3598 P U R 3 distorted distorted 3586 3599 3600 3601 3618 P A R 4 distorted distorted 3606 3619 3620 3621 3640 P C R 5 distorted distorted 3626 3641 3642 3643 3660 P A R 6 distorted distorted 3648 3661 3662 3663 3682 P G R 7 distorted distorted 3668 3683 3684 3685 3705 P U R 8 distorted distorted 3690 3706 3707 3708 3725 P A R 9 distorted distorted 3713 3726 3727 3728 3747 P U R 10 distorted distorted 3733 3748 3749 3750 3767 P U R 11 distorted distorted 3755 3768 3769 3770 ---------------------------------------------------------------------------------