ID code: '2C4R' 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' --------------------------------------------------------------------------------- 3571 C1' A R 1 beta 3566 3572 3569 3593 C1' C R 2 beta 3588 3594 3591 3613 C1' A R 3 beta 3608 3614 3611 3635 C1' G R 4 beta 3630 3636 3633 3658 C1' U R 5 beta 3653 3659 3656 3678 C1' A R 6 beta 3673 3679 3676 3700 C1' U R 7 beta 3695 3701 3698 3720 C1' U R 8 beta 3715 3721 3718 3740 C1' U R 9 beta 3735 3741 3738 3760 C1' G R 10 beta 3755 3761 3758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3569 C2' A R 1 OK 3571 3567 3570 3591 C2' C R 2 OK 3593 3589 3592 3611 C2' A R 3 OK 3613 3609 3612 3633 C2' G R 4 OK 3635 3631 3634 3656 C2' U R 5 OK 3658 3654 3657 3676 C2' A R 6 OK 3678 3674 3677 3698 C2' U R 7 OK 3700 3696 3699 3718 C2' U R 8 OK 3720 3716 3719 3738 C2' U R 9 OK 3740 3736 3739 3758 C2' G R 10 OK 3760 3756 3759 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3567 C3' A R 1 OK 3565 3568 3569 3589 C3' C R 2 OK 3587 3590 3591 3609 C3' A R 3 OK 3607 3610 3611 3631 C3' G R 4 OK 3629 3632 3633 3654 C3' U R 5 OK 3652 3655 3656 3674 C3' A R 6 OK 3672 3675 3676 3696 C3' U R 7 OK 3694 3697 3698 3716 C3' U R 8 OK 3714 3717 3718 3736 C3' U R 9 OK 3734 3737 3738 3756 C3' G R 10 OK 3754 3757 3758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3565 C4' A R 1 OK 3567 3564 3566 3587 C4' C R 2 OK 3589 3586 3588 3607 C4' A R 3 OK 3609 3606 3608 3629 C4' G R 4 OK 3631 3628 3630 3652 C4' U R 5 OK 3654 3651 3653 3672 C4' A R 6 OK 3674 3671 3673 3694 C4' U R 7 OK 3696 3693 3695 3714 C4' U R 8 OK 3716 3713 3715 3734 C4' U R 9 OK 3736 3733 3735 3754 C4' G R 10 OK 3756 3753 3755 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3564 C5' A R 1 3563 3565 3586 C5' C R 2 3585 3587 3606 C5' A R 3 3605 3607 3628 C5' G R 4 3627 3629 3651 C5' U R 5 3650 3652 3671 C5' A R 6 3670 3672 3693 C5' U R 7 3692 3694 3713 C5' U R 8 3712 3714 3733 C5' U R 9 3732 3734 3753 C5' G R 10 3752 3754 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3560 P A R 1 distorted distorted 3561 3562 3563 3582 P C R 2 distorted distorted 3568 3583 3584 3585 3602 P A R 3 distorted distorted 3590 3603 3604 3605 3624 P G R 4 distorted distorted 3610 3625 3626 3627 3647 P U R 5 distorted distorted 3632 3648 3649 3650 3667 P A R 6 distorted distorted 3655 3668 3669 3670 3689 P U R 7 distorted distorted 3675 3690 3691 3692 3709 P U R 8 distorted distorted 3697 3710 3711 3712 3729 P U R 9 distorted distorted 3717 3730 3731 3732 3749 P G R 10 distorted distorted 3737 3750 3751 3752 ---------------------------------------------------------------------------------