ID code: '4IQX' 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' --------------------------------------------------------------------------------- 3687 C1' A B 903 beta 3682 3688 3685 3709 C1' U B 904 beta 3704 3710 3707 3729 C1' G B 905 beta 3724 3730 3727 3752 C1' G B 906 beta 3747 3753 3750 3775 C1' G B 907 beta 3770 3776 3773 3798 C1' C B 908 beta 3793 3799 3796 3818 C1' C B 909 beta 3813 3819 3816 3836 C1' G C 916 beta 3831 3837 3834 3859 C1' G C 917 beta 3854 3860 3857 3882 C1' C C 918 beta 3877 3883 3880 3902 C1' C C 919 beta 3897 3903 3900 3922 C1' C C 920 beta 3917 3923 3920 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3685 C2' A B 903 OK 3687 3683 3686 3707 C2' U B 904 OK 3709 3705 3708 3727 C2' G B 905 OK 3729 3725 3728 3750 C2' G B 906 OK 3752 3748 3751 3773 C2' G B 907 OK 3775 3771 3774 3796 C2' C B 908 OK 3798 3794 3797 3816 C2' C B 909 OK 3818 3814 3817 3834 C2' G C 916 OK 3836 3832 3835 3857 C2' G C 917 OK 3859 3855 3858 3880 C2' C C 918 OK 3882 3878 3881 3900 C2' C C 919 OK 3902 3898 3901 3920 C2' C C 920 OK 3922 3918 3921 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3683 C3' A B 903 OK 3681 3684 3685 3705 C3' U B 904 OK 3703 3706 3707 3725 C3' G B 905 OK 3723 3726 3727 3748 C3' G B 906 OK 3746 3749 3750 3771 C3' G B 907 OK 3769 3772 3773 3794 C3' C B 908 OK 3792 3795 3796 3814 C3' C B 909 OK 3812 3815 3816 3832 C3' G C 916 OK 3830 3833 3834 3855 C3' G C 917 OK 3853 3856 3857 3878 C3' C C 918 OK 3876 3879 3880 3898 C3' C C 919 OK 3896 3899 3900 3918 C3' C C 920 OK 3916 3919 3920 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3681 C4' A B 903 OK 3683 3680 3682 3703 C4' U B 904 OK 3705 3702 3704 3723 C4' G B 905 OK 3725 3722 3724 3746 C4' G B 906 OK 3748 3745 3747 3769 C4' G B 907 OK 3771 3768 3770 3792 C4' C B 908 OK 3794 3791 3793 3812 C4' C B 909 OK 3814 3811 3813 3830 C4' G C 916 OK 3832 3829 3831 3853 C4' G C 917 OK 3855 3852 3854 3876 C4' C C 918 OK 3878 3875 3877 3896 C4' C C 919 OK 3898 3895 3897 3916 C4' C C 920 OK 3918 3915 3917 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3680 C5' A B 903 3679 3681 3702 C5' U B 904 3701 3703 3722 C5' G B 905 3721 3723 3745 C5' G B 906 3744 3746 3768 C5' G B 907 3767 3769 3791 C5' C B 908 3790 3792 3811 C5' C B 909 3810 3812 3829 C5' G C 916 3828 3830 3852 C5' G C 917 3851 3853 3875 C5' C C 918 3874 3876 3895 C5' C C 919 3894 3896 3915 C5' C C 920 3914 3916 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3698 P U B 904 distorted distorted 3684 3699 3700 3701 3718 P G B 905 distorted distorted 3706 3719 3720 3721 3741 P G B 906 distorted distorted 3726 3742 3743 3744 3764 P G B 907 distorted distorted 3749 3765 3766 3767 3787 P C B 908 distorted distorted 3772 3788 3789 3790 3807 P C B 909 distorted distorted 3795 3808 3809 3810 3848 P G C 917 distorted distorted 3833 3849 3850 3851 3871 P C C 918 distorted distorted 3856 3872 3873 3874 3891 P C C 919 distorted distorted 3879 3892 3893 3894 3911 P C C 920 distorted distorted 3899 3912 3913 3914 ---------------------------------------------------------------------------------