ID code: '1BGB' 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' --------------------------------------------------------------------------------- 3631 C1' G C 802 beta 3627 3632 3630 3653 C1' G C 803 beta 3649 3654 3652 3675 C1' G C 804 beta 3671 3676 3674 3697 C1' A C 805 beta 3693 3698 3696 3718 C1' T C 806 beta 3714 3719 3717 3738 C1' A C 807 beta 3734 3739 3737 3759 C1' T C 808 beta 3755 3760 3758 3779 C1' C C 809 beta 3775 3780 3778 3798 C1' C C 810 beta 3794 3799 3797 3817 C1' C C 811 beta 3813 3818 3816 3837 C1' G D 902 beta 3833 3838 3836 3859 C1' G D 903 beta 3855 3860 3858 3881 C1' G D 904 beta 3877 3882 3880 3903 C1' A D 905 beta 3899 3904 3902 3924 C1' T D 906 beta 3920 3925 3923 3944 C1' A D 907 beta 3940 3945 3943 3965 C1' T D 908 beta 3961 3966 3964 3985 C1' C D 909 beta 3981 3986 3984 4004 C1' C D 910 beta 4000 4005 4003 4023 C1' C D 911 beta 4019 4024 4022 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3630 C2' G C 802 3631 3628 3652 C2' G C 803 3653 3650 3674 C2' G C 804 3675 3672 3696 C2' A C 805 3697 3694 3717 C2' T C 806 3718 3715 3737 C2' A C 807 3738 3735 3758 C2' T C 808 3759 3756 3778 C2' C C 809 3779 3776 3797 C2' C C 810 3798 3795 3816 C2' C C 811 3817 3814 3836 C2' G D 902 3837 3834 3858 C2' G D 903 3859 3856 3880 C2' G D 904 3881 3878 3902 C2' A D 905 3903 3900 3923 C2' T D 906 3924 3921 3943 C2' A D 907 3944 3941 3964 C2' T D 908 3965 3962 3984 C2' C D 909 3985 3982 4003 C2' C D 910 4004 4001 4022 C2' C D 911 4023 4020 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3628 C3' G C 802 OK 3626 3629 3630 3650 C3' G C 803 OK 3648 3651 3652 3672 C3' G C 804 OK 3670 3673 3674 3694 C3' A C 805 OK 3692 3695 3696 3715 C3' T C 806 OK 3713 3716 3717 3735 C3' A C 807 OK 3733 3736 3737 3756 C3' T C 808 OK 3754 3757 3758 3776 C3' C C 809 OK 3774 3777 3778 3795 C3' C C 810 OK 3793 3796 3797 3814 C3' C C 811 OK 3812 3815 3816 3834 C3' G D 902 OK 3832 3835 3836 3856 C3' G D 903 OK 3854 3857 3858 3878 C3' G D 904 OK 3876 3879 3880 3900 C3' A D 905 OK 3898 3901 3902 3921 C3' T D 906 OK 3919 3922 3923 3941 C3' A D 907 OK 3939 3942 3943 3962 C3' T D 908 OK 3960 3963 3964 3982 C3' C D 909 OK 3980 3983 3984 4001 C3' C D 910 OK 3999 4002 4003 4020 C3' C D 911 OK 4018 4021 4022 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3626 C4' G C 802 OK 3628 3625 3627 3648 C4' G C 803 OK 3650 3647 3649 3670 C4' G C 804 OK 3672 3669 3671 3692 C4' A C 805 OK 3694 3691 3693 3713 C4' T C 806 OK 3715 3712 3714 3733 C4' A C 807 OK 3735 3732 3734 3754 C4' T C 808 OK 3756 3753 3755 3774 C4' C C 809 OK 3776 3773 3775 3793 C4' C C 810 OK 3795 3792 3794 3812 C4' C C 811 OK 3814 3811 3813 3832 C4' G D 902 OK 3834 3831 3833 3854 C4' G D 903 OK 3856 3853 3855 3876 C4' G D 904 OK 3878 3875 3877 3898 C4' A D 905 OK 3900 3897 3899 3919 C4' T D 906 OK 3921 3918 3920 3939 C4' A D 907 OK 3941 3938 3940 3960 C4' T D 908 OK 3962 3959 3961 3980 C4' C D 909 OK 3982 3979 3981 3999 C4' C D 910 OK 4001 3998 4000 4018 C4' C D 911 OK 4020 4017 4019 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3625 C5' G C 802 3624 3626 3647 C5' G C 803 3646 3648 3669 C5' G C 804 3668 3670 3691 C5' A C 805 3690 3692 3712 C5' T C 806 3711 3713 3732 C5' A C 807 3731 3733 3753 C5' T C 808 3752 3754 3773 C5' C C 809 3772 3774 3792 C5' C C 810 3791 3793 3811 C5' C C 811 3810 3812 3831 C5' G D 902 3830 3832 3853 C5' G D 903 3852 3854 3875 C5' G D 904 3874 3876 3897 C5' A D 905 3896 3898 3918 C5' T D 906 3917 3919 3938 C5' A D 907 3937 3939 3959 C5' T D 908 3958 3960 3979 C5' C D 909 3978 3980 3998 C5' C D 910 3997 3999 4017 C5' C D 911 4016 4018 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3643 P G C 803 OK OK 3629 3644 3645 3646 3665 P G C 804 OK OK 3651 3666 3667 3668 3687 P A C 805 OK OK 3673 3688 3689 3690 3708 P T C 806 OK OK 3695 3709 3710 3711 3728 P A C 807 OK OK 3716 3729 3730 3731 3749 P T C 808 OK OK 3736 3750 3751 3752 3769 P C C 809 OK OK 3757 3770 3771 3772 3788 P C C 810 OK OK 3777 3789 3790 3791 3807 P C C 811 OK OK 3796 3808 3809 3810 3849 P G D 903 OK OK 3835 3850 3851 3852 3871 P G D 904 OK OK 3857 3872 3873 3874 3893 P A D 905 OK OK 3879 3894 3895 3896 3914 P T D 906 OK OK 3901 3915 3916 3917 3934 P A D 907 OK OK 3922 3935 3936 3937 3955 P T D 908 OK OK 3942 3956 3957 3958 3975 P C D 909 OK OK 3963 3976 3977 3978 3994 P C D 910 OK OK 3983 3995 3996 3997 4013 P C D 911 OK OK 4002 4014 4015 4016 ---------------------------------------------------------------------------------