ID code: '3H5X' 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' --------------------------------------------------------------------------------- 3703 C1' G P 2 beta 3698 3704 3701 3726 C1' C P 3 beta 3721 3727 3724 3746 C1' C P 4 beta 3741 3747 3744 3766 C1' C P 5 beta 3761 3767 3764 3786 C1' G P 6 beta 3781 3787 3784 3809 C1' G P 7 beta 3804 3810 3807 3832 C1' G P 8 beta 3827 3833 3830 3856 C1' U T 1 beta 3851 3857 3854 3876 C1' G T 2 beta 3871 3877 3874 3899 C1' C T 3 beta 3894 3900 3897 3919 C1' C T 4 beta 3914 3920 3917 3939 C1' C T 5 beta 3934 3940 3937 3959 C1' G T 6 beta 3954 3960 3957 3982 C1' G T 7 beta 3977 3983 3980 4005 C1' G T 8 beta 4000 4006 4003 4028 C1' C T 9 beta 4023 4029 4026 4050 C1' CSG A 515 beta 4051 4049 4052 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3701 C2' G P 2 OK 3703 3699 3702 3724 C2' C P 3 OK 3726 3722 3725 3744 C2' C P 4 OK 3746 3742 3745 3764 C2' C P 5 OK 3766 3762 3765 3784 C2' G P 6 OK 3786 3782 3785 3807 C2' G P 7 OK 3809 3805 3808 3830 C2' G P 8 OK 3832 3828 3831 3854 C2' U T 1 OK 3856 3852 3855 3874 C2' G T 2 OK 3876 3872 3875 3897 C2' C T 3 OK 3899 3895 3898 3917 C2' C T 4 OK 3919 3915 3918 3937 C2' C T 5 OK 3939 3935 3938 3957 C2' G T 6 OK 3959 3955 3958 3980 C2' G T 7 OK 3982 3978 3981 4003 C2' G T 8 OK 4005 4001 4004 4026 C2' C T 9 OK 4028 4024 4027 4052 C2' CSG A 515 4050 4054 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3699 C3' G P 2 OK 3697 3700 3701 3722 C3' C P 3 OK 3720 3723 3724 3742 C3' C P 4 OK 3740 3743 3744 3762 C3' C P 5 OK 3760 3763 3764 3782 C3' G P 6 OK 3780 3783 3784 3805 C3' G P 7 OK 3803 3806 3807 3828 C3' G P 8 OK 3826 3829 3830 3852 C3' U T 1 OK 3850 3853 3854 3872 C3' G T 2 OK 3870 3873 3874 3895 C3' C T 3 OK 3893 3896 3897 3915 C3' C T 4 OK 3913 3916 3917 3935 C3' C T 5 OK 3933 3936 3937 3955 C3' G T 6 OK 3953 3956 3957 3978 C3' G T 7 OK 3976 3979 3980 4001 C3' G T 8 OK 3999 4002 4003 4024 C3' C T 9 OK 4022 4025 4026 4054 C3' CSG A 515 OK 4056 4055 4052 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3697 C4' G P 2 OK 3699 3696 3698 3720 C4' C P 3 OK 3722 3719 3721 3740 C4' C P 4 OK 3742 3739 3741 3760 C4' C P 5 OK 3762 3759 3761 3780 C4' G P 6 OK 3782 3779 3781 3803 C4' G P 7 OK 3805 3802 3804 3826 C4' G P 8 OK 3828 3825 3827 3850 C4' U T 1 OK 3852 3849 3851 3870 C4' G T 2 OK 3872 3869 3871 3893 C4' C T 3 OK 3895 3892 3894 3913 C4' C T 4 OK 3915 3912 3914 3933 C4' C T 5 OK 3935 3932 3934 3953 C4' G T 6 OK 3955 3952 3954 3976 C4' G T 7 OK 3978 3975 3977 3999 C4' G T 8 OK 4001 3998 4000 4022 C4' C T 9 OK 4024 4021 4023 4056 C4' CSG A 515 OK 4054 4057 4051 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3696 C5' G P 2 3695 3697 3719 C5' C P 3 3718 3720 3739 C5' C P 4 3738 3740 3759 C5' C P 5 3758 3760 3779 C5' G P 6 3778 3780 3802 C5' G P 7 3801 3803 3825 C5' G P 8 3824 3826 3849 C5' U T 1 3848 3850 3869 C5' G T 2 3868 3870 3892 C5' C T 3 3891 3893 3912 C5' C T 4 3911 3913 3932 C5' C T 5 3931 3933 3952 C5' G T 6 3951 3953 3975 C5' G T 7 3974 3976 3998 C5' G T 8 3997 3999 4021 C5' C T 9 4020 4022 4057 C5' CSG A 515 4058 4056 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3692 P G P 2 distorted distorted 3693 3694 3695 3715 P C P 3 distorted distorted 3700 3716 3717 3718 3735 P C P 4 distorted distorted 3723 3736 3737 3738 3755 P C P 5 distorted distorted 3743 3756 3757 3758 3775 P G P 6 distorted distorted 3763 3776 3777 3778 3798 P G P 7 distorted distorted 3783 3799 3800 3801 3821 P G P 8 distorted distorted 3806 3822 3823 3824 3845 P U T 1 distorted distorted 3846 3847 3848 3865 P G T 2 distorted distorted 3853 3866 3867 3868 3888 P C T 3 distorted distorted 3873 3889 3890 3891 3908 P C T 4 distorted distorted 3896 3909 3910 3911 3928 P C T 5 distorted distorted 3916 3929 3930 3931 3948 P G T 6 distorted distorted 3936 3949 3950 3951 3971 P G T 7 distorted distorted 3956 3972 3973 3974 3994 P G T 8 distorted distorted 3979 3995 3996 3997 4017 P C T 9 distorted distorted 4002 4018 4019 4020 ---------------------------------------------------------------------------------