ID code: '3NL0' 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' --------------------------------------------------------------------------------- 3735 C1' U B 904 beta 3730 3736 3733 3755 C1' G B 905 beta 3750 3756 3753 3778 C1' G B 906 beta 3773 3779 3776 3801 C1' G B 907 beta 3796 3802 3799 3824 C1' C B 908 beta 3819 3825 3822 3844 C1' C B 909 beta 3839 3845 3842 3864 C1' C B 910 beta 3859 3865 3862 3882 C1' G C 915 beta 3877 3883 3880 3902 C1' G C 916 beta 3897 3903 3900 3925 C1' G C 917 beta 3920 3926 3923 3948 C1' C C 918 beta 3943 3949 3946 3968 C1' C C 919 beta 3963 3969 3966 3988 C1' C C 920 beta 3983 3989 3986 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3733 C2' U B 904 OK 3735 3731 3734 3753 C2' G B 905 OK 3755 3751 3754 3776 C2' G B 906 OK 3778 3774 3777 3799 C2' G B 907 OK 3801 3797 3800 3822 C2' C B 908 OK 3824 3820 3823 3842 C2' C B 909 OK 3844 3840 3843 3862 C2' C B 910 OK 3864 3860 3863 3880 C2' G C 915 OK 3882 3878 3881 3900 C2' G C 916 OK 3902 3898 3901 3923 C2' G C 917 OK 3925 3921 3924 3946 C2' C C 918 OK 3948 3944 3947 3966 C2' C C 919 OK 3968 3964 3967 3986 C2' C C 920 OK 3988 3984 3987 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3731 C3' U B 904 OK 3729 3732 3733 3751 C3' G B 905 OK 3749 3752 3753 3774 C3' G B 906 OK 3772 3775 3776 3797 C3' G B 907 OK 3795 3798 3799 3820 C3' C B 908 OK 3818 3821 3822 3840 C3' C B 909 OK 3838 3841 3842 3860 C3' C B 910 OK 3858 3861 3862 3878 C3' G C 915 OK 3876 3879 3880 3898 C3' G C 916 OK 3896 3899 3900 3921 C3' G C 917 OK 3919 3922 3923 3944 C3' C C 918 OK 3942 3945 3946 3964 C3' C C 919 OK 3962 3965 3966 3984 C3' C C 920 OK 3982 3985 3986 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3729 C4' U B 904 OK 3731 3728 3730 3749 C4' G B 905 OK 3751 3748 3750 3772 C4' G B 906 OK 3774 3771 3773 3795 C4' G B 907 OK 3797 3794 3796 3818 C4' C B 908 OK 3820 3817 3819 3838 C4' C B 909 OK 3840 3837 3839 3858 C4' C B 910 OK 3860 3857 3859 3876 C4' G C 915 OK 3878 3875 3877 3896 C4' G C 916 OK 3898 3895 3897 3919 C4' G C 917 OK 3921 3918 3920 3942 C4' C C 918 OK 3944 3941 3943 3962 C4' C C 919 OK 3964 3961 3963 3982 C4' C C 920 OK 3984 3981 3983 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3728 C5' U B 904 3727 3729 3748 C5' G B 905 3747 3749 3771 C5' G B 906 3770 3772 3794 C5' G B 907 3793 3795 3817 C5' C B 908 3816 3818 3837 C5' C B 909 3836 3838 3857 C5' C B 910 3856 3858 3875 C5' G C 915 3874 3876 3895 C5' G C 916 3894 3896 3918 C5' G C 917 3917 3919 3941 C5' C C 918 3940 3942 3961 C5' C C 919 3960 3962 3981 C5' C C 920 3980 3982 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3724 P U B 904 distorted distorted 3725 3726 3727 3744 P G B 905 distorted distorted 3732 3745 3746 3747 3767 P G B 906 distorted distorted 3752 3768 3769 3770 3790 P G B 907 distorted distorted 3775 3791 3792 3793 3813 P C B 908 distorted distorted 3798 3814 3815 3816 3833 P C B 909 distorted distorted 3821 3834 3835 3836 3853 P C B 910 distorted distorted 3841 3854 3855 3856 3914 P G C 917 distorted distorted 3899 3915 3916 3917 3937 P C C 918 distorted distorted 3922 3938 3939 3940 3957 P C C 919 distorted distorted 3945 3958 3959 3960 3977 P C C 920 distorted distorted 3965 3978 3979 3980 ---------------------------------------------------------------------------------