ID code: '3KLV' 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' --------------------------------------------------------------------------------- 3740 C1' A B 903 beta 3735 3741 3738 3762 C1' U B 904 beta 3757 3763 3760 3782 C1' G B 905 beta 3777 3783 3780 3805 C1' G B 906 beta 3800 3806 3803 3828 C1' G B 907 beta 3823 3829 3826 3851 C1' C B 908 beta 3846 3852 3849 3871 C1' C B 909 beta 3866 3872 3869 3889 C1' G C 916 beta 3884 3890 3887 3912 C1' G C 917 beta 3907 3913 3910 3935 C1' C C 918 beta 3930 3936 3933 3955 C1' C C 919 beta 3950 3956 3953 3975 C1' C C 920 beta 3970 3976 3973 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3738 C2' A B 903 OK 3740 3736 3739 3760 C2' U B 904 OK 3762 3758 3761 3780 C2' G B 905 OK 3782 3778 3781 3803 C2' G B 906 OK 3805 3801 3804 3826 C2' G B 907 OK 3828 3824 3827 3849 C2' C B 908 OK 3851 3847 3850 3869 C2' C B 909 OK 3871 3867 3870 3887 C2' G C 916 OK 3889 3885 3888 3910 C2' G C 917 OK 3912 3908 3911 3933 C2' C C 918 OK 3935 3931 3934 3953 C2' C C 919 OK 3955 3951 3954 3973 C2' C C 920 OK 3975 3971 3974 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3736 C3' A B 903 OK 3734 3737 3738 3758 C3' U B 904 OK 3756 3759 3760 3778 C3' G B 905 OK 3776 3779 3780 3801 C3' G B 906 OK 3799 3802 3803 3824 C3' G B 907 OK 3822 3825 3826 3847 C3' C B 908 OK 3845 3848 3849 3867 C3' C B 909 OK 3865 3868 3869 3885 C3' G C 916 OK 3883 3886 3887 3908 C3' G C 917 OK 3906 3909 3910 3931 C3' C C 918 OK 3929 3932 3933 3951 C3' C C 919 OK 3949 3952 3953 3971 C3' C C 920 OK 3969 3972 3973 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3734 C4' A B 903 OK 3736 3733 3735 3756 C4' U B 904 OK 3758 3755 3757 3776 C4' G B 905 OK 3778 3775 3777 3799 C4' G B 906 OK 3801 3798 3800 3822 C4' G B 907 OK 3824 3821 3823 3845 C4' C B 908 OK 3847 3844 3846 3865 C4' C B 909 OK 3867 3864 3866 3883 C4' G C 916 OK 3885 3882 3884 3906 C4' G C 917 OK 3908 3905 3907 3929 C4' C C 918 OK 3931 3928 3930 3949 C4' C C 919 OK 3951 3948 3950 3969 C4' C C 920 OK 3971 3968 3970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3733 C5' A B 903 3732 3734 3755 C5' U B 904 3754 3756 3775 C5' G B 905 3774 3776 3798 C5' G B 906 3797 3799 3821 C5' G B 907 3820 3822 3844 C5' C B 908 3843 3845 3864 C5' C B 909 3863 3865 3882 C5' G C 916 3881 3883 3905 C5' G C 917 3904 3906 3928 C5' C C 918 3927 3929 3948 C5' C C 919 3947 3949 3968 C5' C C 920 3967 3969 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3751 P U B 904 distorted distorted 3737 3752 3753 3754 3771 P G B 905 distorted distorted 3759 3772 3773 3774 3794 P G B 906 distorted distorted 3779 3795 3796 3797 3817 P G B 907 distorted distorted 3802 3818 3819 3820 3840 P C B 908 distorted distorted 3825 3841 3842 3843 3860 P C B 909 distorted distorted 3848 3861 3862 3863 3901 P G C 917 distorted distorted 3886 3902 3903 3904 3924 P C C 918 distorted distorted 3909 3925 3926 3927 3944 P C C 919 distorted distorted 3932 3945 3946 3947 3964 P C C 920 distorted distorted 3952 3965 3966 3967 ---------------------------------------------------------------------------------