ID code: '3H5Y' 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' --------------------------------------------------------------------------------- 3738 C1' G P 2 beta 3733 3739 3736 3761 C1' C P 3 beta 3756 3762 3759 3781 C1' C P 4 beta 3776 3782 3779 3801 C1' C P 5 beta 3796 3802 3799 3821 C1' G P 6 beta 3816 3822 3819 3844 C1' G P 7 beta 3839 3845 3842 3867 C1' G P 8 beta 3862 3868 3865 3891 C1' U T 1 beta 3886 3892 3889 3911 C1' G T 2 beta 3906 3912 3909 3934 C1' C T 3 beta 3929 3935 3932 3954 C1' C T 4 beta 3949 3955 3952 3974 C1' C T 5 beta 3969 3975 3972 3994 C1' G T 6 beta 3989 3995 3992 4017 C1' G T 7 beta 4012 4018 4015 4040 C1' G T 8 beta 4035 4041 4038 4063 C1' C T 9 beta 4058 4064 4061 4085 C1' CTP A 515 beta 4090 4077 4086 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3736 C2' G P 2 OK 3738 3734 3737 3759 C2' C P 3 OK 3761 3757 3760 3779 C2' C P 4 OK 3781 3777 3780 3799 C2' C P 5 OK 3801 3797 3800 3819 C2' G P 6 OK 3821 3817 3820 3842 C2' G P 7 OK 3844 3840 3843 3865 C2' G P 8 OK 3867 3863 3866 3889 C2' U T 1 OK 3891 3887 3890 3909 C2' G T 2 OK 3911 3907 3910 3932 C2' C T 3 OK 3934 3930 3933 3952 C2' C T 4 OK 3954 3950 3953 3972 C2' C T 5 OK 3974 3970 3973 3992 C2' G T 6 OK 3994 3990 3993 4015 C2' G T 7 OK 4017 4013 4016 4038 C2' G T 8 OK 4040 4036 4039 4061 C2' C T 9 OK 4063 4059 4062 4086 C2' CTP A 515 OK 4085 4088 4087 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3734 C3' G P 2 OK 3732 3735 3736 3757 C3' C P 3 OK 3755 3758 3759 3777 C3' C P 4 OK 3775 3778 3779 3797 C3' C P 5 OK 3795 3798 3799 3817 C3' G P 6 OK 3815 3818 3819 3840 C3' G P 7 OK 3838 3841 3842 3863 C3' G P 8 OK 3861 3864 3865 3887 C3' U T 1 OK 3885 3888 3889 3907 C3' G T 2 OK 3905 3908 3909 3930 C3' C T 3 OK 3928 3931 3932 3950 C3' C T 4 OK 3948 3951 3952 3970 C3' C T 5 OK 3968 3971 3972 3990 C3' G T 6 OK 3988 3991 3992 4013 C3' G T 7 OK 4011 4014 4015 4036 C3' G T 8 OK 4034 4037 4038 4059 C3' C T 9 OK 4057 4060 4061 4088 C3' CTP A 515 OK 4089 4091 4086 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3732 C4' G P 2 OK 3734 3731 3733 3755 C4' C P 3 OK 3757 3754 3756 3775 C4' C P 4 OK 3777 3774 3776 3795 C4' C P 5 OK 3797 3794 3796 3815 C4' G P 6 OK 3817 3814 3816 3838 C4' G P 7 OK 3840 3837 3839 3861 C4' G P 8 OK 3863 3860 3862 3885 C4' U T 1 OK 3887 3884 3886 3905 C4' G T 2 OK 3907 3904 3906 3928 C4' C T 3 OK 3930 3927 3929 3948 C4' C T 4 OK 3950 3947 3949 3968 C4' C T 5 OK 3970 3967 3969 3988 C4' G T 6 OK 3990 3987 3989 4011 C4' G T 7 OK 4013 4010 4012 4034 C4' G T 8 OK 4036 4033 4035 4057 C4' C T 9 OK 4059 4056 4058 4089 C4' CTP A 515 OK 4088 4092 4090 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3731 C5' G P 2 3730 3732 3754 C5' C P 3 3753 3755 3774 C5' C P 4 3773 3775 3794 C5' C P 5 3793 3795 3814 C5' G P 6 3813 3815 3837 C5' G P 7 3836 3838 3860 C5' G P 8 3859 3861 3884 C5' U T 1 3883 3885 3904 C5' G T 2 3903 3905 3927 C5' C T 3 3926 3928 3947 C5' C T 4 3946 3948 3967 C5' C T 5 3966 3968 3987 C5' G T 6 3986 3988 4010 C5' G T 7 4009 4011 4033 C5' G T 8 4032 4034 4056 C5' C T 9 4055 4057 4092 C5' CTP A 515 4093 4089 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3727 P G P 2 distorted distorted 3728 3729 3730 3750 P C P 3 distorted distorted 3735 3751 3752 3753 3770 P C P 4 distorted distorted 3758 3771 3772 3773 3790 P C P 5 distorted distorted 3778 3791 3792 3793 3810 P G P 6 distorted distorted 3798 3811 3812 3813 3833 P G P 7 distorted distorted 3818 3834 3835 3836 3856 P G P 8 distorted distorted 3841 3857 3858 3859 3880 P U T 1 distorted distorted 3881 3882 3883 3900 P G T 2 distorted distorted 3888 3901 3902 3903 3923 P C T 3 distorted distorted 3908 3924 3925 3926 3943 P C T 4 distorted distorted 3931 3944 3945 3946 3963 P C T 5 distorted distorted 3951 3964 3965 3966 3983 P G T 6 distorted distorted 3971 3984 3985 3986 4006 P G T 7 distorted distorted 3991 4007 4008 4009 4029 P G T 8 distorted distorted 4014 4030 4031 4032 4052 P C T 9 distorted distorted 4037 4053 4054 4055 ---------------------------------------------------------------------------------