ID code: '3BSN' 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' --------------------------------------------------------------------------------- 3772 C1' U P 1 beta 3767 3773 3770 3792 C1' G P 2 beta 3787 3793 3790 3815 C1' C P 3 beta 3810 3816 3813 3835 C1' C P 4 beta 3830 3836 3833 3855 C1' C P 5 beta 3850 3856 3853 3875 C1' G P 6 beta 3870 3876 3873 3898 C1' G P 7 beta 3893 3899 3896 3921 C1' G P 8 beta 3916 3922 3919 3942 C1' U T 1 beta 3937 3943 3940 3962 C1' G T 2 beta 3957 3963 3960 3985 C1' C T 3 beta 3980 3986 3983 4005 C1' C T 4 beta 4000 4006 4003 4025 C1' C T 5 beta 4020 4026 4023 4045 C1' G T 6 beta 4040 4046 4043 4068 C1' G T 7 beta 4063 4069 4066 4091 C1' G T 8 beta 4086 4092 4089 4114 C1' N5M T 9 beta 4115 4113 4116 4153 C1' N5C A 514 beta 4154 4152 4155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3770 C2' U P 1 OK 3772 3768 3771 3790 C2' G P 2 OK 3792 3788 3791 3813 C2' C P 3 OK 3815 3811 3814 3833 C2' C P 4 OK 3835 3831 3834 3853 C2' C P 5 OK 3855 3851 3854 3873 C2' G P 6 OK 3875 3871 3874 3896 C2' G P 7 OK 3898 3894 3897 3919 C2' G P 8 OK 3921 3917 3920 3940 C2' U T 1 OK 3942 3938 3941 3960 C2' G T 2 OK 3962 3958 3961 3983 C2' C T 3 OK 3985 3981 3984 4003 C2' C T 4 OK 4005 4001 4004 4023 C2' C T 5 OK 4025 4021 4024 4043 C2' G T 6 OK 4045 4041 4044 4066 C2' G T 7 OK 4068 4064 4067 4089 C2' G T 8 OK 4091 4087 4090 4116 C2' N5M T 9 OK 4114 4118 4117 4155 C2' N5C A 514 OK 4153 4157 4156 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3768 C3' U P 1 OK 3766 3769 3770 3788 C3' G P 2 OK 3786 3789 3790 3811 C3' C P 3 OK 3809 3812 3813 3831 C3' C P 4 OK 3829 3832 3833 3851 C3' C P 5 OK 3849 3852 3853 3871 C3' G P 6 OK 3869 3872 3873 3894 C3' G P 7 OK 3892 3895 3896 3917 C3' G P 8 OK 3915 3918 3919 3938 C3' U T 1 OK 3936 3939 3940 3958 C3' G T 2 OK 3956 3959 3960 3981 C3' C T 3 OK 3979 3982 3983 4001 C3' C T 4 OK 3999 4002 4003 4021 C3' C T 5 OK 4019 4022 4023 4041 C3' G T 6 OK 4039 4042 4043 4064 C3' G T 7 OK 4062 4065 4066 4087 C3' G T 8 OK 4085 4088 4089 4118 C3' N5M T 9 OK 4120 4119 4116 4157 C3' N5C A 514 OK 4159 4158 4155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3766 C4' U P 1 OK 3768 3765 3767 3786 C4' G P 2 OK 3788 3785 3787 3809 C4' C P 3 OK 3811 3808 3810 3829 C4' C P 4 OK 3831 3828 3830 3849 C4' C P 5 OK 3851 3848 3850 3869 C4' G P 6 OK 3871 3868 3870 3892 C4' G P 7 OK 3894 3891 3893 3915 C4' G P 8 OK 3917 3914 3916 3936 C4' U T 1 OK 3938 3935 3937 3956 C4' G T 2 OK 3958 3955 3957 3979 C4' C T 3 OK 3981 3978 3980 3999 C4' C T 4 OK 4001 3998 4000 4019 C4' C T 5 OK 4021 4018 4020 4039 C4' G T 6 OK 4041 4038 4040 4062 C4' G T 7 OK 4064 4061 4063 4085 C4' G T 8 OK 4087 4084 4086 4120 C4' N5M T 9 OK 4118 4121 4115 4159 C4' N5C A 514 OK 4157 4160 4154 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3765 C5' U P 1 3764 3766 3785 C5' G P 2 3784 3786 3808 C5' C P 3 3807 3809 3828 C5' C P 4 3827 3829 3848 C5' C P 5 3847 3849 3868 C5' G P 6 3867 3869 3891 C5' G P 7 3890 3892 3914 C5' G P 8 3913 3915 3935 C5' U T 1 3934 3936 3955 C5' G T 2 3954 3956 3978 C5' C T 3 3977 3979 3998 C5' C T 4 3997 3999 4018 C5' C T 5 4017 4019 4038 C5' G T 6 4037 4039 4061 C5' G T 7 4060 4062 4084 C5' G T 8 4083 4085 4121 C5' N5M T 9 4122 4120 4160 C5' N5C A 514 4161 4159 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3781 P G P 2 distorted distorted 3769 3782 3783 3784 3804 P C P 3 distorted distorted 3789 3805 3806 3807 3824 P C P 4 distorted distorted 3812 3825 3826 3827 3844 P C P 5 distorted distorted 3832 3845 3846 3847 3864 P G P 6 distorted distorted 3852 3865 3866 3867 3887 P G P 7 distorted distorted 3872 3888 3889 3890 3910 P G P 8 distorted distorted 3895 3911 3912 3913 3951 P G T 2 distorted distorted 3939 3952 3953 3954 3974 P C T 3 distorted distorted 3959 3975 3976 3977 3994 P C T 4 distorted distorted 3982 3995 3996 3997 4014 P C T 5 distorted distorted 4002 4015 4016 4017 4034 P G T 6 distorted distorted 4022 4035 4036 4037 4057 P G T 7 distorted distorted 4042 4058 4059 4060 4080 P G T 8 distorted distorted 4065 4081 4082 4083 4123 P N5M T 9 distorted distorted 4088 4125 4124 4122 ---------------------------------------------------------------------------------