ID code: '3BSO' 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' --------------------------------------------------------------------------------- 3775 C1' G P 2 beta 3770 3776 3773 3798 C1' C P 3 beta 3793 3799 3796 3818 C1' C P 4 beta 3813 3819 3816 3838 C1' C P 5 beta 3833 3839 3836 3858 C1' G P 6 beta 3853 3859 3856 3881 C1' G P 7 beta 3876 3882 3879 3904 C1' G P 8 beta 3899 3905 3902 3928 C1' U T 1 beta 3923 3929 3926 3948 C1' G T 2 beta 3943 3949 3946 3971 C1' C T 3 beta 3966 3972 3969 3991 C1' C T 4 beta 3986 3992 3989 4011 C1' C T 5 beta 4006 4012 4009 4031 C1' G T 6 beta 4026 4032 4029 4054 C1' G T 7 beta 4049 4055 4052 4077 C1' G T 8 beta 4072 4078 4075 4100 C1' C T 9 beta 4095 4101 4098 4133 C1' CTP A 514 beta 4138 4125 4134 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3773 C2' G P 2 OK 3775 3771 3774 3796 C2' C P 3 OK 3798 3794 3797 3816 C2' C P 4 OK 3818 3814 3817 3836 C2' C P 5 OK 3838 3834 3837 3856 C2' G P 6 OK 3858 3854 3857 3879 C2' G P 7 OK 3881 3877 3880 3902 C2' G P 8 OK 3904 3900 3903 3926 C2' U T 1 OK 3928 3924 3927 3946 C2' G T 2 OK 3948 3944 3947 3969 C2' C T 3 OK 3971 3967 3970 3989 C2' C T 4 OK 3991 3987 3990 4009 C2' C T 5 OK 4011 4007 4010 4029 C2' G T 6 OK 4031 4027 4030 4052 C2' G T 7 OK 4054 4050 4053 4075 C2' G T 8 OK 4077 4073 4076 4098 C2' C T 9 OK 4100 4096 4099 4134 C2' CTP A 514 OK 4133 4136 4135 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3771 C3' G P 2 OK 3769 3772 3773 3794 C3' C P 3 OK 3792 3795 3796 3814 C3' C P 4 OK 3812 3815 3816 3834 C3' C P 5 OK 3832 3835 3836 3854 C3' G P 6 OK 3852 3855 3856 3877 C3' G P 7 OK 3875 3878 3879 3900 C3' G P 8 OK 3898 3901 3902 3924 C3' U T 1 OK 3922 3925 3926 3944 C3' G T 2 OK 3942 3945 3946 3967 C3' C T 3 OK 3965 3968 3969 3987 C3' C T 4 OK 3985 3988 3989 4007 C3' C T 5 OK 4005 4008 4009 4027 C3' G T 6 OK 4025 4028 4029 4050 C3' G T 7 OK 4048 4051 4052 4073 C3' G T 8 OK 4071 4074 4075 4096 C3' C T 9 OK 4094 4097 4098 4136 C3' CTP A 514 OK 4137 4139 4134 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3769 C4' G P 2 OK 3771 3768 3770 3792 C4' C P 3 OK 3794 3791 3793 3812 C4' C P 4 OK 3814 3811 3813 3832 C4' C P 5 OK 3834 3831 3833 3852 C4' G P 6 OK 3854 3851 3853 3875 C4' G P 7 OK 3877 3874 3876 3898 C4' G P 8 OK 3900 3897 3899 3922 C4' U T 1 OK 3924 3921 3923 3942 C4' G T 2 OK 3944 3941 3943 3965 C4' C T 3 OK 3967 3964 3966 3985 C4' C T 4 OK 3987 3984 3986 4005 C4' C T 5 OK 4007 4004 4006 4025 C4' G T 6 OK 4027 4024 4026 4048 C4' G T 7 OK 4050 4047 4049 4071 C4' G T 8 OK 4073 4070 4072 4094 C4' C T 9 OK 4096 4093 4095 4137 C4' CTP A 514 OK 4136 4140 4138 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3768 C5' G P 2 3767 3769 3791 C5' C P 3 3790 3792 3811 C5' C P 4 3810 3812 3831 C5' C P 5 3830 3832 3851 C5' G P 6 3850 3852 3874 C5' G P 7 3873 3875 3897 C5' G P 8 3896 3898 3921 C5' U T 1 3920 3922 3941 C5' G T 2 3940 3942 3964 C5' C T 3 3963 3965 3984 C5' C T 4 3983 3985 4004 C5' C T 5 4003 4005 4024 C5' G T 6 4023 4025 4047 C5' G T 7 4046 4048 4070 C5' G T 8 4069 4071 4093 C5' C T 9 4092 4094 4140 C5' CTP A 514 4141 4137 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3764 P G P 2 distorted distorted 3765 3766 3767 3787 P C P 3 distorted distorted 3772 3788 3789 3790 3807 P C P 4 distorted distorted 3795 3808 3809 3810 3827 P C P 5 distorted distorted 3815 3828 3829 3830 3847 P G P 6 distorted distorted 3835 3848 3849 3850 3870 P G P 7 distorted distorted 3855 3871 3872 3873 3893 P G P 8 distorted distorted 3878 3894 3895 3896 3917 P U T 1 distorted distorted 3918 3919 3920 3937 P G T 2 distorted distorted 3925 3938 3939 3940 3960 P C T 3 distorted distorted 3945 3961 3962 3963 3980 P C T 4 distorted distorted 3968 3981 3982 3983 4000 P C T 5 distorted distorted 3988 4001 4002 4003 4020 P G T 6 distorted distorted 4008 4021 4022 4023 4043 P G T 7 distorted distorted 4028 4044 4045 4046 4066 P G T 8 distorted distorted 4051 4067 4068 4069 4089 P C T 9 distorted distorted 4074 4090 4091 4092 ---------------------------------------------------------------------------------