ID code: '3L25' 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' --------------------------------------------------------------------------------- 3875 C1' C C 1 beta 3870 3876 3873 3895 C1' G C 2 beta 3890 3896 3893 3918 C1' C C 3 beta 3913 3919 3916 3938 C1' A C 4 beta 3933 3939 3936 3960 C1' U C 5 beta 3955 3961 3958 3980 C1' G C 6 beta 3975 3981 3978 4003 C1' C C 7 beta 3998 4004 4001 4023 C1' G C 8 beta 4018 4024 4021 4044 C1' C F 1 beta 4039 4045 4042 4064 C1' G F 2 beta 4059 4065 4062 4087 C1' C F 3 beta 4082 4088 4085 4107 C1' A F 4 beta 4102 4108 4105 4129 C1' U F 5 beta 4124 4130 4127 4149 C1' G F 6 beta 4144 4150 4147 4172 C1' C F 7 beta 4167 4173 4170 4192 C1' G F 8 beta 4187 4193 4190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3873 C2' C C 1 OK 3875 3871 3874 3893 C2' G C 2 OK 3895 3891 3894 3916 C2' C C 3 OK 3918 3914 3917 3936 C2' A C 4 OK 3938 3934 3937 3958 C2' U C 5 OK 3960 3956 3959 3978 C2' G C 6 OK 3980 3976 3979 4001 C2' C C 7 OK 4003 3999 4002 4021 C2' G C 8 OK 4023 4019 4022 4042 C2' C F 1 OK 4044 4040 4043 4062 C2' G F 2 OK 4064 4060 4063 4085 C2' C F 3 OK 4087 4083 4086 4105 C2' A F 4 OK 4107 4103 4106 4127 C2' U F 5 OK 4129 4125 4128 4147 C2' G F 6 OK 4149 4145 4148 4170 C2' C F 7 OK 4172 4168 4171 4190 C2' G F 8 OK 4192 4188 4191 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3871 C3' C C 1 OK 3869 3872 3873 3891 C3' G C 2 OK 3889 3892 3893 3914 C3' C C 3 OK 3912 3915 3916 3934 C3' A C 4 OK 3932 3935 3936 3956 C3' U C 5 OK 3954 3957 3958 3976 C3' G C 6 OK 3974 3977 3978 3999 C3' C C 7 OK 3997 4000 4001 4019 C3' G C 8 OK 4017 4020 4021 4040 C3' C F 1 OK 4038 4041 4042 4060 C3' G F 2 OK 4058 4061 4062 4083 C3' C F 3 OK 4081 4084 4085 4103 C3' A F 4 OK 4101 4104 4105 4125 C3' U F 5 OK 4123 4126 4127 4145 C3' G F 6 OK 4143 4146 4147 4168 C3' C F 7 OK 4166 4169 4170 4188 C3' G F 8 OK 4186 4189 4190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3869 C4' C C 1 OK 3871 3868 3870 3889 C4' G C 2 OK 3891 3888 3890 3912 C4' C C 3 OK 3914 3911 3913 3932 C4' A C 4 OK 3934 3931 3933 3954 C4' U C 5 OK 3956 3953 3955 3974 C4' G C 6 OK 3976 3973 3975 3997 C4' C C 7 OK 3999 3996 3998 4017 C4' G C 8 OK 4019 4016 4018 4038 C4' C F 1 OK 4040 4037 4039 4058 C4' G F 2 OK 4060 4057 4059 4081 C4' C F 3 OK 4083 4080 4082 4101 C4' A F 4 OK 4103 4100 4102 4123 C4' U F 5 OK 4125 4122 4124 4143 C4' G F 6 OK 4145 4142 4144 4166 C4' C F 7 OK 4168 4165 4167 4186 C4' G F 8 OK 4188 4185 4187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3868 C5' C C 1 3867 3869 3888 C5' G C 2 3887 3889 3911 C5' C C 3 3910 3912 3931 C5' A C 4 3930 3932 3953 C5' U C 5 3952 3954 3973 C5' G C 6 3972 3974 3996 C5' C C 7 3995 3997 4016 C5' G C 8 4015 4017 4037 C5' C F 1 4036 4038 4057 C5' G F 2 4056 4058 4080 C5' C F 3 4079 4081 4100 C5' A F 4 4099 4101 4122 C5' U F 5 4121 4123 4142 C5' G F 6 4141 4143 4165 C5' C F 7 4164 4166 4185 C5' G F 8 4184 4186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3884 P G C 2 distorted distorted 3872 3885 3886 3887 3907 P C C 3 distorted distorted 3892 3908 3909 3910 3927 P A C 4 distorted distorted 3915 3928 3929 3930 3949 P U C 5 distorted distorted 3935 3950 3951 3952 3969 P G C 6 distorted distorted 3957 3970 3971 3972 3992 P C C 7 distorted distorted 3977 3993 3994 3995 4012 P G C 8 distorted distorted 4000 4013 4014 4015 4053 P G F 2 distorted distorted 4041 4054 4055 4056 4076 P C F 3 distorted distorted 4061 4077 4078 4079 4096 P A F 4 distorted distorted 4084 4097 4098 4099 4118 P U F 5 distorted distorted 4104 4119 4120 4121 4138 P G F 6 distorted distorted 4126 4139 4140 4141 4161 P C F 7 distorted distorted 4146 4162 4163 4164 4181 P G F 8 distorted distorted 4169 4182 4183 4184 ---------------------------------------------------------------------------------