ID code: '4QPX' 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' --------------------------------------------------------------------------------- 3894 C1' U P 1 beta 3889 3895 3892 3914 C1' G P 2 beta 3909 3915 3912 3937 C1' C P 3 beta 3932 3938 3935 3957 C1' C P 4 beta 3952 3958 3955 3977 C1' C P 5 beta 3972 3978 3975 3997 C1' G P 6 beta 3992 3998 3995 4020 C1' G P 7 beta 4015 4021 4018 4043 C1' G P 8 beta 4038 4044 4041 4064 C1' A T 2 beta 4059 4065 4062 4086 C1' C T 3 beta 4081 4087 4084 4106 C1' C T 4 beta 4101 4107 4104 4126 C1' C T 5 beta 4121 4127 4124 4146 C1' G T 6 beta 4141 4147 4144 4169 C1' G T 7 beta 4164 4170 4167 4192 C1' G T 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' --------------------------------------------------------------------------------------------------------------------- 3892 C2' U P 1 OK 3894 3890 3893 3912 C2' G P 2 OK 3914 3910 3913 3935 C2' C P 3 OK 3937 3933 3936 3955 C2' C P 4 OK 3957 3953 3956 3975 C2' C P 5 OK 3977 3973 3976 3995 C2' G P 6 OK 3997 3993 3996 4018 C2' G P 7 OK 4020 4016 4019 4041 C2' G P 8 OK 4043 4039 4042 4062 C2' A T 2 OK 4064 4060 4063 4084 C2' C T 3 OK 4086 4082 4085 4104 C2' C T 4 OK 4106 4102 4105 4124 C2' C T 5 OK 4126 4122 4125 4144 C2' G T 6 OK 4146 4142 4145 4167 C2' G T 7 OK 4169 4165 4168 4190 C2' G T 8 OK 4192 4188 4191 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3890 C3' U P 1 OK 3888 3891 3892 3910 C3' G P 2 OK 3908 3911 3912 3933 C3' C P 3 OK 3931 3934 3935 3953 C3' C P 4 OK 3951 3954 3955 3973 C3' C P 5 OK 3971 3974 3975 3993 C3' G P 6 OK 3991 3994 3995 4016 C3' G P 7 OK 4014 4017 4018 4039 C3' G P 8 OK 4037 4040 4041 4060 C3' A T 2 OK 4058 4061 4062 4082 C3' C T 3 OK 4080 4083 4084 4102 C3' C T 4 OK 4100 4103 4104 4122 C3' C T 5 OK 4120 4123 4124 4142 C3' G T 6 OK 4140 4143 4144 4165 C3' G T 7 OK 4163 4166 4167 4188 C3' G T 8 OK 4186 4189 4190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3888 C4' U P 1 OK 3890 3887 3889 3908 C4' G P 2 OK 3910 3907 3909 3931 C4' C P 3 OK 3933 3930 3932 3951 C4' C P 4 OK 3953 3950 3952 3971 C4' C P 5 OK 3973 3970 3972 3991 C4' G P 6 OK 3993 3990 3992 4014 C4' G P 7 OK 4016 4013 4015 4037 C4' G P 8 OK 4039 4036 4038 4058 C4' A T 2 OK 4060 4057 4059 4080 C4' C T 3 OK 4082 4079 4081 4100 C4' C T 4 OK 4102 4099 4101 4120 C4' C T 5 OK 4122 4119 4121 4140 C4' G T 6 OK 4142 4139 4141 4163 C4' G T 7 OK 4165 4162 4164 4186 C4' G T 8 OK 4188 4185 4187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3887 C5' U P 1 3886 3888 3907 C5' G P 2 3906 3908 3930 C5' C P 3 3929 3931 3950 C5' C P 4 3949 3951 3970 C5' C P 5 3969 3971 3990 C5' G P 6 3989 3991 4013 C5' G P 7 4012 4014 4036 C5' G P 8 4035 4037 4057 C5' A T 2 4056 4058 4079 C5' C T 3 4078 4080 4099 C5' C T 4 4098 4100 4119 C5' C T 5 4118 4120 4139 C5' G T 6 4138 4140 4162 C5' G T 7 4161 4163 4185 C5' G T 8 4184 4186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3903 P G P 2 distorted distorted 3891 3904 3905 3906 3926 P C P 3 distorted distorted 3911 3927 3928 3929 3946 P C P 4 distorted distorted 3934 3947 3948 3949 3966 P C P 5 distorted distorted 3954 3967 3968 3969 3986 P G P 6 distorted distorted 3974 3987 3988 3989 4009 P G P 7 distorted distorted 3994 4010 4011 4012 4032 P G P 8 distorted distorted 4017 4033 4034 4035 4075 P C T 3 distorted distorted 4061 4076 4077 4078 4095 P C T 4 distorted distorted 4083 4096 4097 4098 4115 P C T 5 distorted distorted 4103 4116 4117 4118 4135 P G T 6 distorted distorted 4123 4136 4137 4138 4158 P G T 7 distorted distorted 4143 4159 4160 4161 4181 P G T 8 distorted distorted 4166 4182 4183 4184 ---------------------------------------------------------------------------------