ID code: '5TSN' 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' --------------------------------------------------------------------------------- 3942 C1' U P 1 beta 3937 3943 3940 3962 C1' A P 2 beta 3957 3963 3960 3984 C1' C P 3 beta 3979 3985 3982 4004 C1' C P 4 beta 3999 4005 4002 4024 C1' C P 5 beta 4019 4025 4022 4044 C1' G P 6 beta 4039 4045 4042 4067 C1' G P 7 beta 4062 4068 4065 4090 C1' G P 8 beta 4085 4091 4088 4111 C1' A T 2 beta 4106 4112 4109 4133 C1' C T 3 beta 4128 4134 4131 4153 C1' C T 4 beta 4148 4154 4151 4173 C1' C T 5 beta 4168 4174 4171 4193 C1' G T 6 beta 4188 4194 4191 4216 C1' G T 7 beta 4211 4217 4214 4239 C1' G T 8 beta 4234 4240 4237 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3940 C2' U P 1 OK 3942 3938 3941 3960 C2' A P 2 OK 3962 3958 3961 3982 C2' C P 3 OK 3984 3980 3983 4002 C2' C P 4 OK 4004 4000 4003 4022 C2' C P 5 OK 4024 4020 4023 4042 C2' G P 6 OK 4044 4040 4043 4065 C2' G P 7 OK 4067 4063 4066 4088 C2' G P 8 OK 4090 4086 4089 4109 C2' A T 2 OK 4111 4107 4110 4131 C2' C T 3 OK 4133 4129 4132 4151 C2' C T 4 OK 4153 4149 4152 4171 C2' C T 5 OK 4173 4169 4172 4191 C2' G T 6 OK 4193 4189 4192 4214 C2' G T 7 OK 4216 4212 4215 4237 C2' G T 8 OK 4239 4235 4238 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3938 C3' U P 1 OK 3936 3939 3940 3958 C3' A P 2 OK 3956 3959 3960 3980 C3' C P 3 OK 3978 3981 3982 4000 C3' C P 4 OK 3998 4001 4002 4020 C3' C P 5 OK 4018 4021 4022 4040 C3' G P 6 OK 4038 4041 4042 4063 C3' G P 7 OK 4061 4064 4065 4086 C3' G P 8 OK 4084 4087 4088 4107 C3' A T 2 OK 4105 4108 4109 4129 C3' C T 3 OK 4127 4130 4131 4149 C3' C T 4 OK 4147 4150 4151 4169 C3' C T 5 OK 4167 4170 4171 4189 C3' G T 6 OK 4187 4190 4191 4212 C3' G T 7 OK 4210 4213 4214 4235 C3' G T 8 OK 4233 4236 4237 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3936 C4' U P 1 OK 3938 3935 3937 3956 C4' A P 2 OK 3958 3955 3957 3978 C4' C P 3 OK 3980 3977 3979 3998 C4' C P 4 OK 4000 3997 3999 4018 C4' C P 5 OK 4020 4017 4019 4038 C4' G P 6 OK 4040 4037 4039 4061 C4' G P 7 OK 4063 4060 4062 4084 C4' G P 8 OK 4086 4083 4085 4105 C4' A T 2 OK 4107 4104 4106 4127 C4' C T 3 OK 4129 4126 4128 4147 C4' C T 4 OK 4149 4146 4148 4167 C4' C T 5 OK 4169 4166 4168 4187 C4' G T 6 OK 4189 4186 4188 4210 C4' G T 7 OK 4212 4209 4211 4233 C4' G T 8 OK 4235 4232 4234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3935 C5' U P 1 3934 3936 3955 C5' A P 2 3954 3956 3977 C5' C P 3 3976 3978 3997 C5' C P 4 3996 3998 4017 C5' C P 5 4016 4018 4037 C5' G P 6 4036 4038 4060 C5' G P 7 4059 4061 4083 C5' G P 8 4082 4084 4104 C5' A T 2 4103 4105 4126 C5' C T 3 4125 4127 4146 C5' C T 4 4145 4147 4166 C5' C T 5 4165 4167 4186 C5' G T 6 4185 4187 4209 C5' G T 7 4208 4210 4232 C5' G T 8 4231 4233 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3951 P A P 2 distorted distorted 3939 3952 3953 3954 3973 P C P 3 distorted distorted 3959 3974 3975 3976 3993 P C P 4 distorted distorted 3981 3994 3995 3996 4013 P C P 5 distorted distorted 4001 4014 4015 4016 4033 P G P 6 distorted distorted 4021 4034 4035 4036 4056 P G P 7 distorted distorted 4041 4057 4058 4059 4079 P G P 8 distorted distorted 4064 4080 4081 4082 4122 P C T 3 distorted distorted 4108 4123 4124 4125 4142 P C T 4 distorted distorted 4130 4143 4144 4145 4162 P C T 5 distorted distorted 4150 4163 4164 4165 4182 P G T 6 distorted distorted 4170 4183 4184 4185 4205 P G T 7 distorted distorted 4190 4206 4207 4208 4228 P G T 8 distorted distorted 4213 4229 4230 4231 ---------------------------------------------------------------------------------