ID code: '3SQW' 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' --------------------------------------------------------------------------------- 4045 C1' U B 2 beta 4040 4046 4043 4058 C1' U B 3 beta 4053 4059 4056 4078 C1' U B 4 beta 4073 4079 4076 4098 C1' U B 5 beta 4093 4099 4096 4118 C1' U B 6 beta 4113 4119 4116 4138 C1' U B 7 beta 4133 4139 4136 4158 C1' U B 8 beta 4153 4159 4156 4192 C1' ANP A 800 beta 4187 4193 4190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4043 C2' U B 2 OK 4045 4041 4044 4056 C2' U B 3 OK 4058 4054 4057 4076 C2' U B 4 OK 4078 4074 4077 4096 C2' U B 5 OK 4098 4094 4097 4116 C2' U B 6 OK 4118 4114 4117 4136 C2' U B 7 OK 4138 4134 4137 4156 C2' U B 8 OK 4158 4154 4157 4190 C2' ANP A 800 OK 4192 4188 4191 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4041 C3' U B 2 OK 4039 4042 4043 4054 C3' U B 3 OK 4052 4055 4056 4074 C3' U B 4 OK 4072 4075 4076 4094 C3' U B 5 OK 4092 4095 4096 4114 C3' U B 6 OK 4112 4115 4116 4134 C3' U B 7 OK 4132 4135 4136 4154 C3' U B 8 OK 4152 4155 4156 4188 C3' ANP A 800 OK 4186 4189 4190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4039 C4' U B 2 OK 4041 4038 4040 4052 C4' U B 3 OK 4054 4051 4053 4072 C4' U B 4 OK 4074 4071 4073 4092 C4' U B 5 OK 4094 4091 4093 4112 C4' U B 6 OK 4114 4111 4113 4132 C4' U B 7 OK 4134 4131 4133 4152 C4' U B 8 OK 4154 4151 4153 4186 C4' ANP A 800 OK 4188 4185 4187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4038 C5' U B 2 4037 4039 4051 C5' U B 3 4050 4052 4071 C5' U B 4 4070 4072 4091 C5' U B 5 4090 4092 4111 C5' U B 6 4110 4112 4131 C5' U B 7 4130 4132 4151 C5' U B 8 4150 4152 4185 C5' ANP A 800 4184 4186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4034 P U B 2 distorted distorted 4035 4036 4037 4047 P U B 3 distorted distorted 4042 4048 4049 4050 4067 P U B 4 distorted distorted 4055 4068 4069 4070 4087 P U B 5 distorted distorted 4075 4088 4089 4090 4107 P U B 6 distorted distorted 4095 4108 4109 4110 4127 P U B 7 distorted distorted 4115 4128 4129 4130 4147 P U B 8 distorted distorted 4135 4148 4149 4150 4167 P U B 9 distorted distorted 4155 4168 4169 4170 ---------------------------------------------------------------------------------