ID code: '3I5Y' 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' --------------------------------------------------------------------------------- 3989 C1' U B 1 beta 3984 3990 3987 4009 C1' U B 2 beta 4004 4010 4007 4022 C1' U B 3 beta 4017 4023 4020 4042 C1' 5BU B 4 beta 4037 4043 4040 4063 C1' U B 5 beta 4058 4064 4061 4083 C1' U B 6 beta 4078 4084 4081 4103 C1' U B 7 beta 4098 4104 4101 4123 C1' U B 8 beta 4118 4124 4121 4143 C1' U B 9 beta 4138 4144 4141 4163 C1' U B 10 beta 4158 4164 4161 4193 C1' ANP A1000 beta 4188 4194 4191 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3987 C2' U B 1 OK 3989 3985 3988 4007 C2' U B 2 OK 4009 4005 4008 4020 C2' U B 3 OK 4022 4018 4021 4040 C2' 5BU B 4 OK 4042 4038 4041 4061 C2' U B 5 OK 4063 4059 4062 4081 C2' U B 6 OK 4083 4079 4082 4101 C2' U B 7 OK 4103 4099 4102 4121 C2' U B 8 OK 4123 4119 4122 4141 C2' U B 9 OK 4143 4139 4142 4161 C2' U B 10 OK 4163 4159 4162 4191 C2' ANP A1000 OK 4193 4189 4192 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3985 C3' U B 1 OK 3983 3986 3987 4005 C3' U B 2 OK 4003 4006 4007 4018 C3' U B 3 OK 4016 4019 4020 4038 C3' 5BU B 4 OK 4036 4039 4040 4059 C3' U B 5 OK 4057 4060 4061 4079 C3' U B 6 OK 4077 4080 4081 4099 C3' U B 7 OK 4097 4100 4101 4119 C3' U B 8 OK 4117 4120 4121 4139 C3' U B 9 OK 4137 4140 4141 4159 C3' U B 10 OK 4157 4160 4161 4189 C3' ANP A1000 OK 4187 4190 4191 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3983 C4' U B 1 OK 3985 3982 3984 4003 C4' U B 2 OK 4005 4002 4004 4016 C4' U B 3 OK 4018 4015 4017 4036 C4' 5BU B 4 OK 4038 4035 4037 4057 C4' U B 5 OK 4059 4056 4058 4077 C4' U B 6 OK 4079 4076 4078 4097 C4' U B 7 OK 4099 4096 4098 4117 C4' U B 8 OK 4119 4116 4118 4137 C4' U B 9 OK 4139 4136 4138 4157 C4' U B 10 OK 4159 4156 4158 4187 C4' ANP A1000 OK 4189 4186 4188 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3982 C5' U B 1 3981 3983 4002 C5' U B 2 4001 4003 4015 C5' U B 3 4014 4016 4035 C5' 5BU B 4 4034 4036 4056 C5' U B 5 4055 4057 4076 C5' U B 6 4075 4077 4096 C5' U B 7 4095 4097 4116 C5' U B 8 4115 4117 4136 C5' U B 9 4135 4137 4156 C5' U B 10 4155 4157 4186 C5' ANP A1000 4185 4187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3998 P U B 2 distorted distorted 3986 3999 4000 4001 4011 P U B 3 distorted distorted 4006 4012 4013 4014 4031 P 5BU B 4 distorted distorted 4019 4032 4033 4034 4052 P U B 5 distorted distorted 4039 4053 4054 4055 4072 P U B 6 distorted distorted 4060 4073 4074 4075 4092 P U B 7 distorted distorted 4080 4093 4094 4095 4112 P U B 8 distorted distorted 4100 4113 4114 4115 4132 P U B 9 distorted distorted 4120 4133 4134 4135 4152 P U B 10 distorted distorted 4140 4153 4154 4155 ---------------------------------------------------------------------------------