ID code: '3SQX' 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' --------------------------------------------------------------------------------- 4002 C1' U B 3 beta 3997 4003 4000 4022 C1' U B 4 beta 4017 4023 4020 4042 C1' U B 5 beta 4037 4043 4040 4062 C1' U B 6 beta 4057 4063 4060 4082 C1' U B 7 beta 4077 4083 4080 4102 C1' U B 8 beta 4097 4103 4100 4136 C1' ANP A 800 beta 4131 4137 4134 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4000 C2' U B 3 OK 4002 3998 4001 4020 C2' U B 4 OK 4022 4018 4021 4040 C2' U B 5 OK 4042 4038 4041 4060 C2' U B 6 OK 4062 4058 4061 4080 C2' U B 7 OK 4082 4078 4081 4100 C2' U B 8 OK 4102 4098 4101 4134 C2' ANP A 800 OK 4136 4132 4135 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3998 C3' U B 3 OK 3996 3999 4000 4018 C3' U B 4 OK 4016 4019 4020 4038 C3' U B 5 OK 4036 4039 4040 4058 C3' U B 6 OK 4056 4059 4060 4078 C3' U B 7 OK 4076 4079 4080 4098 C3' U B 8 OK 4096 4099 4100 4132 C3' ANP A 800 OK 4130 4133 4134 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3996 C4' U B 3 OK 3998 3995 3997 4016 C4' U B 4 OK 4018 4015 4017 4036 C4' U B 5 OK 4038 4035 4037 4056 C4' U B 6 OK 4058 4055 4057 4076 C4' U B 7 OK 4078 4075 4077 4096 C4' U B 8 OK 4098 4095 4097 4130 C4' ANP A 800 OK 4132 4129 4131 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3995 C5' U B 3 3994 3996 4015 C5' U B 4 4014 4016 4035 C5' U B 5 4034 4036 4055 C5' U B 6 4054 4056 4075 C5' U B 7 4074 4076 4095 C5' U B 8 4094 4096 4129 C5' ANP A 800 4128 4130 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3991 P U B 3 distorted distorted 3990 3992 3993 3994 4011 P U B 4 distorted distorted 3999 4012 4013 4014 4031 P U B 5 distorted distorted 4019 4032 4033 4034 4051 P U B 6 distorted distorted 4039 4052 4053 4054 4071 P U B 7 distorted distorted 4059 4072 4073 4074 4091 P U B 8 distorted distorted 4079 4092 4093 4094 4111 P U B 9 distorted distorted 4099 4112 4113 4114 ---------------------------------------------------------------------------------