ID code: '2XPJ' 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' --------------------------------------------------------------------------------- 3956 C1' C D 1 beta 3951 3957 3954 3976 C1' C D 2 beta 3971 3977 3974 3996 C1' C D 3 beta 3991 3997 3994 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3954 C2' C D 1 OK 3956 3952 3955 3974 C2' C D 2 OK 3976 3972 3975 3994 C2' C D 3 OK 3996 3992 3995 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3952 C3' C D 1 OK 3950 3953 3954 3972 C3' C D 2 OK 3970 3973 3974 3992 C3' C D 3 OK 3990 3993 3994 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3950 C4' C D 1 OK 3952 3949 3951 3970 C4' C D 2 OK 3972 3969 3971 3990 C4' C D 3 OK 3992 3989 3991 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3949 C5' C D 1 3948 3950 3969 C5' C D 2 3968 3970 3989 C5' C D 3 3988 3990 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3965 P C D 2 distorted distorted 3953 3966 3967 3968 3985 P C D 3 OK OK 3973 3986 3987 3988 ---------------------------------------------------------------------------------