ID code: '4AFY' 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' --------------------------------------------------------------------------------- 3926 C1' G C 1 beta 3921 3927 3924 3949 C1' G C 2 beta 3944 3950 3947 3973 C1' G D 1 beta 3968 3974 3971 3996 C1' G D 2 beta 3991 3997 3994 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3924 C2' G C 1 OK 3926 3922 3925 3947 C2' G C 2 OK 3949 3945 3948 3971 C2' G D 1 OK 3973 3969 3972 3994 C2' G D 2 OK 3996 3992 3995 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3922 C3' G C 1 OK 3920 3923 3924 3945 C3' G C 2 OK 3943 3946 3947 3969 C3' G D 1 OK 3967 3970 3971 3992 C3' G D 2 OK 3990 3993 3994 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3920 C4' G C 1 OK 3922 3919 3921 3943 C4' G C 2 OK 3945 3942 3944 3967 C4' G D 1 OK 3969 3966 3968 3990 C4' G D 2 OK 3992 3989 3991 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3919 C5' G C 1 3918 3920 3942 C5' G C 2 3941 3943 3966 C5' G D 1 3965 3967 3989 C5' G D 2 3988 3990 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3915 P G C 1 distorted distorted 3916 3917 3918 3938 P G C 2 OK OK 3923 3939 3940 3941 3962 P G D 1 distorted distorted 3963 3964 3965 3985 P G D 2 distorted distorted 3970 3986 3987 3988 ---------------------------------------------------------------------------------