title: Standard conformations for the canonical structures of immunoglobulins.
abstract: A comparative analysis of the main-chain conformation of the L1, L2, L3, H1 and H2 hypervariable regions in 17 immunoglobulin structures that have been accurately determined at high resolution is described. This involves 79 hypervariable regions in all. We also analysed a part of the H3 region in 12 of the 15 VH domains considered here. On the basis of the residues at key sites the 79 hypervariable regions can be assigned to one of 18 different canonical structures. We show that 71 of these hypervariable regions have a conformation that is very close to what can be defined as a "standard" conformation of each canonical structure. These standard conformations are described in detail. The other eight hypervariable regions have small deviations from the standard conformations that, in six cases, involve only the rotation of a single peptide group. Most H3 hypervariable regions have the same conformation in the part that is close to the framework and the details of this conformation are also described here.
authors.affiliation: University of Cambridge Clinical School, Hills Road, Cambridge, CB2 2QH, England.
authors.forename: B
authors.initials: B
authors.lastname: Al-Lazikani
authors.forename: A M
authors.initials: AM
authors.lastname: Lesk
authors.forename: C
authors.initials: C
authors.lastname: Chothia
mesh_terms: D001665:Binding Sites; D018604:Epitope Mapping; D007135:Immunoglobulin Variable Region / Q000737:chemistry; D007136:Immunoglobulins / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D007135:Immunoglobulin Variable Region; D007136:Immunoglobulins