Canonical Classes

CDRs are classified in abYsis using sequence rules which specify loop length and permitted amino acids at required positions. In this way classifications can be made for all numbered sequences, whether or not structural data are available. Use the Region dropdown to select a particular CDR.

Three separate CDR classification methods are implemented within abYsis. These differ in the key residues allowed at different positions. Use the Canonical Method dropdown to select a particular method.

The table shows details of the sequence rules for all the canonical classes corresponding to a particular CDR/method combination.

The row below Chothia position, permitted amino acids indicates the subset of numbered positions that are relevant for the selected CDR/method combination.

There is then one row for each canonical class.

The first column shows the canonical class name. The second column shows the accession for a representative structure in abYsis. The third column shows the required loop length (AbM definition). The following columns show the permitted amino acids at each required position.

For a query sequence to have an exact match, the loop length must agree and the amino acids at each required position must match one of the permitted amino acids. For a similar match, the loop length must agree but there may be one or more position where the amino acids do not match one of the permitted amino acids.

Methods

Auto Method

Likely to give the most accurate results because it is based on strict templates derived automatically from available crystal structures. The templates are generated using an automatic protocol involving cluster analysis and analysis of buried hydrophobic and hydrogen bonding residues (Martin and Thornton, J. Mol. Biol. 263(1996),800-815).

The canonical class identifiers consist of the equivalent Chothia class followed by a structural cluster number consisting of the loop length followed by a letter to describe the individual cluster. Where there is no equivalent Chothia class, a '?' appears (e.g. for CDR-H1, there are classes ?/10C and ?/10D).

AbM Method

The AbM key residues are based on Chothia templates (Whitelegg N & Rees AR, Protein Eng. 13(2000),819-24 and Methods Mol. Biol. 248(2004),51-91). The classes are expanded from the Chothia definitions: some additional allowed residues have been specified together with some additional required residues and extra classes. Classes with a * in the name are not defined by Chothia. Modfications and references are detailed for each class.

Strict Method

These classes result from strict application of templates derived from various papers by Chothia et al.

Note

There are some confusing discrepancies in the canonical class numbers used by Chothia. For example CDR-L1 Class 5 is used in earlier papers to refer to a 13-residue lambda light while later papers use class 5 for a 15-residue kappa. Similarly CDR-L1 Class 6 is used in earlier papers to refer to a 14-residues lambda, but later papers use class 6 for a 12-residue kappa. We have used the earlier class numbers.