Numbering Schemes

Three numbering schemes are implemented within abYsis:

The Scheme name dropdown can be used to select a numbering scheme.

All three schemes can also be viewed side-by-side view. Note the side-by-side view shows a highly artificial situation in which all insertions have their maximum allowed length. In general the correspondence between schemes is non-trivial and depends on the length of the insertions.

Region Definitions

Four region definitions (defining the location of the loops or CDRs) are implemented within abYsis:

Note

The Chothia region definition for the CDR-H1 loop, and the Contact definition for the CDR-L1 loop, have a complex specification when using the Kabat numbering scheme (footnotes are provided for the Kabat numbering scheme). However, for a given sequence, the regions are ultimately independent of the numbering scheme. Internally, abYsis uses the Chothia numbering scheme to delineate regions.