Figure 4.

Ab positions that contact the Ag. (A,B) The lower graphs show the percentage of Abs with known 3-D structure that have a residue in a given position (i.e., in other Abs there is a gap in the MSTA in that position). The upper graphs show the percentage of Abs that contact the Ag out of those Abs that have a residue in that position. (A) Depicts the heavy chain and (B) depicts the light chain. In the upper graphs, the ABRs are colored red and the FRs are colored blue. An example of a position within an ABR that is not in contact with the Ag in any of the Abs, is marked by a green arrow. An example of a position in the FRs that is in contact with the Ag in many (8%) of the Abs is marked by an orange arrow. (C) The Ab Fv domain (PDB ID: 1QFU) is colored according to the percentage of all Abs with known 3-D structure in which the residue in that position is in contact with the Ag: from red (100% of the Abs) to blue (0%). ABR residues are presented as lines. The definition of the ABRs is according to the Paratome server. A 6-Å cutoff value was used to define residues in contact. Percentages of contacts were calculated based on an MSTA of all protein Ab-Ag complexes in the PDB (30).