Figure 7.

Visualization of the contribution of the different physical properties of amino acid to the peptide binding to MHC-II. Variable importance projection (VIP) of the PLS regression prediction of ln(ic50) of peptide binding using the first three principal components of each of the amino acids in the 15-mer as predictors. (PC1) Principal component 1, polarity correlate; (PC2) principal compent 2, size correlate, (PC3) principal component 3, electronic correlate. Coloration is column-relative indicated by the scales for each position in the binding domain (a copy of this figure with details of color scaling can be found in Additional File 8; Figure S7). The amino acid in the binding domain of the particular MHC-II allele in each column is indicated on the left. A 15-amino acid binding domain is shown using the standard for the MHC binding groove numbered N-terminus to C-terminus 1 through 9 along with the additional 3 N-terminal and 3 C-terminal residues. The colors compare the relative importance of the particular numbered residue of the binding domain among the MHC-II alleles indicated. Cells in the matrix with VIP >1 are the most relevant in explaining the binding affinity.