The interaction between recombinant Fab57P and the coat protein of tobacco mosaic virus was studied using quantitative structure–activity relationship (QSAR) method. The development of quantitative multivariate model has shown to be a promising approach for unraveling protein–protein interactions by designed mutations in peptide sequence. This approach makes it possible to stereo-chemically determine which residue properties contribute most to the interaction. A set of side-chain descriptors was proposed and applied in structural characterization of three positions (positions 142, 145 and 146) in the peptide antigen. Quantitative sequence–kinetics relationship (QSKR) models describing the dissociation rates (log kd) were developed successfully using orthogonal signal correction–partial least squares method. The results showed that peptides will have high log kd values when the amino acids in position 142 and 145 have high net charge index, and when residue 145 has high hydrophobicity and residue 146 has low hydrophobicity.