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Figure 1: A picture of the alignment of HLA-${\text{A}}^{*}$0201 peptides along with positionwise similarity indices calculated by (1). $S_{{\text{ISA}}_i}^{\text{AB}}$ similarity indices for the query peptide [B] aligned against the reference peptide [A] for positions ${\text{P}}_{-4}$ to ${\text{P}}_{+2}$, the similarity indices have been calculated by (1) using the property—isotropic surface area (ISA).