The hydrophobic interaction drives the association of non-polar molecules in water. It governs the assembly of biomolecules, and plays a central role in biological phenomena ranging from protein folding to viral-host cell interactions. In these contexts, domains defined by non-polar amino acids are found proximal to polar and charged groups, thus generating nanoscale patterns of chemical functional groups. Atomistic simulations have advanced our understanding of how hydrophobic interactions arise in such systems, but few experiments permit unambiguous conclusions regarding the effects of chemical heterogeneity on hydrophobic interactions. One prior set of studies used conformationally rigid β-peptide oligomers and single-molecule force measurements to reveal that the identity of charged groups placed adjacent to non-polar domains can profoundly impact hydrophobic interactions encoded by the non-polar domains. However, the impact of chemical heterogeneity on hydrophobic interactions has not been characterized in experimental systems beyond β-peptide oligomers. This thesis will focus on the use of single-molecule force measurements to understand hydrophobic interactions encoded by oligopeptides formed from a-amino acids. In contrast to prior studies of oligomers of β-peptides, the oligopeptides to be discussed in this talk possess conformations that are coupled to their interactions. First, single-molecule force measurements of α-peptide sequences capable of forming parallel coiled-coil dimers will be described to explore how charged residue identity (lysine versus arginine) influences their hydrophobic interactions. These measurements, when combined with infrared spectroscopic characterization of peptide conformations, reveal that lysine-bearing sequences assume conformations that encode stronger hydrophobic interactions than arginine-containing sequences. Importantly, the results reveal that the influence of charged group identity on hydrophobic interactions, which had previously been observed using conformationally rigid β-peptide oligomers, extends to the interactions of α-peptides that form coiled-coil complexes. Second, the capability to characterize coiled-coil complexes is used to provide insight into hydrophobic interactions encoded by heptad repeat sequences proximal to the N-terminus (HRN) and C-terminus (HRC) within the SARS-CoV-2 spike (S) protein. HRC and HRN play an important role in the fusion of host cell and viral membranes: a disordered HRC trimer has been proposed to pack against the grooves of a coiled-coil HRN trimer to create a six-helix bundle (6HB) necessary for successful membrane fusion and infection. Single molecule force measurements reveal that hydrophobic interactions dominate intermolecular forces acting between HRC and/or HRN sequences, and that the interaction between HRC and HRN gives rise to stronger hydrophobic interactions than their self-interactions. This result suggests a thermodynamic driving force for the formation of the 6HB in which HRC packs against the HRN trimer. Finally, single molecule force measurements of hydrophobic interactions mediated by fusion peptide (FP) sequences within SARS-CoV-2 and MERS-CoV S proteins will be described. These measurements reveal that a 11 amino acid SARS-2 FP sequence exhibits a three-fold stronger hydrophobic interaction than its MERS counterpart due to substitution of a single amino acid (Phe versus Ala). The outsized influence of this single amino acid substitution arises from the strong coupling between hydrophobic interaction and peptide conformation.