We present a multilevel molecular modeling study aimed at elucidating physical and chemical properties of gold clusters capped by a monolayer of thiolated oligopeptides. The protecting peptides are based on the α-aminoisobutyric acid unit, form intramolecular C=O⋯H-N bonds, and can form intermolecular hydrogen bonds. This study is motivated by recent breakthroughs into the determination of crystal structures of small gold clusters protected with small thiolated molecules. Such structures are characterized by surface gold atoms in the so-called "staple motifs", as opposed to the commonly assumed structures in which thiolates bind to a high-symmetry gold cluster. It is unclear, however, whether the staple motif is common to all kinds of protecting layers, especially those made of polypeptides that are largely stabilized by intermolecular hydrogen bonding. Structural and spectroscopic properties are presented to understand the nature of peptide-peptide interactions, their structural arrangements, and their effect on the gold-thiol structural motif.