Understanding the competition between protein secondary structure formation and protein aggregation is important from a biomedical viewpoint where many diseases have been linked to protein misfolding and subsequent aggregation. In downstream bioprocessing, the aggregation of partially folded intermediates leads to reduced yields and, thus, many approaches are being developed to prevent these un-wanted side reactions. In this work we use Monte Carlo simulations to study the interactions between a pair of poly-alanine molecules and a pair of poly-lysine molecules. These homopolypeptides have well-defined elements of secondary structure, are relatively simple, and are known to form either amorphous precipitates or fibrils. For simulations where the homopolypeptides are treated as rigid molecules, the pair potential of mean force is anisotropic where an end-to-end configuration is favoured. The determined interactions for a pair of conformationally flexible polyalanine molecules are similar to those of a rigid model for separations larger than the helix-helix contact separation. Alternatively, a pair of flexible poly-lysine helices melts upon approaching each other. For separations less than the helix-helix contact distance, the configurations are trapped in a state where a non-helical peptide is wrapped around a helical peptide.