In recent years, protein methylation has been established as a major intracellular post translational modification (PTM). It has also been proposed to modulate protein-protein interactions (PPIs) in the interactome. To investigate the effect of PTMs on PPIs, we recently developed the conditional two hybrid (C2H) system. It allows the co‑expression of a modifying enzyme such as a methyltransferase, acetyltransferase, or kinase alongside the bait and prey proteins. Any increase or decrease in interaction due to the modification of the proteins can be measured by an increased or decreased level of reporter gene expression. With this, we demonstrated that arginine methylation can modulate PPIs in the yeast interactome. Here, we used the C2H system to investigate the effect of lysine methylation. Specifically, we asked whether Ctm1p-mediated trimethylation of yeast cytochrome c Cyc1p, on lysine 78, modulates its interactions with Erv1p, Ccp1p, Cyc2p and Cyc3p. We show that the interactions between Cyc1p and Erv1p, and between Cyc1p and Cyc3p, are significantly increased upon trimethylation of lysine 78. This increase of interaction helps explain the reported facilitation of Cyc1p import into the mitochondrial intermembrane space upon methylation. This is one of the first demonstrations in a two-hybrid system that lysine methylation can modulate PPIs. It will be of interest to understand how widespread this process is in the eukaryotic cell.