However, this effect also impacts protein-protein interactions. Many protein interfaces feature amino acids that are so tightly packed that when mapped to Martini 3 side chains, which are made up of beads of various sizes, may also fall within the repulsive regime of their respective LJ potentials. Indeed this is the case in the Barnase-Barstar complex, which we use as an example here. Analyzing the crystal complex mapped to Martini 3, the interface contains 215 residues with 1806 possible LJ pair interactions (within the Martini non-bonded cutoff of 1.1 nm 1 ) out of which 215 are involved in repulsive interactions (Figure , D & E). Interactions between specific amino acid residues will be especially susceptible to this issue. In the Martini 3 interaction matrix, "super repulsive" interaction levels 1 have A contact is deemed repulsive if the pair distance is shorter than the distance associated with the LJ minimum for that particular pair interaction. Here, interface residues were defined as those within 0.8 nm of the opposite protein partner. Interface water molecules were defined as those within 0.4 nm of both protein chains. Barnase-Barstar protein complex showcasing the interface amino acid residues (E) and water molecules (F) engaged in repulsive interactions. The Martini 3 structure was directly mapped from the experimental crystal structure. Barnase and barstar are represented in white and brown, respectively. Sidechains engaged in repulsive interactions are shown and colored by residue type (basic in blue, acidic in red, polar in green, and hydrophobic in white) and water molecules engaged in repulsive interactions are represented in blue.