Identifying hot-spot residues – residues that are critical to protein–protein binding – can help to elucidate a protein’s function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein–protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36–57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein–protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins.