AbstractThe subunit interfaces of 122 homodimers of known three‐dimensional structure are analyzed and dissected into sets of surface patches by clustering atoms at the interface; 70 interfaces are single‐patch, the others have up to six patches, often contributed by different structural domains. The average interface buries 1,940 Å2 of the surface of each monomer, contains one or two patches burying 600–1,600 Å2, is 65% nonpolar and includes 18 hydrogen bonds. However, the range of size and of hydrophobicity is wide among the 122 interfaces. Each interface has a core made of residues with atoms buried in the dimer, surrounded by a rim of residues with atoms that remain accessible to solvent. The core, which constitutes 77% of the interface on average, has an amino acid composition that resembles the protein interior except for the presence of arginine residues, whereas the rim is more like the protein surface. These properties of the interfaces in homodimers, which are permanent assemblies, are compared to those of protein‐protein complexes where the components associate after they have independently folded. On average, subunit interfaces in homodimers are twice larger than in complexes, and much less polar due to the large fraction belonging to the core, although the amino acid compositions of the cores are similar in the two types of interfaces. Proteins 2003. © 2003 Wiley‐Liss, Inc.