Table 1.

Protein interfaces used in the analysis

Code	Protein	Species	Interface size	Residue number	Sequence number
Heterodimer
1allAB_A	phycobiliprotein allophycocyanin	Spirulina platensis	1431	34	10,10
1hcgAB_A	coagulation factor X	Homo sapiens	887	32	23,12
1lucAB_A	luciferase	Vibrio harveyi	2055	52	19,8
1scuDE_E	succinyl-CoA synthetase	Escherichia coli	1744	47	17,11
1tcoAB_B	calmodulin-dependent phosphatase	Bos taurus	1909	55	12,12
1tcoBC_B	calmodulin-dependent phosphatase	Bos taurus	415	12	12,12
1tcrAB_A	T cell receptor α chain	Mus musculus	2120	60	11,7
1ubsAB_A	tryptophan synthase α subunit	Salmonella typhimurium	1308	37	18,12
1wdcAC_C	myosin light chain	Argopecten irradians	1856	46	10,12
2pcdBN_N	protocatechuate 3,4-dioxygenase	Pseudomonas putida	3568	89	12,10
8atcAB_A	aspartate carbamoyltransferase	Escherichia coli	767	25	27,13
9atcAB_B	aspartate carbamoyltransferase	Escherichia coli	767	17	13,9
Homodimer
1bncAB_A	acetyl-CoA carboxylase	Escherichia coli	1224	35	40,13
1daaAB_A	D-amino acid aminotransferase	Bacillus sp YM-1	2302	57	25,10
1dpgAB_A	glucose-6-phosphate 1-dehydrogenase	L mesenteroides	2285	59	13,13
1ecpBD_B	purine nucleoside phosphorylase	Escherichia coli	1694	40	10,10
1efuBD_B	translation elongation factor Ts	Escherichia coli	1081	27	20,15
1frpAB_A	fructose bisphosphatase	Sus scrofa	2358	60	10,10
1fuqAB_A	fumarate hydratase	Escherichia coli	1977	48	12,13
1gdhAB_A	D-glycerate dehydrogenase	H. methylovorum	3127	72	46,13
1gesAB_A	pyruvate dehydrogenase	Escherichia coli	3393	85	23,14
1glqAB_A	Glutathione S-transferase pi	Mus musculus	1282	31	11,11
1gp1AB_A	glutathione peroxidase	Bos taurus	775	18	20,10
1gpmBD_B	GMP synthase	Escherichia coli	965	26	14,10
1hurAB_A	ADP-ribosylation factor 1	Homo sapiens	550	15	17,11
1hyhAB_A	L-lactate dehydrogenase	Weissella confusa	818	23	22,11
1idsAC_A	superoxide dismutase	M. tuberculosis	2182	52	18,14
1iesBE_B	ferritin	Equus caballus	1395	31	10,10
1lehAB_A	leucine dehydrogenase	Bacillus sphaericus	1274	30	19,10
1masAB_A	IU-nucleoside hydrolase	Crithidia fasciculata	875	25	15,11
1mldAB_A	malate dehydrogenase	Sus scrofa	1534	38	10,9
1nhkLR_L	nucleoside diphosphate kinase	Myxococcus xanthus	1166	33	16,14
1oroAB_A	orotate phosphoribosyltransferase	Escherichia coli	1217	35	23,10
1osjAB_A	3-isopropylmalate dehydrogenase	Thermus thermophilus	2138	52	12,12
1pkyAC_A	pyruvate kinase	Escherichia coli	1074	27	16,14
1poly12_1	spermidine/putrescine-binding protein	Escherichia coli	1004	31	20,12
1qorAB_A	quinone oxidoreductase	Escherichia coli	1194	32	22,10
1rahBD_B	aspartate carbamoyltransferase	Escherichia coli	1143	27	12,10
1rvv12_1	riboflavin synthase, β subunit	Bacillus subtilis	1362	36	14,12
1scuBE_B	succinyl-CoA synthase, β subunit	Escherichia coli	840	26	17,11
1setAB_A	seryl-tRNA synthetase	Thermus thermophilus	2282	60	12,15
1sftAB_A	alanine racemase	G. stearothermophilus	3151	83	10,3
1tph12_1	triosephosphate isomerase	Gallus gallus	1637	38	19,9
1xikAB_A	ribonucleoside-diphosphate reductase	Escherichia coli	2976	69	11,13
2cstAB_A	aspartate aminotransferase	Gallus gallus	3642	91	12,10
2eipAB_A	Inorganic Pyrophosphatase	Escherichia coli	666	18	21,11
2hhmAB_A	inositol monophosphatase	Homo sapiens	1693	43	21,9
2pcdMP_M	protocatechuate 3,4-dioxygenase	Pseudomonas putida	1603	40	12,10
2polAB_A	DNA polymerase III, β subunit	Escherichia coli	1271	30	25,14
3ladAB_A	lipoamide dehydrogenase	Azotobacter vinelandii	3386	93	14,13
3mdeAB_A	acyl-CoA dehydrogenase medium chain	Sus scrofa	1703	45	31,10
6gsvAB_A	glutathione S-transferase μ	Rattus rattus	1309	32	17,11
8catAB_A	catalase	Bos taurus	4718	108	10,10
Transient
1apmIE_E	cAMP dependent kinase	Mus musculus	1051	38	30,12
1efuAB_B	elongation factor EF-Ts	Escherichia coli	1815	45	20,15
1g3nAB_A	cyclin-dependent kinase 4	Homo sapiens	885	23	10,12
1g3nAC_A	cyclin-dependent kinase 4	Homo sapiens	1188	29	10,12
1gotAB_B	G protein β subunit	Bos taurus	1248	38	16,12
1k9oIE_E	trypsin	Rattus norvegicus	914	33	16,12
1k9oIE_I	serpin	Rattus norvegicus	914	17	14,12
1rrpAB_A	ran GTPase	Homo sapiens	2361	65	19,11
1ughIE_E	uracil DNA glycosylase	Homo sapiens	1096	31	35,10
1ytfAD_A	TATA binding protein	S. cerevisiae	423	11	27,10

Each chain that formed an interface was assigned a code that consists of the PDB code, the chains forming the interface, and the chain that was used as part of the MSAs (e.g., lubsAB_A is PDB code IUBS, chains A and B form the interface, and chain A was aligned with related sequences). The interface size is the average size (Angstrom²) of the two interfaces, and residue number is the number of residues that are found at the interface. The numbers of sequences that are aligned to the structural template are shown for diverse and close homologs, respectively.