Table 1.

Salt bridges in putative models of Apaf-1/cytochrome c complex before and after energy minimization

Model	Models before energy minimization			Models after energy minimization
	cyt c	Dist, Å	Apaf-1	cyt c	Dist, Å	Apaf-1
Cryo-EM fitting [PDB:3J2T]	GLU 90	2.80	ARG1131	GLU 90	2.68	ARG1131
	LYS 73	2.58	ASP1023	LYS 73	2.68	ASP1023
	LYS 87	3.13	ASP1106	LYS 87	3.22	ASP1064
	ARG 91	3.91	GLU1045	ARG 91	3.76	GLU1045
PatchDock model	LYS 8	3.34	ASP1106	LYS 22	2.68	ASP 903
	LYS 22	3.07	ASP 903	LYS 79	2.66	GLU 981
	LYS 79	2.68	GLU 981
PatchDock’ model	LYS 8	2.19	ASP1147	LYS 7	2.65	ASP 902
	LYS 72	3.23	ASP1023	LYS 7	2.77	ASP 903
	LYS 79	3.07	GLU 981	LYS 8	2.65	ASP1147
				LYS 25	2.63	ASP 877
				LYS 27	3.80	GLU 925
				LYS 39	2.67	ASP 792
				LYS 72	2.64	ASP1023
				LYS 73	2.63	GLU1045
				LYS 79	2.63	GLU 981
ZDOCK model 1	GLU 21	2.02	LYS1004	LYS 79	2.57	ASP 902
	LYS 25	3.47	GLU 925
	LYS 55	3.63	ASP 658
	LYS 79	3.60	ASP 902
ZDOCK model 2	GLU 4	3.31	HIS 840	GLU 21	2.94	LYS 802
	GLU 21	3.95	LYS 802	ASP 62	3.67	LYS1003
	GLU 61	3.28	LYS1003	LYS 5	2.63	ASP 792
	ASP 62	3.17	LYS1003	LYS 8	2.64	GLU 798
	LYS 5	2.47	ASP 792	LYS 25	2.63	ASP 902
	LYS 25	3.36	GLU 659	LYS 55	2.62	GLU1045
	LYS 53	3.01	ASP1106
ClusPro model	LYS 22	3.79	GLU 981	LYS 22	2.64	GLU 981
	LYS 25	2.62	GLU 925	LYS 25	2.62	GLU 925
	HIS 33	3.48	ASP1023	HIS 33	3.48	ASP1023
	LYS 39	2.69	ASP1147	LYS 39	2.69	ASP1147
	LYS 53	2.67	ASP1147	LYS 53	2.67	ASP1147
	LYS 73	2.64	GLU 659	LYS 73	2.97	GLU 659
	LYS 79	2.60	ASP 902	LYS 79	2.60	ASP 902
	GLU 21	2.74	LYS1004	GLU 21	2.74	LYS1004

Bonds, as formed by conserved cytochrome c residues known to be involved in activation of the apoptosome, are shown in bold font