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

From: Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly

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