Table 2. Numbers of concordantly and discordantly evolving site pairs mappable to protein structures and correlations between strength of excess (deficit) of rapid consecutive substitutions and distances between sites on protein structures.

gene	concordant (+)	nominal p-value threshold for FDR<0.3	#pairs	rho (Spearman’s) association statistics vs. 3D distances	rho p-value association statistics vs. 3D distances
	discordant (-)
ATP6
	+	0.0262	1764	-0.15	6.96E-10
	-	0.05	5213	-0.01	0.4795
CYTB
	+	0.0099	2216	-0.24	<2.2e-16
	-	0.05	12782	-0.01	0.2759
COX1
	+	0.0316	12114	-0.24	<2.2e-16
	-	0.05	11431	-0.004	0.63
COX2
	+	0.0135	875	-0.24	8.64E-13
	-	0.05	3522	-0.07	6.37E-05
COX3
	+	0.0368	3375	-0.16	<2.2e-16
	-	0.05	4637	-0.07	6.18E-06

For each protein the following statistics are shown: the numbers of significantly concordantly ('+') and discordantly ('-') evolving site pairs with known distances between sites in protein structures, those nominal p-values were below thresholds corresponding to FDR<0.3 (#pairs). For concordantly evolved site pairs the association statistics equal to partial correlations and for discordantly evolved site pairs they equal to pseudo-correlations. The Spearman's correlations (rho) between distances on the protein structures and association statistics as well as corresponding p-values (rho p-value) are shown. For concordantly evolving pairs of sites, a significantly negative value of rho means that strongly associated sites tend to be closer on the structure; for discordantly evolving pairs of sites, a significantly negative rho means that strongly associated sites tend to be apart from each other.