I have information Km and Vmax dependence on pH: 

pH	6.0	6.3	6.5	7.0	7.5	8.0
KM (mM)	0.120	0.163	0.216	0.250	0.210	0.160
Vmax	0.430	0.480	0.526	0.530	0.450	0.313

and I have to determine which amino acids are in the active site. Which is a better way to find pKa and determine the amino acids? To look at logKm dependence on pH, or at logVmax dependence on pH? Thank you.

Have you thought about looking at V_max/K_M?  It turns out that each parameter that you examine tells a slightly different story.  

20 hours ago, BabcockHall said:

Have you thought about looking at V_max/K_M?  It turns out that each parameter that you examine tells a slightly different story.  

I created pH dependence on log(Vmax/Km) graph, but I'm not sure how I can get pKa values from it, because it's form is strange.

 Then I created pH dependence on log(Vmax) graph:

and painted lines to find pKa values. Am I doing it right?

Your estimates do not look bad, but it might be possible to improve them.  Ideally one would use nonlinear regression.

Provided certain assumptions are correct, pK_a values in the V_max graph pertain to the E•S complex, whereas pK_a values in the V/K graph pertain to free E or to free S.  CRC Critical Reviews in Biochemistry (Knowles JR 1976, p. 165) has a good intermediate-level discussion of this topic.  In your case the graph of V/K vs. pH has an unusual shape, which I find a bit puzzling.   It may be that the data do not span as a large range of velocities as one might like.