The possibility to describe accurately the internal dynamics of proteins in terms of movements of few approximately rigid subparts is an appealing biophysical problem with important implications for the analysis and interpretation of data from experiments or numerical simulations. The problem is tackled here by means of a novel variational clustering scheme which exploits information about equilibrium fluctuations of inter-residues distances, provided e.g. by atomistic molecular dynamics simulations or coarse-grained models. No contiguity in primary sequence nor in space is enforced a priori for amino acids grouped in the same rigid unit. The identification of the rigid protein moduli, or dynamical domains, provides valuable insight into functionally-oriented aspects of protein internal dynamics. To illustrate this point we first discuss the decomposition of adenylate kinase and HIV-1 protease and then extend the investigation to several representatives of the hydrolase enzymatic class. The known catalytic site of these enzymes is found to be preferentially located close to the boundary separating the two primary dynamical subdomains.