A novel approach was proposed to evaluate the steadiness of polar clusters containing the RNA-binding sites on the protein surface. The degree of clustering of RNA-binding polar residues was used as a measure of the steadiness of the corresponding polar clusters. Escherichia coli ribosomal protein L25 utilizes two binding sites, S1 and S2, to complexate with a 5S rRNA fragment. The cluster distribution of RNA-contacting polar residues on the protein surface was studied using the structural data on the complex (in crystal and in solution) and the free state (in solution). The degree of polar residue clustering in S1 and S2 in crystal was estimated at 71.4 and 100%, respectively. For the free state in solution, the degree of clustering of the two sites was 22.8 and 68.6%, respectively. Thus, the steadiness was quantitatively estimated for the RNA-binding sites of two different types, one preexisting in the protein and the other induced by the RNA structure upon complexation. The difference between the protein structures in crystal and in solution was found to be functionally significant. The results can be extrapolated to numerous complexes of proteins with double-stranded RNA and DNA.