The proteins composed of short polypeptides (about 70 amino acid residues) participating in large complexes (ribosome) and proteins interacting with DNA/RNA were taken for analysis and classified according to the hydrophobicity excess/deficiency distribution as a measure of structural and functional specificity and similarity. The characterization of this group of proteins is the introductory part to the analysis of the so called "Never Born Proteins" (NBP) in search for protein compounds exhibiting biological activity that may be valuable in pharmacological research. The entropy scale (classification between random and deterministic limits) organized in ranking list allows the comparative analysis of the proteins under consideration. The comparison of the hydrophobicity deficiency appeared to be useful for similarity recognition, the examples of which are shown in the paper. The specificity of proteins participating in large protein-nucleic acid complexes generation is presented.