The frequency distribution of clustered ionizations produced by a proton beam was measured in a nanodosimetric volume of the size of a DNA segment by means of an ion-counting nanodosimeter in the energy range from 0.4 to 3.5 MeV. In order to meet the needs of the ion-counting nanodosimeter, the accelerator's primary beam was reduced in intensity by means of Rutherford scattering. The comparison between experimental results and Monte Carlo simulations show a good agreement in the energy dependence of the mean cluster size, while the experimental cluster size distributions show a higher amount of large ionization clusters compared with those obtained with the simulations.