We study the charge and mass distributions within a nucleon and compute the associated squared radii based on a potential model approach. Different constituent quark configurations such as \(\Delta\), \(Y\), and quark-diquark are considered and compared, with model parameters calibrated by experimental measurements of the proton and neutron charge radius. The results suggest that while the charge radius is dictated by quark dynamics, the mass radius is strongly influenced by nonperturbative QCD contributions to a nucleon's mass that are not sensitive to the constituent quarks. As a result, the mass radius could become substantially different from the charge radius. The obtained nucleon mass distributions of different configurations are further used for simulations of the initial conditions in heavy ion collisions. The computed eccentricities \(\varepsilon_2\) and \(\varepsilon_3\) are found to demonstrate a considerable sensitivity to the input nucleon profiles, especially to the mass radius in the peripheral region as well as for systems with fewer participants.