What part of the atom determines physical properties?

Physical properties are the properties which can be observed without any change in chemical composition of a substance. For example, color, odor, mass, density etc are all physical properties.

An atom contains protons, neutrons and electrons. The nucleus of atom contains protons and neutrons. The mass of an electron is negligible as compared to protons.

Therefore, mass of an atom is due to the number of protons.

Hence, we can conclude that protons of the atom determines physical properties.