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Nearly one hundred percent of the mass of an atom (99.94%) is contained in the nucleus. The mass of the protons and the mass of the neutrons are almost the same. Electromagnetic force binds the electron cloud to the nucleus. A nearly identical force can allow atoms to bind together, forming molecules. Atoms exist as either electrically neutral, or ions.
The number of protons in a nucleus is the same for all the atoms of a particular element. It corresponds to the atomic number of that element. For example, if a nucleus contains three protons, then it is part of an atom of lithium (atomic number 3). The neutron has a similar mass to the proton but has no charge. The neutrons help keep the nucleus together.