How do protons react with the main atom?
Positively charged protons are what comprise the nucleus of an atom, along with the electrically neutral neutrons. Generally, protons are stable forms of matter, and their stability is what allows an atom of a particular element to exist. However, if you involve the protons or neutrons in some kind of transformation, you have initiated a nuclear reaction, and this change in the nucleus will change the atom to some other element. Protons and neutrons can interchange through the process of Beta Decay. A proton can turn into a neutron; a given atom will then transform into an element to the left of the initial element on the Periodic Table; a neutron can turn into a proton, in which case a given atom will transform into an element to the right of the initial element. See link for more info:
I would encourage you to restate the question or look it up again because it does not seem to make sense as written. Here's why:
Typically, protons do not react with an atom (and it's not clear what you mean by "the main atom").
Instead, protons are simply one of the components of the nucleus of every atom. An atom's nucleus is made up of protons and neutrons and it is these particles that give the atom its mass.
Atoms do indeed react with other atoms, but it is not protons that determine whether two atoms will interact. Instead, it is the number of electrons that the atoms have that determines if they can interact.