could hydrogen an atoms be arranged differently?
Definitely, it is possible to arrange hydrogen differently.\n\nThe first way hydrogen can be arranged is in the type of isotopes.  There are three different kinds of hydrogen:\nProtium (1 proton, 0 neutron, 1 electron)\nDeuterium (1 proton, 1 neutron, 1 electron)\nTritium (1 proton, 2 neutrons, 1 electron)\n\nAdditionally, how hydrogen is arranged at current atmospheric pressures and temperatures is as a diatomic gas that shares between them two electrons.  At lower temperatures and higher pressures, hydrogen can become a liquid, and a solid.\n\nAt extremely high pressures (like GPa and above), the properties of hydrogen change so drastically that it becomes a metallic solid.
Are you looking at any protein in particular?  Look up in situ hybrdization for proteins ( at least it will give you an idea where it is localised).  I think that it would really depend on the system ad proteins that you want to study, so I am not sure how much else I can tell you, sorry.