The amino acid alanine is choosen as a model molecule for protein structure. To study the effect of metals upon protein Na, K, Ca, Mg, Fe and Zn were respectively coordinated to alanine through the H-bonding of Carboxyl group. Both Na and K are coordinated with one alanine unit while Ca, Mg, Fe and Zn are coordinated with two alanine units. Calculations are conducted with density functional theory at B3LYP/6-31g(d,p) level of theory. The geometrical parameters are calculated including bond lengths and bond angle of COOH group. The total dipole moment, HOMO/LUMO band gap energy and C=O vibration of COOH group are also calculated. Results indicate that, the bond length LC-O is decreased while LC=O and LO-H are increased, a shift in the characteristic band of carboxyl group (C=O) toward lower wavenumbers is recorded. The total dipole moment and band gap energy are changed. It could be concluded that the studied elements are changing both the structural, Physical and vibrational characteristics of protein.