Accurate quantification of the hydrophobic/hydrophilic properties of protein surfaces requires detailed knowledge of the
hydrophobicity of amino acids at the atomic level. As discussed previously in various published papers, molecular
modeling can be used with effect to acquire such knowledge. In this study, molecular dynamics methods have been
employed to examine the role of the distance between an amino acid atom and its nearest water molecule in relation to its
intrinsic atom hydrophobicity. This distance is the radius of the water-excluding-region around the atom; therefore, it can
provide information on the solvent accessibility and steric hindrance that may influence the atom hydrophobicity.
Molecular models of tripeptide in the form of GXG, and pentapeptides in the form of AcWLXLL-NH2 and AcGGXGGNH2
for 20 natural amino acids in the X position were constructed and allowed to dynamically interact with surrounding
water for a sufficient period of time. The distance value for each atom in all natural amino acids were calculated and
analyzed against the atom/amino acid's other parameters such as radial distribution function, solvent-accessible surface
area, and hydrogen bonding. It was observed that, when the dynamic factor is taken into account, peptide molecular
conformation is modified noticeably with residue type. For protein surface identification purposes, preliminary results
are consistent with those reported in the literature on the need to include the amino acid structural properties as well as
the effects of its neighboring residues. Further investigation is envisaged in order to verify these observations.