Hydrophobic-hydrophilic interactions, protein binding

Hydrophobic interactions are usually calibrated to the number of protein-ligand contacts or the size of the contact surface buried upon complex formation. By assigning a hydrophobicity character to the atoms or surface patches, more specific contact counts or surface measures can be obtained, such as hydrophobic-hydrophobic contacts as favorable and hydrophobic-hydrophilic contacts as unfavorable contributions to binding affinity. 

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