Tertiary and Quaternary Structure
Part I. C. Hydrophobic Interactions
C. Hydrophobic Interactions in Tertiary Structure
Hydrophobic interactions involve the side chains of Non-Polar amino acids:
Hydrocarbon -- Ala Val Leu Ile Pro Met
Aromatics ----- Phe Trp (Tyr)
Hydrophobic interactions are due to clustering of Non-polar amino acid side chains and are not directed bonds like hydrogen or ionic bonds. These clusters are found in the interior of proteins. The reasons I do not call these hydrophobic bonds is because hydrophobic interactions do not usually involve direct interactions between 2 amino acid side chains and are formed by groups of hydrophobic amino acid side chains in cluster formation.
Figure 5. Hydrophobic Cluster in a protein.
These hydrophobic clusters exclude water and are very tightly packed together.
Aromatic AA side chains can form a special hydrophobic interaction called a Pi-stack:
Figure 6. Pi-Stack Hydrophobic Interaction.
©Wilbur H. Campbell, 1995; wcampbel@mtu.edu