The hydrophobic effect

The hydrophobic effect is entropically driven - hydrophobic (non-polar) atoms like to pack away from the water solvent. Hydrophobic atoms exposed to solvent cause ordering of the surrounding solvent; this order is entropically unfavourable.

The practical effect of this in proteins is that hydrophobic sidechains (such as valine, leucine, isoleucine, etc.) tend to pack on the inside of a protein, while hydrophilic sidechains (such as glutamine, asparagine, serine, etc.) tend to be on the outside of a protein.

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Practical work

View this structure (lysozyme, 7lyz) using RasMol. We will now colour all the hydrophilic residues in red and the hydrophobic residues in blue.

• In the RasMol command window, type:
  select ala or cys or phe or gly or ile or leu or met or pro or val or trp
  colour blue
  select asp or glu or his or lys or asn or gln or arg or ser or thr or tyr
  colour red
  select backbone
  colour white
  select *

Rotate the structure and you should see that most of the red sidechains are on the outside of the structure with the blue sidechains on the inside.

• From the RasMol menus, choose Display->Spacefill

You can now see the surface of the protein and you will see that, while there certainly are a number of exposed blue (hydrophobic) sidechains, most of the surface sidechains are red (hydrophilic).

• From the RasMol menus, choose Options->Slab Mode
• Press and hold the Control key. At the same time, press the left mouse button and move the mouse down until the image looks normal.

You are now in slab mode - this allows you to slice the front of the molecule off.

• Press and hold the Control key. At the same time, press the left mouse button and gradually move the mouse up or down. (Note that whether you have to move up or down seems to depend on the particular i computer you are on!)

You will see the front of the molecule gradually disappearing. When you get about half way through the protein, look at the colours. You should see quite clearly that the centre of the protein is mostly blue and the red sidechains are mostly on the outside.