Hydrophobicity is one of the component considerations that goes into making up your score on a fold.
IntroAmino acids are either hydrophobic, or hydrophilic. The sidechains of an amino acid will be orange or blue depending on whether they are hydrophobic or hydrophilic.
- hydro means "water"
- phobic means "that fears"
- philic means "that loves"
So, hydrophobic fears water, while hydrophilic loves water.
- Ok that's great for them, but how can that help me?
The proteins in all cells are immersed in water. So:
- all the "water fearing" amino-acids will tend to be inside the protein (where they can't touch the surrounding water)
- all the "water loving" amino acids will tend to be outside the protein (where they can be in contact with the water)
When folding, you should then try to get as much hydrophobic inside, and as much hydrophilic outside. Exceptions, however, will almost always exist. While hydrophobic hiding is a good strategy to follow, it is almost never possible to put every single hydrophobic amino acid on the inside of a fold. Often, in fact, the biological function of the protein requires some hydrophobic amino acids on the outside.
Proteins are not all in water. A lot of them are actually implanted in the cell membrane. The cell membrane is made of lipids, that has the opposite effect of water:
- the "water loving" amino acids will fear lipids
- the "water fearing" amino acids will love lipids
Some parts of the proteins can actually be inside the membrane, and some other parts outside, for real.
- hydrophobicity in Wikipedia