Alpha helices are often embedded in a protein so that one side faces the surface and the other
side faces the interior. Such helices are often termed amphipathic because the surface side is
hydrophilic and the interior side is hydrophobic. A simple way to decide whether a sequence
of aminoacids might form an amphipathic helix is to arrange the aminoacids around what is
known as “helix-wheel projection”, which is a 2d projection of the aminoacid positions (see
Fig. 1). If the hydrophobic and hydrophilic aminoacids are segregated on opposite sides of
the wheel, the helix is amphipathic. Using the helix-wheel projection, decide which of the
three peptides here might form an amphipathic helix
1. S L I K S V I E M V D E W F R T F L
2. F L I R V L R K V F R V L T R I L S
3. R L F R S R V L K I A V I R F L L I
(underlined aminoacids are hydrophobic one, they can be memorized by the mnemonic
“FAMILY VW”).
1.2 Amphipatic beta sheets
Like alpha helices, beta sheets often have a one side facing the surface of the protein and one
side facing the interior, giving rise to an amphipathic sheet with one hydrophobic surface
and one hydrophilic surface. From the sequences listed below pick the one that could form
a strand in an amphipathic beta sheet.
1. A L S C D V E T Y W L I
2. D K L V T S I A R E F M
3. D S E T K N A V F L I L
4. T L N I S F Q M E L D V
5. V L E F M D I A S V L D
1.3 Buried Aminoacids
Small proteins may have only one or two amino acid side chains that are totally inaccessible
to solvent. Even in large proteins, only about 15% of the amino acids are fully buried. A list
Figure 1: You can use this figure to decide which of the three sequences might form an
amphipatic helix (problem 1.1).