Amphipathic alpha helices
This model corresponds to a 19 amino acid residue stretch with alpha helix secondary structure.
(Specifically, it is helix E of the beta subunit of human haemoglobin.)
Let's study the polarity of its sidechains; to highlight them, we have coloured the backbone. At the current orientation of this helix, in front you can observe a large number of oxygen and nitrogen atoms. This is, hence, a face of the helix with high polarity.
If we turn the model around to see the face that was behind we can now notice how there are much fewer electronegative atoms on this face, and more carbon atoms: this is a quite nonpolar face.
Due to this dual polar-nonpolar nature (or hydrophilic-hydrophobic), the helix is said to be amphipathic.
We can see it a bit better if we colour the whole residues according to the usual scheme: hydrophilic and hydrophobic (try again the former buttons).
This amphipathy matches well the tertiary structure of the protein, since
- the hydrophobic face is oriented inwards in the protein, where there are no water molecules and it can interact with hydrophobic amino acids from other helices,
- the hydrophilic face is oriented outwards, in contact with water.
We can see this if we display the few water molecules included in the model (only oxygens are shown). (Try again the former buttons.)
Which of the two faces in the helix has more water molecules associated to it?