The only bonds in the secondary structure of a protein are regular repeated hydrogen bonds from the peptide bonds of the amide groups and carbonyl groups. You can also classify protein families by their secondary structures.
Helices
This is the most common secondary structure of proteins.
The carbonyl oxygen atom act as a hydrogen bond acceptor and the hydrogen attached to the nitrogen atom of the amide group act as the hydrogen bond donor.
The carbonyl oxygen atom (n) bonds to the hydrogen of the amide group four residues along (n+4) by hydrogen bonding.
Can be formed when the R-groups in the primary structure is not 'bulky'.
If proline is present, the hydrogen bond formation would stop because the amine group is bonded to the R-group in proline. This is why proline is known as the 'helix breaker'.
The first amine group and the last carbonyl group of the helix are not involved in the hydrogen bonding of the secondary structure.
The helix forms a cylinder shape, with the hydrogen bonds forming the walls of the cylinder and the R-groups pointing outwards.
The properties of the R-groups that make up the primary structure dictates the interactions the helix has with other parts of the protein chain and with other molecules. It also means that the helix can be amphipathic (e.g. one side of the helix is hydrophobic and the other side is hydrophilic).
They can be right-handed (going clockwise) or left-handed (anti-clockwise) but left-handed helices are very rare.
The helices can be any length because they have no limit.
Other variations of the alpha helix exist but are also very rare.
