The very common secondary structures maximize the number of hydrogen bonds involving these backbone groups . The peptide bond has a dipole moment Because all the hydrogen bonds in an a -helix are oriented along the helix axis, all the peptide bond units are also aligned in the same orientation along the helix axis. The helix dipole moment plays an important role in binding charged ligands to proteins, as we shall see later. In this drawing the alpha carbons are red. In this drawing the alpha carbons are red.
Loops have irregular lengths and shapes and are on the surface of the protein.
The elements of the loop do not usually form hydrogen bonds to each other, but do form hydrogen bonds to water. Since a b -turn has several unsatisfied backbone hydrogen bond donors and acceptors, it is polar, and is usually found near the surface of the protein. A nice summary of secondary structure and the Ramchandran plot is found at this site. Note that the direction of the b -strand is indicated by the arrow point. There are a few proteins which form long filaments.