Basics of protein structure
===========================

Proteins are linear polypeptides with distinct structural details and
four different levels, termed the primary, secondary, tertiary and
quanternary structure. The key points are:

- polypeptides, amino acids
     - chemical structure of the 20 aa     
     - natural aa: L-form (note: look down H-Ca and read CORN == L, otherwise D)
     - peptide bond 
     - repeating unit: residue, same backbone, differing sidechain R
     - sequence, *primary structure*
- hydrogen bonds: donor-H...acceptor
- secondary structure
     - :math:`\alpha` -helix (n..n+4 H-bonds of main chain, ~3.6 res
       per turn)
       
       - peptide units: :math:`\phi`, :math:`\psi` angles: flexible,
         :math:`\omega` (peptide bond) fixed (cis/trans) 

       - must be right handed (otherwise clashes; only very short helices are left-handed) 
     - :math:`\beta` sheet (extended), parallel/anti-parallel
     - (coiled coil)
     - :math:`3_{10}` helix (n..n+3, 10 atoms between donor and acceptor, 3 res
       per turn)
     - :math:`\pi` helix (n..n+5)
- tertiary structure:
    - packing of helices, sheets, hairpins, loops
    - coiled-coil
- quaternary structure
    - assemblies of multiple proteins (identical copies: homomers,
      different protein molecules: heteromers)
    - proteins and co-factors (e.g., heme group)

.. Note:: For more background see the illustrations in the
   *introductory slides on protein structure* :download:`(PDF)
   </files/practical_visualization.pdf>` and [BrandenTooze]_.