These questions are mostly the same as the previous block. If you divide the
percentage SEA < 10 by the percentage SEA > 30 and take the logarithm,
you get something close to the scales 1 and 4 from the previous question.
And the algoritm is pictured in the Accessibility page of the SFB course
at swift.cmbi.umcn.nl/teach/B2/ (and that is NOT exam-material for the present
course).
Obviously, Arg, Lys, Glu, Gln, etc are most often at the surface, and Trp,
Phe, Ile, etc., are most ofte buried. If that is still a problem at this moment,
then you better talk with one of the teaching assistants soon...
The reason that Methionine is so often at the surface, is that it comes from AUG
and that is also the start codon. The start codon codes for the first amino
acid of the chain, and that one most often carries the very positive N-terminal
NH3 group. That group is very polar and thus better be at the surface, and
that is why the rest of Methionine often is (also) at the surface.
Proline is often seen in turns, and at the start of helices. And turns and
beginnings and ends of helices tend to be at the surface. So, proline, in a
forced mariage with its preference for turns and hlix starts, is seen more
often at surface than you would expect from its biophysical hydrophobicity
that is determined by the three CH2 groups in its side chain.