Secondary structure Flashcards
rule 1 - rotation
no rotation around planar peptide bond
transconfiguration
rule 2 - other chains
other parts of chain must be rhythmically flexible
phi - Ф bond
bond between amino group and alpha carbon
psi - ψ bond
bond between alpha carbon and carboxyl group
R bond defines
define phi and psi
rule 3 - stability
structure has max no. stabilising force between residue
must be independent
alpha helix - length, bonding
5.4A per complete turn (0.54nm)
3.6 amino acids per turn - 1.5A length per residue
NH of one residue H bond to C=O 4 amino acids away
alpha helix from above
clockwise
4 residues - between 3 residues - angle is 100 degrees
one space the angle is 60 degrees
disrupting folding of alpha-helix
can’t have glycine or proline
cyclic sidechains restrict rotation of angles phi - -50 degrees
no H atom on N of peptide bond - can’t H bond to another peptide bond
amphipathic helices
polar and nonpolar - helix has 2 different sides
one side is polar and other nonpolar
beta sheets
one peptide chain
parallel or antiparallel
beta turn
residue x+3 and residue x
H bond between beta strand 1 and beta strand 2
chou-Fasman - alpha helix
4/6 contiguous residues should have alpha helix values >100
chou-Fasman - beta sheet
3/5 contiguous residues should have beta sheet value >100
Ramachandran plot
shows phi and psi angle on graph to see which structure the protein is
+180 -> R groups are more extended
