torsion angle coordinates for beta strands & alpha helices in a Ramachandran plot
(-phi,+psi) for beta strands
(-phi,-psi) for alpha helices
Beta strands are in the +y region, alpha helices are in the -y region. They both only occur on the -x axis side. See slide #13
Why are certain torsion angle combinations not allowed from the Ramachandran plot?
The protein structures would be unstable due to large possibility of steric clashes between atoms.
How many intrahelical H bonds are present with 18 residues?
(# of H bonds) = (# of residues) - 4
See slide #4
How many residues are there per helical turn?
: 18 residues x (1 turn/3.6 residues) = 5 turns
: 7 turns x (3.6 residues/1 turn) = 25 residues when rounded to the nearest whole #
amino acids whose side chains can participate in favorable electrostatic interactions
DEKR (all charged molecules)
(also participate in H bonding)
functional significance of a disulfide bond
strengthens the shape of a protein or peptide
1 disulfide bond = 2 Cysteines
Which secondary protein structure never occurs alone (self-stabilizes) & why?
Beta strands. There would be steric constraints between the H bonds within 1 strand. Interstrand H bonding occurs between 2 strands to help them stabilize.
See slide #10
Which secondary protein structures are self-stabilizing?
Alpha helixes & beta turns. In alpha helixes, intrahelical H bonding occurs between the carbonyl O & amide N
See slide #3 & 11A
How many residues are in one helical layer?
18 (See slide #6)
An alpha helix has 35 intrahelical H bonds. How many layers will it occupy? (3 sig figs)
35 H bonds + 4 = 39 residues.
39 residues x (1 layer/18 residues) = 2.17 layers
An alpha helix has 8 turns. How many helical layers will it occupy? (3 sig figs)
8 turns x (3.6 residues/1 turn) = 28.8 residues
28.8 residues x (1 layer/18 residues) = 1.60 layers
A coiled coil has 42 residues. How many total a & d positions will there be?
42/7 = 6 perfect heptad repeats. Each heptad has 2 a & d residues making a total of 12 a & d positions.
See slide #9
A coiled coil has 8 a & d positions. How many total residues would there be? Assume it has perfect heptad repeats.
A heptad has 2 a & d positions so there would be 4 heptad repeats. Each heptad has 7 residues so 4 x 7 = 28 residues
Phi is defined by __ & controls __ distance.
N-C(alpha); carbonyl C
Psi is defined by __ & controls __ distance
C(alpha)-C; amide N
Omega is defined by __ & controls __ distance
C-N (no rotation due to partial double bond); alpha C