BIOC1600

Amino acids, proteins, and protein

structures

Part II
bcwwong@hku.hk
• Peptide bond – cis/trans configuration
• Dihedral angles: phi (φ) and psi (ψ)
• Steric hindrance and Ramachandran plot
• Common secondary structures: alpha helix
and beta strand
Formation of peptide bonds

Peptide bond
 R1 R3 R5

R2 R4 R6

Residue i i+1 i+2 i+3 i+4 i+5

Backbone: -N-Cα-C-N-C α-C-N-C α-C-N-C α-C-N-C α-C-

Side chain: R
 N-terminus R1 C-terminus

ψ1 ψ2 ω2
φ1 ω1 φ2
R2

For each residue, there are three bonds where rotation is possible:

N – Cα : φ
Cα– C : ψ Rotations about these bonds
C – N : ω (0° or 180°) determine the shape of the
(peptide bond) polypeptide chain
Peptide bond is planar: rotation about
the peptide bond is restricted

Peptide bond

The peptide bond has a partial double bond character:

• C-N bond in a peptide link is intermediate in length (1.33 Å) between a C-
N single bond (1.46 Å) and a C=N double bond (1.27 Å)
• Peptide bond is planar, not free to rotate
• All 4 atoms attached to the C-N bond are located in the same plane: two
possible configurations for the peptide bond
Two possible configurations for the
peptide bond

trans: similar substituents cis: similar substituents

on opposite side on same side

The 2 alpha carbons attached to the peptide bond are

almost always trans to each other (on opposite sides of
the peptide bond)
Most peptide bonds are in trans
configuration

Clash!
trans is preferred over cis
Steric clash between the side chains
attached to α-carbon atoms
Biochemistry, Seventh Edition. W.H. Freeman and Company
trans or cis configuration in X-Pro
peptide bonds

Peptide
bond
(ω = 180°) (ω = 0°)

Cis peptide bonds can be found in X-Pro

linkages. There are steric clashes in
both the trans and cis configurations.
 N-terminus R1 C-terminus

ψ1 ψ2 ω2
φ1 ω1 φ2
R2

For each residue, there are three bonds where rotation is possible:
The peptide bond is either in trans
N – Cα : φ (ω = 180°) or cis (ω = 0°).
Cα– C : ψ
C – N : ω (180° or 0°) Not all combinations of φ and ψ
angles are permitted due to steric
(peptide bond) hindrance.
Only limited combinations of φ/ψ values
are allowed in nature: Ramachandran plot

G.N. Ramachandran

Ramachandran plot shows φ and ψ

allowed for rotation about the main
chain α carbon based on steric
hindrance.

Allowable combinations are colored.

Most combinations of φ and ψ are
not allowed due to steric hindrance
between non-bonded atoms.
 Secondary structures
• Segment of regular conformations, with repeating
characteristic φ and ψ angles allowed by steric constraints
and stabilized by H-bonds along the peptide backbone
• Right-handed α-helix and 310-helix: stabilized by H-bonds
between the N–H and C=O groups of the main chain
• β sheets: stabilized by H-bonds between N–H and C=O groups
on adjacent strands

Proteins: Concepts in Biochemistry (Garland Science, 2016)

H-bond between amide N-H and
C=O groups
• H-bond between amide N-H and C=O groups
in backbone give rise to secondary structures
in proteins

H-bond acceptor
δ-

δ+ Hydrogen bond
H-bond donor
Secondary structure
• The core of most protein structures is
composed of secondary structures such as
α helix and β sheet.

• Formation of hydrogen bond between main

chain carbonyl oxygen and amide hydrogen
in the hydrophobic core of the protein.
Common protein secondary structures:
alpha helix and beta strand

Ribbons to represent Arrows to

alpha helices represent beta
strands (N → C)
Alpha helix Beta sheet
Different representations of protein
structure

Backbone only Cartoon view

(linking Cα only)
Lysozme (PDB - 1LYZ)
 β sheet: H-bond
between β strands

N C

The side chains along

each strand alternate
above and below the
sheet.
C N phi (φ) ≈ -135°
psi (ψ) ≈ +135°
Antiparallel β sheet
 β sheet: H-bond
between β strands

N N

The side chains along

each strand alternate
above and below the
sheet.
phi (φ) ≈ -120°
C C psi (ψ) ≈ +120°

Parallel β sheet
β strands can combine into mixed β sheets:
some parallel and some antiparallel
α-helix: intrachain H-bonds

Left Right
handed handed
helix helix
H points towards N terminus
O points towards C terminus
Right handed helix,
phi (φ) ≈ -60° side-chains point
psi (ψ) ≈ -50° outward from the
helix axis
 α-helix: intrachain H-bonds
• In an α-helix: CO group of residue i
forms a hydrogen bond with the
NH group of residue i+4
• 3.6 residue per turn; right-handed
3.6 residues
5.4Å • 13 atoms in the closed loop formed
by one hydrogen bond (α-helix also
called 3.613-helix)
R1 R3 R5

R2 R4 R6

Residue i i+1 i+2 i+3 i+4 i+5

• Side chain
protrude outward Helix on
from the helix surface of
• No hole in the protein
centre of the
helix

Helix
completely
buried

Helix
completely
exposed to
solvent
hydrophilic
hydrophobic
Only limited combinations of φ/ψ values
are allowed in nature: Ramachandran plot

G.N. Ramachandran

Ramachandran plot shows φ and ψ

allowed for rotation about the main
chain α carbon based on steric
hindrance.

Allowable combinations are colored.

Most combinations of φ and ψ are
not allowed due to steric hindrance
between non-bonded atoms.
Torsion (dihedral) angle

4 atoms A, B, C, D to define torsion

angle about the B-C bond
• Atoms A, B, C form one plane
• Atoms B, C, D form one plane
• Torsion (dihedral) angle is the
angle between these two planes
 Torsion (dihedral) angle

If a system of four atoms A — B — C— D is projected onto a plane normal to B

— C, the angle between the projection of A — B and the projection of C — D is
described as the torsion angle about bond B — C; this angle can also be
described as the angle between the plane containing atoms A, B and C, and
the plane containing atoms B, C and D.
 +θ +θ

-θ -θ

The angle is positive if the front bond is rotated in a clockwise

direction in order to eclipse the bond to the back; negative if
the front bond is rotated in a counter-clockwise direction.
Torsion angles are usually expressed as having values between
–180° and +180°
 N-terminus R1 C-terminus

ψ1 ψ2 ω2
φ1 ω1 φ2
R2

For each residue, there are three bonds where rotation is possible:
N – Cα : φ
Cα– C : ψ
C – N : ω (0° or 180°)
Cα C N
(peptide bond)
 Most peptide bonds are in trans
configuration

Cα (ω = 180°) (ω = 0°)

N
CN

Cα
Clash!
trans is preferred over cis
Steric clash between the side chains
Torsion angle ω defined by Cα―C―N―Cα
attached to α-carbon atoms
Biochemistry, Seventh Edition. W.H. Freeman and Company
N-terminus R1 C-terminus

ψ1 ψ2
φ1 φ2
R2

Since the peptide bonds (C―N) cannot rotate, the conformation

of the main chain of the polypeptide can be described by
rotations about the N―Cα and Cα―C bonds:
N―Cα : φ
Cα―C : ψ
R1

φ ψ

R2

C
N Cα

R
R1

φ ψ

R2

C
Cα
N
R
Which combination of φ (phi), Ψ(psi) angles
is shown in the following amino acid residue?

A.φ = 120°, Ψ = 120°

Cα B.φ = 180°, Ψ = 0°
C φ ψ N C.φ = 180°, Ψ = 180°
N C D.φ = 0°, Ψ = 180°
E. φ = -60°, Ψ = -40°
Only limited combination of φ/ψ values
are allowed in nature: Ramachandran plot

G.N. Ramachandran

Ramachandran plot shows φ

and ψ allowed for rotation
about the main chain α carbon
based on steric hindrance.
http://proteopedia.org/wiki/index.php/Tutorial:Ramachandran_principle_a
nd_phi_psi_angles
 Only limited combination of φ/ψ values
are allowed in nature: Ramachandran plot

φ = 0°, ψ = 180°
Steric clash between carbonyl oxygen;
not favourable
 Only limited combination of φ/ψ values
are allowed in nature: Ramachandran plot

φ = 0°, ψ = 0° (not favourable due to

steric clash between carbonyl oxygen
and amide hydrogen)
 Only limited combination of φ/ψ values
are allowed in nature: Ramachandran plot

φ = 180°, ψ = 0°
(not favourable due to steric
clash between amide hydrogen)
 Questions
• Why φ = +120° is
unfavourable?

• Why ψ = -120° is
unfavourable?
 Readings
• Berg JM et al (2012) Biochemistry 7th ed. WH
Freeman. Chapter 2
• Nelson DL, and Cox MM (2008) Lehninger
Principles of Biochemistry, 5th ed. WH
Freeman. Chapter 4
END