Backbone of peptide chain Subscribe to my youtube channel for such great contents www.youtube.com/c/AwesomeBiochemistry

1. Dr. Kalpeshkumar C Nakarani
Tutor cum Second year Resident
Backbone linkages of
Peptide chain

2. General
 The –COOH group of one amino acid can be joined to the –NH2 group of
another amino acid by a covalent bond called as peptide bond.
 Thus it is the peptide linkage which holds various amino acids together in
a specific sequence and number.

3. Dimensions of fully extended
polypeptide chain
Bond distance
N-H bond  0.100 nm
C=O bond  0.123 nm
C-N bond  0.132 nm
N-Cα bond  0.147 nm
Cα-C bond  0.153 nm
Cα-Cα distance  0.360
nm

4. Peptide bond
 Peptide bond is planar • Thus for a pair of amino acid
linked by a peptide bond, six
atoms lie in the same plane.
• Ca, C, O, N, H, Ca

5. Peptide bond is partial Double bond
 Peptide bond resonates between a single bond and double
bond
 Partial double bond
Proof of Partial double bond
• In peptide bond C-N distance
is 0.132 nm
• But
• C-N = 149 nm
• C=N = 127 nm

6. Considering peptide as a ‘partial double
bond’ – 2 configurations are possible
‘Trans’ Configuration ‘Cis’ Configuration

7. Considering peptide as a ‘partial double
bond’ – 2 configurations are possible
‘Trans’ Configuration ‘Cis’ Configuration
 Allmost all peptide bonds
(99.6%) are in ‘trans’
configuration because
stearic clashes between
groups attached to the Ca
atoms do not arise in trans
configuration as groups are
far apart
 Stearic clashes arise in ‘cis’
configuration as groups will
be near.
 Rarely occurs (0.4 %)
 Mostly occurs in X-Pro
linkages

8. Considering peptide as a ‘partial double
bond’ – 2 configurations are possible
‘Cis’ Configuration
 Stearic clashes arise in ‘cis’ configuration as
groups will be near.
 Rarely occurs (0.4 %)
 Mostly occurs in X-Pro linkages
 Because the N of Proline is bonded to 2
tetrahedral carbon atoms limiting the stearic
differences between the ‘trans’ and ‘cis’
forms
 E.g. Ribonuclease A
 It contains 4 proline, 2 are in ‘trans, and
rest 2 are in ‘trans/cis’

9. Torsion angles (Dihedral angles)
(Between -180 to +180)
N-Ca bond (Φ)
 The angle of rotation is known as phi
(Φ)
 Phi (Φ) Rotation
Ca-C bond (Ψ)
 The angle of rotation is known as psi
(Ψ)
 Psi (Ψ) Rotation
• View from previous to next
• Keep previous bond at “12
o’clock” position
• Measure its angle with next
bond
• If Clockwise  +ve value
• If anti clockwise  -ve
value

10. Possible Φ and Ψ angles
 GM Ramchandran recognized that many combinations are forbidden because of stearic
collisions between atoms
 Explanation Video
 Allowed Φ and Ψ values can be seen on a plot known as ‘Ramchandran plot’.

13. Thank You