Chandigarh Call Girls Service ❤️🍑 9809698092 👄🫦Independent Escort Service Cha...
Backbone of peptide chain
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’.