Table 2 Hydrogen bonds predicted by ChimeraX between receptor and peptide chains and receptor and G protein chains

From: Understanding VPAC receptor family peptide binding and selectivity

Receptor - Peptide

PAC1R-PACAP27

VPAC1-PACAP27

VPAC1-VIP

Peptide

Receptor

Distance (Ã…)

Peptide

Receptor

Distance (Ã…)

Peptide

Receptor

Distance (Ã…)

D3

Y1.47

3.34

H1

Q3.37

2.65

H1

Q3.37

3.16

D3

Y1.47

3.36

S2

E7.42

3.29

S2

M7.39

3.37 (bb)

D3

R2.60

3.31 (s)

D3

Y1.47

3.36

D3

R2.60

2.87 (s)

D3

R2.60

2.55 (s)

D3

R2.60

2.94 (s)

T7

K2.67

2.46

T7

K2.67

2.50

T7

K2.67

2.51

N9

Y1.36

3.38

D8

N300ECL2

2.86

S11

D287ECL2

2.93

T11

D287ECL2

3.01

S11

Y2.72

3.18

R12

N290ECL2

2.99

L27

Y118ECD

2.35 (bb)

S11

D298ECL2

2.91

Y13

D1.29

3.20 (bb)

   

R12

D301ECL2

2.90 (s)

Y13

T1.33

2.77

   

Y22

N60ECD

3.27

K20

G123ECD

3.43 (bb)

   

Receptor – G proteins

PAC1R-PACAP27-Gs

VPAC1-PACAP27-Gs

VPAC1-VIP-Gs

Gs

Receptor

Distance (Ã…)

Gs

Receptor

Distance (Ã…)

Gs

Receptor

Distance (Ã…)

D381

K5.64

2.56

N384

L244ICL2

2.83

N384

L244ICL2

2.64

N384

L255ICL2

2.75

N384

K5.64

2.93

R385

K5.64

3.54 (bb)

N384

K5.64

2.87

R385

K5.64

3.27 (bb)

R380

S247

3.41

R385

K5.64

3.10 (bb)

R385

K5.64

3.48 (bb)

N384

K5.64

2.78

E392

G405H8

2.72

Y391

H1.50

3.20

D323

R329ICL3

3.08

L393

S6.41

3.16

E392

G393H8

2.91

E392

G393H8

2.82

   

L393

S6.41

2.73

   

Gβ

Receptor

Distance (Ã…)

Gβ

Receptor

Distance (Ã…)

Gβ

Receptor

Distance (Ã…)

H311

R413H8

2.43

n/a

  

n/a

  

D312

R413H8

3.15

      
  1. Hydrogen bonds were predicted using relaxed parameters and distances are shown in Ã…. (s) indicates a salt bridge. (bb) indicates interactions with the backbone. n/a: no hydrogen bonds present. Receptor residues are labelled according to the Wootten et al. numbering system.
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