Table 3

Comparison of interface residues of avidin, putative BBPs and AVR-proteins. Residues at subunit interfaces in avidin are determined according to Livnah et al. [17]. Equivalent residues in the other proteins are shown based on their alignment.

Secondary structure and type of interaction of amino acid residues of avidin in different subunit interfaces

Residue in avidin

Differences found in other proteins

Secondary

M-chain

S-chain

BBP-A

BBP-B

AVRs^a

1–4 interface

β4

H-bonds

H50

K^b

R^c

L

β4

H-bond

Q53

-

-

-

β4

H-bonds

N54

Q^d

Q^d

H

B4

H-bond

H-bond

T55

P^b

Q^b

gap

L4

H-bond

N57

T^d

S^d

K

L4

H-bonds

R59

G^b

V^b

A

β5

H-bond

G65

-

A^d

-

β5

H-bond

H-bond

T67

-

-

-

β5

H-bonds

N69

Q^e

W^f

L/H

L5

H-bonds

W70

-

-

-

L5

H-bond

K71

Q^d

D^b

N

L5

H-bonds

S73

A^d

-

-

β6

H-phobic

V78

-

A^d

-

β6

H-bond

T80

V^f

A^f

V

β6

H-bonds

Q82

-

-

-

β7

H-bond

M96

A^b

T^b

K

β7

H-phobic

L98

-

M^d

-

β7

H-bond

R100

-

-

-

β7

H-bond

S101

E^g

E^g

L

L7

H-bond

V103

-

-

-

β8

H-bonds

T113

-

-

-

1–2 interface

L7

H-phobic

W110

-

-

-

B8

H-bond

T113

-

-

-

B8

H-bond

V115

-

-

-

1–3 interface

B7

H-bond

H-phobic

M96

A

T^b

K

B8

H-phobic

V115

-

-

-

B8

H-phobic

I117

T

R^h

N/Y

^aDifferences found in all AVR-proteins 1–7 in previous studies [27, 31] and current study (AVR-A, B, C)

^bNo interaction according to the model

^cSalt bridge to D26 in subunit 4 according to the model

^dInteraction similar to avidin according to the model

^eInteraction similar to avidin without linking water molecule according to the model

^fHydrophobic interaction according to the model

^gSide-chain hydrogen bond according to the model

^hSalt bridge to E13 in subunit 3 according to the model

Niskanen et al. BMC Genomics 2005 6:41   doi:10.1186/1471-2164-6-41