. 2005 Mar 18;6:41. doi: 10.1186/1471-2164-6-41

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