Table 1 The dataset of PPI families with available alanine scanning data [10,14]. The complexes tested by experimental alanine scanning, are detailed in columns 1–3. Column 4 presents the number of PPI family members created by molecules with the same functional description by PDB [56] and SCOP [54]. In the case of multiple structures of exactly the same complexes, we have arbitrarily chosen half of the structures. Crystal structures with resolution lower than 2.5Å were ignored. Column 5 details the PDB codes and the chain identifiers of the proteins in PPIs. Column 6 provides the percentage of sequence identity between the complexes in each family, measured by structure based sequence alignment method Staccato [63])

1a4y:A

RNase inhibitor

Angio genin

4

1a4y A:B, 1z7x Z:Y, 1dfj I:E, 2bex A:C

48

1brs:A

Barnase

Barstar

6

1brs A:D, 1b2s A:D, 1b27 A:D, 1x1u A:D, 1x1w A:D, 1b2u A:D

94

1brs:D

Barstar

Barnase

6

1brs A:D, 1b2s A:D, 1b27 A:D, 1x1u A:D, 1x1w A:D, 1b2u A:D

94

1cbw:I

BPTI

Trypsin

7

1cbw I:HG, 1taw B:A, 1ca0 I:HG, 1ejm B:A, 3tgk I:E,1fak I:H, 1p2k I:A, 1f7z I:A

24

1gc1:C

CD4

gp120

6

1gc1 C:G, 1g9n C:G, 1rzk C:G, 1rzj C:G, 1g9m C:G, 1yym M:G

54

1bxi:A

Im9

E9 DNase

6

1bxi A:B, 1emv A:B, 1fr2 A:B, 1znv A:B, 1mz8 A:B, 1ujz A:B

56

1dan:L

Factor VII

Tissue Factor

6

1dan LH:TU, 1fak LH:TU, 2aer LH:T, 1wun LH:T, 1wtg LH:T, 1wqv L:T, 2a2q L:T

49

1jck:A

TCR Vb

SEC3

6

1jck A:B, 2aq1 A:B, 2aq2 A:B, 2aq3 A:B

13

1jck:B

SEC3

TCR Vb

6

1jck A:B, 2aq1 A:B, 2aq2 A:B, 2aq3 A:B

13

1vfb:C

HEL

D.1.3

6

1vfb C:AB, 1a2y C:AB, 1fdl Y:LH, 1g7h C:AB, 1g7i C:AB, 1kip C:AB

45

3hfm:Y

HEL

HYHEL

8

3hfm Y:LH, 1ua6 Y:LH, 1j1o Y:LH, 1j1p Y:LH, 1uac Y:LH, 1ic7 Y:LH, 1c08 C:AB, 1nby C:AB

57

3hhr:A

hGH

hGHbp

4

3hhr A:B, 1a22 A:B, 1axi A:B, 1hwg A:B

89