DATA SET OF COMPLEXES USED

The dataset was non-redundant, and generated as in Chapter 2 (2.1.3). Five

additional complexes were found, giving a data set of 64 protein-protein

Table 4.1 Data set of 64 proteins of the non-redundant data set (column 1 gives PDB code and SCOP numbering)

1 2 1 2 1 2

I p p c : p ro te ase/ I d a n : C o ag u latio n facto r/ I r i b : tra n sth y retin / 2 . 4 4 . 1 . 2 . 1 in h ib ito r 2 . 1 . 2 . 1 . 1 sol. tissu e facto r 2 . 3 . 3 . 1 . 1 retin o l b in d in g p ro tein

7 . 3 . 2 . 1 . 2 2 . 4 4 . 1 . 2 . 1 2 . 5 6 . 1 . 1 . 4

I s b w : p ro te ase/ I h w h : h o rm o n e/ l a v z : ty ro sin e k in a se / 2 . 4 4 . 1 . 2 . 1 in h ib ito r 2 . 1 . 2 . 1 . 1 recep to r 2 . 3 2 . 2 . 1 . 2 n eg a tiv e facto r

7 . 3 . 1 3 . 1 . 1 1 . 2 7 . 1 . 1 . 6 4 . 8 5 . 1 . 1 . 1

I c g i : p ro te ase/ 2 t e c : th erm itase/ I d n l : sy n tax in /

2 . 4 4 . 1 . 2 . 7 in h ib ito r 3 . 3 5 . 1 . 1 . 4 in h ib ito r com plex 1 . 7. 2. 1. 1 b in d in g p ro tein

7 . 1 5 . 1 . 1 . 4 4 . 3 4 . 1 . 1 . 1 (ex o cy to sis)

I m t n : p ro te ase/ 2 s i c : su b tilisin / I s m p : m e tallo p ro tea se / 2 . 4 4 . 1 . 2 . 7 in h ib ito r 3 . 3 5 . 1 . 1 . 7 in h ib ito r 2 . 5 7 . 2 . 1 . 1 in h ib ito r

7 . 8 . 1 . 1 . 1 4 . 6 9 . 1 . 1 . 2 4 . 7 6 . 1 . 4 . 2

l a v g : p ro te ase/ I s p b : su b tilisin p ro seg m e n t/ l u d i : h y d ro lase/ 2 . 4 4 . 1 . 2 . 1 2 in h ib ito r 3 . 3 5 . 1 . 1 . 7 su b tilisin 3 . 1 4 . 1 . 1 . 2 in h ib ito r

2 . 5 6 . 1 . 3 . 1 4 . 4 8 . 3 . 2 . 1 4 . 1 5 . 4 . 1 . 2

l a c b : p ro te ase/ I b i S : k in a se / l e a y : C h eA /C h eY

2 . 4 4 . 1 . 2 . 7 in h ib ito r 1 . 1 1 0 . 2 . 1 . 5 an tio n eo g en e 3 . 1 6 . 2 . 1 . 1 sig n al tran d u ctio n 4 . 3 4 . 1 . 1 . 1 4 . 1 2 3 . 1 . 1 . 2 4 . 4 8 . 2 1 . 1 . 1

l a v w : p ro te ase/ I n l l : N F -k a p p a-B / I d h k : am y lase/

2 . 4 4 . 1 . 2 . 2 in h ib ito r 1 . 1 1 0 . 2 . 1 . 7 A nk repeat 3 . 1 . 7 . 1 . 8 in h ib ito r

2 . 4 0 . 4 . 1 . 4 2 . 2 . 5 . 1 . 6 2 . 2 8 . 1 . 1 . 1 6

l a z z : p ro te ase/ I q n i z : k in a se / l a v a : am y lase/

2 . 4 4 . 1 . 2 . 9 in h ib ito r 4 . 1 2 3 . 1 . 1 . 1 cyclin 3 . 1 . 7 . 1 . 1 6 in h ib ito r

2 . 1 5 . 1 . 1 . 1 1 . 72 . 1 . 1 . 1 2 . 4 0 . 4 . 1 . 5

I w q l : R A S/ l b 6 c : iso m erase/ k in ase I n o c : o x id o re d u ctase/ 3 . 3 1 . 1 . 7 . 1 G T P ac tiv atin g 4 . 1 2 3 . 1 . 1 . 1 3 . 6 4 . 1 . 1 . 1 tran sferase 1 . 1 0 8 . 1 . 2 . 1 4 . 2 4 . 1 . 1 . 1 4 . 1 5 2 . 1 . 1 . 1

l a g r : n u cletid e b in d in g / l a i n ; d eo x y rib o n u clea s/ I f s s : .serine esterase/ 3 . 3 1 . 1 . 7 . 1 3 reg u lato r 3 . 5 0 . 1 . 1 . 4 actin 3 . 6 4 . 1 . 1 . 1 toxin

1 . 8 7 . 1 . 1 . 1 4 . 1 3 0 . 1 . 1 . 4 7 . 7 . 1 . 1 . 3

I g u a : R A P / I d k g : n u cleo tid e ex ch an g e l a y ? : rib o n u c lease/ 3 . 3 1 . 1 . 7 . 3 G R A F 3 . 5 0 . 1 . 1 . 3 factor/ 3 . 8 . 1 . 1 . 1 b arsta r 4 . 1 3 . 3 . 1 . 1 2 . 6 8 . 1 . 1 . 1 ch ap ero n e 4 . 1 . 1 . 1 . 1

I a 2 k : n u clear tra n sp o rt I g l a : k in a se / I d f j : rib o n u e lease/ 3 . 3 1 . 1 . 7 . 6 facto r/ 3 . 5 0 . 1 . 3 . 1 g lu c o se sp ecific facto r 3 . 9 . 1 . 1 . 1 in h ib ito r 4 . 1 5 . 3 . 2 . 1 R A S 2 . 7 9 . 3 . 2 . 1 4 . 5 . 1 . 1 . 1

l n 2 c : n itro g en ase protein I h l u ; ac tin / I t c o : S er-T h r

3 . 3 1 . 1 . 9 . 3 com plex 3 . 5 0 . 1 . 1 . 4 profilin 4 . 1 3 8 . 1 . 3 . 3 P h o sp h a tase/ 3 . 8 1 . 1 . 1 . 2 4 . 9 1 . 1 . 1 . 1 (acéty latio n ) 4 . 2 4 . 1 . 1 . 2 Isom erase

I z b d : G T P b in d in g /effec to r l u e a : m etalloprolea.se/ I x d t : to x in / 3 . 3 1 . 1 . 7 . 5 2 . 3 8 . 3 . 1 . 1 in h ib ito r 4 . 1 4 4 . 1 . 1 . 3 g row th factor

7 . 4 8 . 1 . 1 . 2 4 . 7 6 . 1 . 9 . 4 7 . 3 . 1 1 . 1 . 1 4

l a i p : elo n g atio n facto r l a O r : tra n sd u c in / I s t f : p ro te in ase/ 3 . 3 1 . 1 . 7 . 1 5 co m p lex 2 . 6 4 . 3 . 1 . 1 p h o sd u cin 4 . 1 5 . 1 . 2 . 3 in h ib ito r

4 . 3 7 . 1 . 1 . 2 3 . 4 2 . 1 . 6 . 1 4 . 3 . 1 . 1 . 2

l f 6 0 : elo n g atio n facto r l b h 8 : tra n sc rip tio n I b n d : g ro w th facto r co m p lex 3 . 3 1 . 1 . 7 . 1 7 com plex 1 . 2 3 . 1 . 3 . 3 regulation hetero 7 . 1 7 . 1 . 3 . 1

1 4 . 4 8 . 1 2 . 1 . 1 1 . 2 3 . 1 . 3 . 4 com plex

I c x z : R h o A /R h o e ffec to r 2 p c c : O x id o red u ctase l f 3 v : T N F l/ 3 . 3 1 . 7 . 1 . 1 6 1 . 3 . 1 . 1 . 9 /e lectro n transpor t 2 . 7 . 1 . 1 . 1 rece p to r asso cia ted

2 . 4 0 . 4 . 1 . 5 1 . 8 9 . 1 . 1 . 3 ? protein

I b k d : o n co g e n e p ro te in / l a 2 x : tro p o n in C / l a l O P ro tease/ 3 . 3 1 . 1 . 7 . 1 e x c h an g e facto r 1 . 4 1 . 1 . 5 . 3 tro p o n in 1 4 . 3 4 . 1 . 1 . 2 in h ib ito r

1 . 1 0 9 . 1 . 1 . 1 3 . 3 5 . 1 . 1 . 3

l a k 4 C y clo p h ilin A/ l e b d D eh y d ro g en ase/ I t n r T N F / 2 . 5 8 . 1 . 1 . 1 C ap sid pro tein 3 . 3 . 1 . 5 . 9 A cety ltran sferase 2 . 2 1 . 1 . 1 . 3 recep to r

1 . 7 1 . 1 . 1 . 1 1 . 9. 1. 1 .1 7 . 2 4 . 1 . 1 . 1

l d s 6 : R ac /R h o reg u latio n l a v z ; ty ro sin e k in a se / I s p p S em in al p la sm a 3 . 3 1 . 1 . 7 . 2 co m p lex 2 . 3 2 . 2 . 1 . 2 n eg ativ e factor 2 . 2 2 . 1 . 1 g ly co p ro tein

2 . 1 . 1 . 5 . 1 8 4 . 8 5 . 1 . 1 . 1 2 . 2 2 . 1 . 1 h etero co m p lex

I m k w Th rom hi n -preth rom bi n I d d h M H C I- I w w w N erv e gro w th facto r- 2 . 4 4 . 1 co m p lex 4 . 1 7 . 1 P -m icroglohulin 2 . 1 . 1 . 4 . 1 5 recep to r

2 . 4 4 . 1 2 . 1 . 1 . 2 7 . 1 7 . 1 . 3 . 4

I t b g T ra n sd u c in Py: 2 . 6 4 . 3 . 1 . 1 rece p to r

4.3.0 GENERATION OF INTERACTION POTENTIALS, SCORES