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Table 1 Top amino-acid pairs in transmembrane helices of the consensus sequences of classified Pfam-A families

From: Genomic analysis of membrane protein families: abundance and conserved motifs

List 1: top 50 pairs and their significance from Senes et al. [12]

List 2: top 50 pairs and their occurrences from random pairs

List 3: top 50 pairs and their occurrences in lists 1 and 2

GG4

6.35 × 10-34

GG4

46

GG4

46

II4

8.36 × 10-24

GG3

32

GL3

28

GA4

3.61 × 10-21

GG1

30

GG7

21

IG1

4.79 × 10-21

GG2

29

GL1

18

IG2

1.29 × 10-16

GL3

28

AG7

18

VG2

5.73 × 10-16

LL1

25

GA7

17

IV4

2.12 × 10-15

LG2

25

AG4

17

IP1

4.52 × 10-15

GF4

24

PL2

16

VV4

3.75 × 10-14

FL3

24

AS4

16

VI4

1.09 × 10-12

LL7

23

AL6

16

AV1

2.17 × 10-12

GL4

23

LP1

15

GL3

9.69 × 10-12

GG6

23

PG9

15

AG4

9.06 × 10-10

LL5

23

GA4

15

WQ1

3.87 × 10-09

LL3

22

FG1

15

IL4

4.89 × 10-09

LG3

22

SL1

14

AA3

1.33 × 10-08

LG6

21

SG4

14

VG1

1.83 × 10-08

LL8

21

PL1

14

GG7

2.95 × 10-08

GG7

21

AA7

13

VL4

7.71 × 10-08

GA1

21

AG5

12

IS2

8.98 × 10-08

LG10

21

LF8

12

SI2

1.52 × 10-07

GG8

21

IA1

12

GI1

2.93 × 10-07

LA1

21

GV1

12

IY10

4.55 × 10-07

LL2

20

AI1

12

YY3

6.3 × 10-07

FG7

20

AA2

12

IF10

1.63 × 10-06

FL1

20

GL2

12

GI2

3.27 × 10-06

LG4

20

AA3

11

PI3

3.99 × 10-06

GA3

20

SL2

11

PV1

4.97 × 10-06

FG4

19

PG5

11

PL1

5.35 × 10-06

GG5

19

PG6

11

LP1

5.35 × 10-06

GL7

19

IL4

11

CG4

5.4 × 10-06

GL1

18

GS5

10

VY9

5.58 × 10-06

AG7

18

VL4

10

GV2

6.04 × 10-06

FG8

18

GV2

10

VP1

7.45 × 10-06

LL4

18

IG1

10

IA1

7.93 × 10-06

GV3

18

PG10

10

PL2

1.13 × 10-05

AG3

18

LY6

10

GN4

1.38 × 10-05

GF1

18

LF10

10

GS5

1.43 × 10-05

LA2

18

SA6

10

VA2

2.51 × 10-05

AG1

17

LG5

10

HQ1

2.7 × 10-05

FL5

17

SA3

10

VY10

2.95 × 10-05

AG4

17

PF1

10

IQ2

3.1 × 10-05

FG5

17

GS4

10

LN2

5.74 × 10-05

FF1

17

IV4

9

IM9

6.84 × 10-05

GA7

17

LS1

9

PA9

8.25 × 10-05

FG2

17

GY8

9

VC5

9.87 × 10-05

AF3

17

IG2

9

QD3

9.95 × 10-05

GP2

17

LF9

9

LY10

1.19 × 10-04

PL2

16

VF8

8

SV2

1.24 × 10-04

FF5

16

VG6

8

DE4

1.51 × 10-04

AS4

16

GN4

8

  1. A pair XYn corresponds to amino acids X and Y separated by (n-1) residues. List 1 shows the top 50 amino-acid pairs and their significances by the TMSTAT method [12]; list 2 shows the top 50 amino-acid pairs generated from random amino-acid pairs and their occurrences in the consensus sequences of Pfam-A families of polytopic membrane domains; and list 3 shows the top 50 amino-acid pairs generated from the intersection of lists 1 and 2 (that is, the top 200 pairs as judged by TMSTAT and their occurrences in the consensus sequences of Pfam-A families of polytopic membrane domains). Pairs of small-side-chain amino acids, such as GG4 and AS7, are in bold.