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Table 3 Details of the intersection between binding sites and destabilizing regionsa.

From: Relating destabilizing regions to known functional sites in proteins

Pdb idb

N sitec

N des.d

N IRe

Sens.f

PPVg

Exp N IRh

P-value

Small

       

1e1a

13

38

7

53.8

18.4

1.6

0.00023

1e3f

32

18

8

25.0

44.4

1.2

5.9e-06

1gu7

62

53

10

16.1

18.9

4.5

0.00999

1gud

24

36

14

58.3

38.9

3.0

1.5e-08

1gus

24

73

0

0.0

0.0

4.4

1.0

1gusi

84

73

41

48.8

56.2

15.2

6.2e-14

1gxy

24

18

7

29.2

38.9

1.9

0.00100

1hf8

8

46

0

0.0

0.0

0.7

1.0

1hhq

102

126

30

29.4

23.8

14.3

1.2e-05

1is5

88

16

16

18.2

100.0

2.6

8.2e-14

1jcf

34

46

12

35.3

26.1

4.7

0.00061

1odl

150

190

60

40.0

31.6

20.3

3.3e-18

1ofn

30

46

13

43.3

28.3

3.4

2.9e-06

1tm2

19

26

6

31.6

23.1

1.6

0.00232

1usg

30

56

14

46.7

25.0

2.4

5.6e-09

1usl

36

28

15

41.7

53.6

3.2

5.5e-09

1w1h

10

7

6

60.0

85.7

0.5

9.6e-08

1w2i

16

24

0

0.0

0.0

2.1

1.0

1w37

48

101

16

33.3

15.8

4.1

6.5e-07

1y2t

108

66

0

0.0

0.0

12.6

1.0

Polysaccharide

       

1nof

12

43

7

58.3

16.3

1.4

7.3e-05

1o88

15

34

12

80.0

35.3

1.4

3.2e-11

1ob0

41

24

8

19.5

33.3

2.0

0.00037

1ogb

32

53

4

12.5

7.5

1.7

0.08496

1qhz

14

29

10

71.4

34.5

1.3

1e-08

1qjv

10

45

4

40.0

8.9

1.3

0.03039

1uuq

16

35

10

62.5

28.6

1.4

3.1e-08

1w0n

8

10

0

0.0

0.0

0.7

1.0

1w6z

20

14

6

30.0

42.9

2.2

0.00887

Peptide

       

1c7k

9

7

0

0.0

0.0

0.5

1.0

1e5t

18

33

4

22.2

12.1

0.8

0.00748

1ea7

7

41

0

0.0

0.0

0.9

1.0

1gt9

21

28

4

19.0

14.3

1.6

0.07134

1kl4

68

22

12

17.6

54.5

3.1

5.6e-06

1oes

16

27

5

31.2

18.5

1.5

0.01154

Protein

       

1e3f

60

18

0

0.0

0.0

2.3

1.0

1e6l

10

6

3

30.0

50.0

0.5

0.00632

1e6l

15

6

0

0.0

0.0

0.7

1.0

1f2x

24

4

0

0.0

0.0

0.4

1.0

1gcp

21

10

2

9.5

20.0

3.1

0.89027

1gqv

36

8

6

16.7

75.0

2.1

0.00465

1obq

44

19

11

25.0

57.9

2.3

9.6e-07

1uns

19

4

0

0.0

0.0

0.9

1.0

1uns

20

4

4

20.0

100.0

0.9

0.00852

1uol

18

7

2

11.1

28.6

0.7

0.12811

1uq4

42

5

4

9.5

80.0

0.8

0.00254

Nucleic acid

       

1o7i

5

4

0

0.0

0.0

0.2

1.0

1okb

30

24

12

40.0

50.0

3.2

3.7e-06

1uol

19

7

0

0.0

0.0

0.7

1.0

1gqv

9

8

0

0.0

0.0

0.5

1.0

1uq4

17

5

0

0.0

0.0

0.3

1.0

Lipid

       

1obq

42

19

7

16.7

36.8

2.2

0.00305

1qmd

14

37

4

28.6

10.8

1.4

0.04088

Metal

       

1e6l

7

6

0

0.0

0.0

0.3

1.0

1qmd

6

37

1

16.7

2.7

0.6

0.47097

Peptide-Protein

       

1mix

26

21

6

23.1

28.6

2.6

0.03234

Small-Metal

       

1h1y

38

33

17

44.7

51.5

2.9

8.6e-12

2poo

16

25

10

62.5

40.0

1.1

2.8e-09

1oid

19

60

14

73.7

23.3

2.2

1.2e-10

Polysaccharide-Metal

       

1gkb

76

88

48

63.2

54.5

7.0

1.4e-36

Lipid-Metal

       

1umv

34

19

0

0.0

0.0

2.6

1.0

Protein-Metal

       

1o6v

49

40

12

24.5

30.0

4.2

0.00032

Small

   

34.4 (21.4) j

32.3 (25.5) k

  

Polysaccharide

   

43.7 (27.3)

26.2 (17.4)

  

Peptide

   

18.3 (14.0)

16.6 (16.7)

  

Protein

   

13.0 (10.9)

36.2 (33.9)

  

Nucleic acid

   

8.0 (17.9)

10.0 (22.4)

  

Lipid

   

15.1 (14.4)

15.9 (18.9)

  

Metal

   

35.7 (29.4)

25.3 (22.6)

  
  1. aNo destabilizing regions were detected in 11 entries of the dataset (1utx, 1gv2, 1eao, 1e7l, 1vyi, 1w9s, 1upq, 1w53, 1tgr, 1r29, 1sif) and these entries are not listed in this table.
  2. bPdb identifier of structure used for energy calculations.
  3. cNumber of residues in binding site.
  4. dNumber of residues in destabilising region.
  5. eNumber of residues in intersection region.
  6. fSensitivity (in %).
  7. gPositive predictive value (in %).
  8. hExpected number of residues in intersection region (see text).
  9. i1gus appears twice here because it has 2 distinct binding sites for small ligands. The same observation applies to 1e6l and 1uns that have 2 distinct binding sites for different proteins.
  10. jAverage sensitivity (and standard deviation) for the given ligand type.
  11. kAverage PPV (and standard deviation) for the given ligand type.