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Table 2 Annotation of residue positions predicted in five enzymes as being important by H2rs and H2r

From: H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments

Protein

Residue

H2rs

H2r

PSICOV

Residue’s role

stTrpA

L100

2.2

3.2

1

Near binding site

 

S125

1.1

6.8

1

Stabilizes the active site

 

L127

2.0

 

2

Near binding site

 

A129

1.9

5.7

5

Near active site

 

I153

0.9

4.6

1

Near active site

 

L162

0.7

6.1

0

TrpA/TrpB interface

stTrpB

P7

1.3

6.8

0

ND

 

C62

2.2

7.3

0

ND

 

G83

1.8

7.2

2

Near binding site

 

T88

2.4

 

1

Near binding site

 

Q90

2.4

7.5

0

Near binding site

 

V91

2.1

 

0

Near binding site

 

L121

1.8

6.3

1

ND

 

C170

4.5

 

4

End of substrate tunnel

 

T190

2.2

 

6

Metal binding site

 

P257

2.2

6.7

0

Near metal ion

 

G268

2.3

 

0

Coordination of ion binding

 

F280

2.4

2.8

0

End of substrate tunnel

 

M282

2.6

 

4

Near binding site

 

S297

4.2

 

3

Near metal ion

 

F306

-0.8

5.0

0

Metal binding site

 

S308

2.4

8.5

0

Metal binding site

 

Q312

2.9

 

0

ND

ssTrpC

I48

2.4

 

3

ND

 

A50

1.4

6.1

1

Near active site

 

Y76

1.1

4.0

1

ND

 

M109

1.9

4.3

2

Near active site

 

I133

2.6

9.8

3

Catalytically important

 

V134

2.3

 

2

Near active site

 

I136

2.1

 

1

ND

 

L142

2.7

 

1

Catalytically important

 

N161

1.4

6.9

2

Near active site

 

L187

1.8

4.6

1

Mutation L187A is neutral

 

A209

2.1

 

3

Near binding site

 

S234

2.1

9.5

4

Phosphate binding site

ecDHFR

A9

2.2

 

2

Near active site

 

W30

2.3

 

0

Binding site

 

K32

2.3

 

0

Binding site

 

M92

3.4

 

0

Near active site

 

G121

2.7

2.8

0

Near active site

 

D144

1.9

5.1

0

ND

 

H149

2.1

4.4

0

Coupled motion

smHK

T69

2.8

 

1

Domain interface

 

A215

2.6

 

2

End of domain 1

 

C217

2.7

13.9

0

End of domain 1

 

A218

2.3

 

0

End of domain 1

 

C224

2.2

 

0

Begin of domain 2

 

V230

2.1

 

3

Near binding site

 

V256

2.1

 

2

Domain interface

 

K290

2.2

 

0

Near binding site

 

D367

1.5

9.8

2

ND

 

T409

2.4

 

1

Near C224

 

V412

2.0

 

0

Near binding site

  1. For the enzymes stTrpA, stTrpB, ssTrpC, ecDHFR, and smHK, H2r and H2r were used to identify important residue positions. For these residues, annotation was deduced from literature. The first column lists the name of the enzyme. The second column gives the residue and its position. The third column gives the conz(k)-value deduced by H2rs from all U vNE ()-values based on a p-value of 10-11. The column H2r lists mean conn(k)-values resulting from 25 randomization tests. The column PSICOV lists the number of contacting pairs the residue belonged to. The last column lists the role of the residues, for details see Results. “ND” indicates that we did not find clues to the function of this residue.
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BMC Bioinformatics

ISSN: 1471-2105

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