Annotations_BasedOnT..

chardfriendlyΤεχνίτη Νοημοσύνη και Ρομποτική

16 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

97 εμφανίσεις

A.

List of proteins in training set.

Acetylcholinesterase



(E.C. 3.1.1.7)


1ACE

3
-
Ketoacetyl
-
Coa Thiolase


(E.C. 2.3.1.16)


1AFW

Ornithine carbamoyltransferase


(E.C. 2.1.3.3)


1AKM

Glutamate racemase



(E.C. 5.1.1.3)


1B74

Alanine racemase



(E.C. 5.1.1.
1)


1BD0

Adenosine kinase



(E.C. 2.7.1.20)


1BX4

Subtilisin Carlsberg



(E.C. 3.4.21.62)

1CSE

Micrococcal nuclease



(E.C. 3.1.31.1)

1EY0

Oxalate oxidase



(E.C. 1.2.3.4)


1FI2

DNA
-

Lyase




(E.C. 4.2.99.18)

1HD7

2
-
amino
-
4
-
hydroxy
-
6
-
hydroxymethyldihyd
ropteridine

pyrophosphokinase



(E.C. 2.7.6.3)


1HKA

Colicin E3 Immunity Protein


(E.C. 3.1.21.
-
)

1JCH

L
-
lactate dehydrogenase


(E.C. 1.1.1.27)

1LDG

Papain





(E.C. 3.4.22.2)


1PIP

Mannose
-
6
-
phosphate isomerase

(E.C. 5.3.1.8)


1PMI

Pepsin





(E.C. 3
.4.23.1)

1PSO

Triosephosphate Isomerase


(E.C. 5.3.1.1)


1TPH

Aldose Reductase



(E.C. 1.1.1.21)

2ACS



HIV
-
1 Protease



(E.C. 3.4.23.16)

2AID



Mandelate Racemase



(E.C. 5.1.2.2)


2MNR


B.

Testing result on the 64 proteins from CatRes.


The following

table gives the THEMATICS
-
SVM results for 64 CSA proteins. The first
and second columns give the PDB ID and the protein name. The third column gives the
list of residues annotated as active site residues in CSA.
Boldface
indicates a CSA
ionizable active s
ite residue correctly predicted by the SVM alone.
Bold italics

indicates
a
CSA active site residue missed by the SVM result but correctly predicted by
SVM+Region.
Plain italics

designate annotated residues missed by both the SVM and
the SVM+Region. The fou
rth column lists the THEMATICS
-
SVM predicted residues,
with the members of the same cluster bounded by square brackets. Residues in
boldface

are CSA annotated residues. []ab means the same clusters appear in both chain a and b.
[XXXab] means residue XXX in

both chains a and b occurs in the same cluster. Columns
5 and 6 give the recall and filtration ratio as percentages for the SVM alone / the
SVM+Region. Recall and precision here are based on all residues, not just ionizable
residues. Column 7 indicates wh
ether the SVM / SVM+Region prediction is Correct,
Partially correct, or Incorrect.



PDB Code

Protein Name

CSA
Positive

SVM
Reported
Positive

Recall (%)

True positive /
ActualPositive

Filtration
ratio (%)

Predicted
positive /
Total residue

Result

Chains
w
e

used

Our

Comments

1.

1AL6

Citrate (si)
-
synthase

H274
H320
[H246a
H249a R413a
E420a H246b
67/100

5/17

Correct/Correct

A


There is no chain B
for this structure

-

ONLY chain A

D375

H249b R413b
E420b]
[Y231b
H235b H238a
H274a

R329b
D375b

R401b
R421a]
[Y231a
H235a H238b
H274b

R329a
D375a

R401a
R421b]
[D174
D257]a,b

[Y158
Y167]a, b

[Y318
Y330]
a,b



Also, the CSA
annotates residues
S
244

as catalytic as
well!!! I used only the
annotations here!

2.

1APX

Heme peroxidase

R38 H42

N71

[E65 H68]
[H163 D208]
[H116 E244]

0/33

2/10

Incorrect/Partial
correct

A, B,
C, D


3.

1AQ2

Phosphoenol pyruvate
carboxykinase

H232
K254
R333

[R65 K70
C125 Y207
E210 K212
K213
H232

C233
K254

D268 D269
E270 H271
E282 C285
Y286 E311
R333

Y336]
[C408 Y421
Y524]

[E36 H146]

100/100

5/16

Correct/C
orrect

A


4.

1B3R

Adenosylhomocysteinase

D130

K185
D189

N190

C194

[C52 H54
D129
D130

E154 E155
D189

C194

C227]

[Y220 Y256]

60/100

3/20

Correct/Correct

A, B,
C, D

I took out the
following CSA
annotations:

H
300
,
H
54

for all
chai
ns
.



5.

1B6B

Aralkylamine N
-
acety
ltransferase

S97

L111

H122

L124

Y168


[E54 H127]a

[H120
H122
]ab

[H145
H174]a

[E50 E52]b

[E190 E192]b

[C160
Y168
]b

30/70

5/17

Partial
correct/Correct

A,

B


6.

1B93

Methylglyoxyl synthase

H19

G66

D71

D91

H98

D101


[
H19 D71
H98 D101
]

67/100

3/11

Correct/Correct

A, B,
C


7.

1BG0

Arginine Kinase

R126
E225
R229
R280
R309

[Y68 Y89
H90 H99
R124
R126

C127 D192
E224
E225

D226
R229

C271
R280
R309

E314
H315 R330
E335]

[H185 H284]

100/100

7/20

Correct/Correct

A


[Y145 R208]

[Y134 K151]

8.

1BOL

Ribonuclease T2

H46

E105
H10
9

[Y116 Y121
E128 D129
D132 Y202]
[
E105 H109
]

67/100

4/13

Correct/Correct

A


9.

1BWD

L
-
arginine:Inosamine
-
phosphate
amidinotransferase

D108
R127

D179
H227
D229
H331
C332

[E9 E37 Y53
H87 H102
D103 C105
R107
D108

E130
D179
H227

D229

H278 C279
H331
C332
]ab

[D30

Y161]b

86/100

5/15

Correct/Correct

A, B


10.

1BZY

Hypoxanthine
-
guanine
phosphoribosyltransferase

E133

D134

D137
K165

R169

[R100 K102
D193]

[Y104
D137
K165
]

[
E133 D134
]

80/100

4/12

Correct/Correct

A, B,
C
,

D


11.

1CD5

Glucosamine
-
6
-
phosphate
isomerase

D72

D141

H143
E148

[
D72

E73
Y74 Y85]

[H19 E198]

[K124 Y128]

25/25

3/9

Partial correct/
Partial correct

A


12.

1CHD

Protein
-
glutamate
methylesterase

S164

T165

H190

M283

D286

[H233 E235
H248]

[
H190

H256
D286
]

40/80

3/10

Partial correct /
Correct

A


13.

1COY

Cholesterol
Oxidase

E361
H447
N485

[R44 C57
R65 Y92
Y107 Y219
Y446]

[Y21 K225]

[R328 Y376]

0/33

2/10

Incorrect /
Partial correct

A


14.

1CQQ

Picornain 3C

H40 E71
G145
C147

[Y97 C100
K153]


0/0

2/5

Incorrect /
Incorrect

A


15.

1CTT

Cytidine Deaminase

E104

[H102
E104

C129 H1
31
C132]ab

[E138 H203
E229]ab

[C217
Y252]b

100/100

3/11

Correct/Correct

A

There is no chain B


ONLY A

16.

1D0S

Nicotinate
-
nucleotide
-
dimethylbenzimidazole
phosphoribosyltransferase

E174

E317

G176

K213

[D69 H70
E174

D242
D263]


25/75

1/8

Partial Correct /
Cor
rect

A



R
esidues 174, 176 and
213 are
NOT

annotated by the CSA

or by
CATRES
.


I added them as
annotations to be
consistent for the
comparison.

17.

1DAA

Aminotransferase class
-
IV

E177
K145

L201

[R22a R98a
H100a Y31b
E32b H47b
R50b Y88b
Y114b
K145b
]

[Y31a E32
a
H47a R50a
Y88a
K145a

67/100

4/14

Correct / Correct

A
,

B


R98b]

[C142
E177
]ab

[R22 R93]b

18.

1DAE

Dethiobiotin synthase

T11

K15
K37

S41

[D10ab
C151ab
H154ab]

[
K15 K37
]ab

50/75

2/11

Correct/Correct

A

There is no chain B


ONLY A

19.

1DB3

GDP
-
mannose 4,6
-
dehydra
tase

T132

E134

Y156
K160

[D13 Y128
Y177 C179
H186]

[D105
E134
Y156 K160
]

[H228 D231
E344]

[K2 Y26]

[E315 E317]

75/100

5/16

Correct/Correct

A


20.

1DL2

Mannosyl
-
oligosaccharide
1,2
-
alpha
-
mannosidase

E132
R136

D275
E435

[D86
E132

E207
D275

E279 K283
D336 H337
Y
389 E399
E435

E438
E503 Y507
E526 H528]

[K216 Y235
E290 Y293]

[D52 H68]

75/100

5/16

Correct/Correct

A


21.

1DNK

Deoxyribonuclease I

E78 H134
D212
H252

[E39 Y76
E78 H134

D168
D212
H252
]

[R31 Y32]

100/100

4/10

Correct/Correct

A


22.

1DNP

Deoxyribodipyrimidine
phot
olyase

W306
W359
W382

[H44 E106
E109 C251
R278 R282
D372
D374]ab

[R8 D10
D130]a

[E318
Y365]ab

[D409
D431]ab

[D327
D331]b

[D354
H453]ab

[K353
Y464]a

0/0

7/15

Incorrect /
Incorrect

A, B


23.

1DZR

dTDP
-
4
-
dehydrorhamnose
3,5
-
epimerase

H63

D170

[R60
H63

D84 H120
Y
133 Y139
E144]

50/100

4/14

Correct/Correct

A, B


24.

1E2A

Histidine Kinase IIAlac

H78
Q80

D81 H82

[
H78abc

D81abc
H82abc
]

[E32 H94
H95]b

[E32 H94
H95]c

[E32 H95]a

75/75

5/21

Correct/Correct

A, B,
C


25.

1EBF

Homoserine dehydrogenase

D219
K223

[K117 E208
D210 D2
13
D214
D219
K223
]

100/100

2/10

Correct/Correct

A, B


26.

1FRO

Lactoylglutathione lyase

E172

[R37a E99a
Y114a D165a
D167a R122b
100/100

6/27

Correct/Correct

A, B,
C, D


H126b
E172b
]

[R37c E99c
Y114c D165c
D167c H126d
E172d]

[R37b E99b
Y114b
D165b
D167b H126a
E172a
]

[Y70 H102
E107]abcd

[H126c
E172c

E
99d]

[C138b
K151b]

[K150d
K158d]

[D165d
D167d]

[H115ab]

27.

1GOG

Galactose Oxidase

C228
Y272
W190

Y495

[C228
Y272

H334 C383
Y405 H442
Y495

H496
H581]

[H85 D166
H522 D524]

[D324 D404]

75/100

2/8

Correct/Correct

A

In the

CSA W290 is
annotated as catalytic
instead of W190. For
the sake of comparing,
I used W190

28.

1GRC

Phosphoribosylglycinamide
formyltransferase

N106

H108
S135

D144

[H54ab
E70ab H73ab
E74ab
Y78ab]

[
H108

H137
D144
]a

[Y67 R90]ab

[E44ab]

50/50

5/14

Correct/Corre
ct

A, B


29.

1HXQ

UDP
-
glucose
--
hexose
-
1
-
phosphate
uridylyltransferase

C160

H164
H166

Q168

[E182 E232
H281 H296
H298]

[H115 E152
H164 H166
]

[R13 Y201
R211 R324]

[E121 D267
H342]

[D183 H292]

50/75

5/18

Correct/Correct

A, B


30.

1I7D

DNA topoisomerase III

E7 K8
R3
30

[
E7 K8

H44
D103 D105
E107 E114
D136 Y320
D332 C333
H340 C372
D379 H381
H382 Y410
D520 E525]

[H100 D113]

[E286 E458]

67/67

4/11

Correct/Correct

A

According to the
CSA, residue
F
328 A

is also annotated as
catalytic. I took it out
to be consistent with
th
e comparison.

31.

1IDJ

Pectin lyase

R176

R236

[D186 D217
D221
R236

K239 D242]

[H247 E272]

[H178 H210]

50/50

3/10

Correct/Correct

A, B


32.

1KAS

3
-
oxoacyl
-
[acyl
-
carrier
protein] synthase

C163
H303
H340
F400

[
C163 H303

D311 E314
K335
H340

E349
C395]ab

[H168ab
75/100

3/14

Correct/Correct

A

There is no chain B


ONLY A

H17
2ab
D181ab]

[E115ab
H118ab]

33.

1LBA

T7 Lysomsome

Y46

K128

[H17 C18
Y46

H47
H68 C80
H122 C130]

50/100

5/18

Correct/Correct

A


34.

1MAS

Purine nucleosidase

D14
N168

H241

[H157ab
E158ab
D192ab
H195a]

[D10

D14

D15 E166
H241

D242]b

[D10
D14

D15
H241

D242]a

[E265ab]

[K44 Y92]a

67/100

4/13

Correct/Correct

A
, B

According to the
CSA, residue D10 is
catalytic instead of
D14. I changed the
annotation to be D14
for consistency of
comparison.

35.

1MHY

Methane Monooxyg
enase

C151
T213

[D74a K78a
H80a E89a
R171a D172a
C173a R179a
K45b Y46b
K49b R186b
D190b
D196b E199b
C200b D270b
D418b
H439b
H446b
D450b E454b
E460b E462b
R463b Y464b
E465b C466b
H467b E471b
R45c D51c
Y54c E58c
E62c H112c
R116c K12c
D133c]

[H39a C57a
Y99a H
109a
H110a D176a
E71b D75b
E111b E114b
D143b E144b
H147b
H149b
C151b

D170b R172b
R175b E209b
D242b E243b
H246b]

[H166 K189
H252 D256
R264]a

[K104 Y162
H168 R360]b

[Y112a
K116a Y290a
K65b]

[R98 Y288
Y351]b

[D243
E246]a

50/100

8/25

Correct/Correct

B, D,
G

Th
ere is no chain A or
C, ONLY B, D and
G!!!!

36.

1MPP

Mucoropepsin

D32
S35
Y75

D215

[D9 D11 E13
D32

D215
]

50/75

1/4

Correct/Correct

A

I took out the
double
occupancy residues in
the
following residue

positions
: 11, 47,
115,131
,
186
,
205
,
235
,
255, 263, 278,

37.

1NI
D

Nitrite Reductase (Copper
Containing)

D98
H255

[H95a
D98a

H100a H135a
C136a H145a
H255c

E279c
H306c]

[H95c
D98c

H100c H135c
C136c H145c
H255b

E279b
H306b]

[H95b
D98b

H100b
H135b C136b
H145b
H255a

E279a
H306a]

[E180 D182
H245
E310]abc

[D251abc]

[H260 Y293

R296]abc

100/100

5/19

Correct/Correct

A

There are no chains B
and C

-

ONLY A

38.

1NSP

Nucleoside
-
diphosphate
kinase

K16
N119

H122

[
C16

H55
Y56 E58
R109
H122

E133]

67/100

5/15

Correct/Correct

A


39.

1NZY

4
-
Chlorobenzoyl Coenzyme
A Dehalogenase

F64

H90

G114

W137

D145

[D160abc
E163abc
E175abc
D178abc]

[D123b
D145b

Y150b R154b
H218b C228c
E232c]

[C228a
E232a
H90c

D145c

Y150c
R154c
H218c]

[
D145a

Y150a R154a
H218a C228b
E232b]

[H138
D168]b

40/60

4/16

Partial correct /
Correct

A, B,
C


40.

1PGS

Peptide
Aspartylglucosamini
dase

D60 E206

[Y62 R80
Y116]

[Y161 Y293]

[Y183 K302]

[H224 Y277]

0/0

3/14

Incorrect /
Incorrect

A


41.

1PJB

Alanine dehydrogenase

K74 H95
E117
D269

[E8 E13 R15
K72
K74

E75
Y93
H95

Y116
E117
]

75/75

3/9

Correct / Correct

A


42.

1PKN

Pyruvate Kinase

R72
R119

K269

T327
S361

E363

[
R72

D112
E117
K269

E271 D295
E299]

[C316 D356
C357 E385
R444 R466]

[D224 D227]

[K265 Y465]

33/67

3/12

Partial correct /
Correct

A


43.

1PNL

Penicillin Acylase

S1 A69
[E152a
0/0

4/18

Incorrect /
A, B

Note that the catalytic
N241

K179a H192a
D73b D74b
D76b Y180b
Y190b
Y196b
D252b]

[D12a H18a
Y3
1a D38a
R39a Y96a
Y33b H38b
H520b]

[R145a Y27b
Y31b Y52b]

[R263
K394]b

[D484
D501]b

[R479
Y528]b

[E80 H123]b

[Y33 K106]a

Incorrect

annotations only refer
to chain B

44.

1PUD

Queuine tRNA
-
ribosyltransferase (tR
NA
-
guanine transglycosylase)

D102

[K55a D315b
C318b C320b
C323b E348b
H349b]

[D315a
C318a C320a
C323a E348a
H349a K55b]

[R38 R60
R362]ab

[
D102

D280]ab

100/100

3/10

Correct / Correct

A

There is no chain B
-

ONLY A

45.

1QFE

3
-
dehydroquinate
dehydratase

E86 H143

K170

[E46
E86

D114 E116
H143
K170
]ab

[D50 H51]ab

100/100

3/12

Correct / Correct

A, B


46.

1QPR

Quinolinate
phosphoribosyltransferase
(decarboxylating) (Type II)

K140

E201
D222

[R139 R146
K150 H161
R162 K172
D173 E199
E201

D203
D222

E246]

[D57 D80]

67/67

5/13

Correct / Correct

A, B,
C, D,

E,

F

The CSA also
annotates residue
R105 as catalytic. I
took it out to remain
consistent.

47.

1QQ5

2
-
haloacid dehalogenase

D8
T12

R39
N115

K147
S171
N173
F175

D176

[
D8 R39

Y89
K147

Y153
D176
]

[Y95 R192]

56/100

4/13

Correct / P
artial
Correct

A, B


48.

1QUM

Deoxyribonuclease IV

E261

[H69 D70
E94 E145
C177 D179
C181 H182
H216
E261
]

100/100

4/12

Correct / Correct

A


49.

1RA2

Dihydrofolate reductase

I5 M20
D27 L28
F31 L54
I94

[K38 K109
Y111]

0/0

2/6

Incorrect /
Incorrect

A


50.

1UAE

UDP
-
N
-
a
cetylglucosamine
1
-
carboxyvinyltransferase

N23

C115

D305

R397

[K22 R91
C115

R120
E188 E190
D231 E234
50/100

4/14

Correct / Correct

A


H299 R331
D369 R371
H394
R397

Y399 K405]

51.

1UAG

UDP
-
N
-
acetylmuramoylalanine
--
D
-
glutamate ligase

K115
N138

H183

[
K115 H183

Y
187 Y194
R302 K319
D346 K348
C413 R425]

67/100

9/8/2

Correct / Correct

A


52.

1ULA

Purine
-
nucleoside
phosphorylase (type 1)

H86 E89

N243

[D134a
H135a Y166a
E201c E205c
Y249c]

[E201a
E205a Y249a
D134b
H135b
Y166b]

[E201b
E205b Y249b
D134c H135c
Y166c]

[H257
E2
58]ac

[
H86
E89
]abc

67/67

3/11

Correct / Correct

A

There are no chains B,
C
-

ONLY A

53.

1UOK

Oligo
-
1,6
-
glucosidase

D199
E255
D329

[Y12 Y15
Y39 D60
D64 D98
H103 H161
D169
D199
E255

H283
D285 Y324
H328
D329

R332 R336
H356 Y365
E368 E369
D385E387
D416 R419
Y464
R471
Y495 R497]

[D21 D29]

100/100

6/20

Correct/ Correct

A


54.

1VAO

Vanillyl Alcohol Oxidase

Y108
D170
H422
Y503
R504

[
Y108 D170

Y187 R312
D317 R398
E410 E464
H466
Y503
R504
]

[D59 H61
H422

H506]

[Y148 D167
H193]

[H467 C470]

[H313 Y440]

[Y276 Y358]

100/100

4
/15

Correct / Correct

A, B


55.

1WGI

Inorganic pyrophosphatase

D117

[E48 K56
E58 Y89
E101 H107
D115
D117

D120 D147
D152 Y192]a

[E48 K56
E58 E101
D115
D117

D120 D147
D152 Y192]b

[E123 D159
D162]b

[H87ab]

100/100

5/15

Correct /
Correcy

A, B


56.

1YTW

Protein Tyros
ine
Phosphatase

E290
D356

H402
C403

R409
T410

[C259 Y261
H270 Y301
H350
H402
C403
]

33/67

2/11

Partial Correct /
Correct

A


57.

2CPO

Heme Chloroperoxidase

H105
E183

[E104
H105

D106 H107
D113 E161
D168
E183
]

100/100

3/7

Correct / Correct

A


58.

2HDH

3
-
hydroxyacyl
-
CoA
dehydrogenase

S137

H158
E170

N208

[R209a
Y214ab
E217ab
R220ab
R224a Y242a
H275a]

[
H158a
E170b
]

[
H158b
E170a
]

[H266b
H275b]

50/100

3/10

Correct / Correct

A, B


59.

2HGS

Glutathione Synthase

R125

S151
G369

R450

[D24a H107b
E214b R221b
E224b R236b
Y265b R26
7b
Y270b E287b
K293b C294b
D296b
Y432b]

[H107a
E214a R221a
E224a R236a
Y265a R267a
Y270a E287a
K293a C294a
D296a Y432a
D24b]

[
R125

D127
E144 K305
K364 E368
Y375 E425
R450

K452]a

[
R125

D127
E144 K305
K364 E368
Y375 E425
R450
]b

[H163
D469]ab

50/100

5/21

Corr
ect / Correct

A

There is no chain B


ONLY A

60.

2JCW

Superoxide dismutase

H63
R143

[H46 H48
H63 H71
H80 D83
H120
D124]ab

50/100

5/16

Correct / Correct

A

There is no chain B


ONLY A

61.

2PFL

Formate C
-
acetyltransferase

W333

C418

C419
G734

[D74a H84a
R141ab
K142
ab
H144ab
R174ab
D180ab
Y181ab
R183a
R218ab
E221ab
E222ab
E225ab
50/100

6/19

Correct / Correct

A,B


Y240a Y259a
Y262ab
K267a
E368ab
D413ab
H498ab
Y499ab
H501ab
D502ab
D503ab
Y504ab
Y506ab
E507ab
H514ab
R520ab
Y594ab
R595ab]

[Y172 R176
R319 Y323
E400
C418
C419

R435
Y490 Y612
H704 R731
Y735]a
b

[H84 Y240
Y259 K267]b

[C159
Y444]b

[R316
D330]ab

62.

2PLC

1
-
phosphatidylinositol
phosphodiesterase

H45 D46
R84 H93

D278

[
H45 D46

D82 E128
D204 H236
D278
]

[Y71 K115]

60/100

3/11

Correct / Correct

A


63.

2THI

Thiamine pyridin
ylase

C113
E241

[Y16 Y50
D64
C113

E171 D175
Y222 Y239
E241

D265
Y270
D272]ab

[E37ab
D84ab
E284ab]

[Y323
Y333]b

[Y180
R349]ab

[H282ab]

100/100

5/16

Correct / Correct

A, B


64.

8TLN

Metalloproteinase M4

E143

H231

[D138 H142
E143

E166
D170 E177
D185 E190]

[K18
D72
Y76 K182]

50/100

4/13

Correct / Correct

E




Questions I need to ask Tong:

1) Which are the 4 proteins that you didn’t use in the test

set for which the
results are
reported in
Table 2 (when comparing with other methods)
?

2) Can you tell me
exactly
wh
ich chains you used for each structure?
This inf
ormation is
not stated anywhere

and there are also some inconsistencies regarding the chain
annotations. For example:

(i) i
n the fourth column of
T
able

B

in the supplementary
material, it states that some res
idue clusters were found for chain b

of structure 1AL6
,
however this structure

does not have a chain b
. The same goes for structures
1KAS,
1DAE, 1CTT, 1PUD,
2HGS and2 JCW
; (ii) same as before but for structure 1MHY,
there are no chains a or c, o
nly b, d an
d g; (iii) same as before but for structure
s

1NID

and
1ULA
, there are no chains b and c
.

3
)

There are some contradictions between the
literature
annotations stated in the CSA and
the ones you used (according to the third column of
T
able

B

in the
s
upplemen
tary
material)
. For example
: (i)

you did not consider residues
H
300 and
H
54 which are
annotated by the CSA as catalytic in structure
1B3R; (ii)
residues
174, 176 and 213 are
not annotated by the
CSA (
http://www.ebi.ac.uk/thornton
-
srv/databases/cgi
-
bin/CSA/CSA_Site_Wrapper.pl

) or
CATRES

(
http://www.ebi.ac.uk/thornton
-
srv/databases/CATRES/

)

for str
ucture 1D0S
, though you consider them to be
; (iii)

in
structure 1GOG, the W290 is annotated in the CSA instead of W190 that you used
; (iv)
in structure 1I7D,
the CSA
as well as CATRES
also annotate
residue
F
328 as catalytic

whereas you do not
; (v) for str
ucture 1qpr, t
he CSA also annotates residue R105 as
catalytic

whereas you do not;

Which version of the CSA did you use?
Is it possible that
these are mistakes?