Project name: adali

Status: done

Started: 2026-03-27 15:21:29
Chain sequence(s) H: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDYADSVEGRFTISRDNAKNSLYLDMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKI
input PDB
Selected Chain(s) H
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with H chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:54)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/146ae787b715f4c/tmp/folded.pdb                (00:01:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:10)
Show buried residues
Minimal score value
-2.7775
Maximal score value
2.5395
Average score
-0.4738
Total score value
-101.4017
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 E H -2.1396
2 V H -1.0346
3 Q H -1.0218
4 L H 0.0000
5 V H 1.1691
6 E H 0.2113
7 S H -0.4451
8 G H -1.0140
9 G H -0.7646
10 G H -0.4159
11 L H -0.0541
12 V H 0.0000
13 Q H -1.7615
14 P H -1.8758
15 G H -2.1679
16 R H -2.7207
17 S H -2.0695
18 L H -1.4579
19 R H -2.1118
20 L H 0.0000
21 S H -0.3800
22 C H 0.0000
23 A H -0.0584
24 A H 0.0000
25 S H -0.9920
26 G H -1.3227
27 F H -0.7983
28 T H -0.7977
29 F H 0.0000
30 D H -1.7592
31 D H -1.1971
32 Y H -0.0385
33 A H 0.0000
34 M H 0.0000
35 H H 0.1439
36 W H 0.0000
37 V H 0.0000
38 R H 0.0000
39 Q H -0.1924
40 A H -0.8943
41 P H -0.7868
42 G H -1.1871
43 K H -1.5771
44 G H -0.6530
45 L H 0.8227
46 E H 0.2022
47 W H 0.4103
48 V H 0.0000
49 S H 0.0000
50 A H 0.0000
51 I H 0.0000
52 T H -0.5641
53 W H -0.6636
54 N H -1.7416
55 S H -1.0062
56 G H -1.0445
57 H H -0.9815
58 I H -0.3111
59 D H -0.9590
60 Y H -1.0061
61 A H 0.0000
62 D H -2.1583
63 S H -1.3421
64 V H -1.4529
65 E H -2.3825
66 G H -1.4868
67 R H -1.2180
68 F H 0.0000
69 T H -0.8367
70 I H 0.0000
71 S H -0.2266
72 R H -1.0017
73 D H -1.5945
74 N H -1.8991
75 A H -1.4097
76 K H -2.2069
77 N H -1.8304
78 S H 0.0000
79 L H 0.0000
80 Y H -0.4825
81 L H 0.0000
82 D H -1.3143
83 M H 0.0000
84 N H -1.8122
85 S H -1.7421
86 L H 0.0000
87 R H -2.5373
88 A H -1.6491
89 E H -2.2293
90 D H 0.0000
91 T H -0.8208
92 A H 0.0000
93 V H 0.3086
94 Y H 0.0000
95 Y H 0.4261
96 C H 0.0000
97 A H 0.0000
98 K H 0.0000
99 V H 0.0000
100 S H 0.1202
101 Y H 1.1823
102 L H 1.0127
103 S H 0.5001
104 T H 0.2851
105 A H 0.2384
106 S H 0.1337
107 S H -0.2966
108 L H -0.3675
109 D H -1.2765
110 Y H -0.4540
111 W H 0.0241
112 G H 0.0000
113 Q H -0.8011
114 G H -0.2422
115 T H -0.0865
116 L H -0.0575
117 V H 0.0000
118 T H -0.4150
119 V H 0.0000
120 S H -0.6269
121 S H -0.5747
122 A H -0.3279
123 S H -0.4480
124 T H -0.7756
125 K H -1.0137
126 G H -1.3064
127 P H -0.5224
128 S H -0.0819
129 V H 0.0000
130 F H 1.1296
131 P H 0.6310
132 L H 0.8536
133 A H 0.3531
134 P H -0.0329
135 S H -0.2657
136 S H -0.3262
142 G H -0.6282
143 T H -0.4743
144 A H -0.3243
145 A H 0.0671
146 L H 0.0000
147 G H 0.0000
148 C H 0.0000
149 L H 0.8713
150 V H 0.0000
151 K H -0.2629
152 D H -0.5782
153 Y H 0.0000
154 F H -0.1653
155 P H 0.0000
156 E H -0.6272
157 P H -0.7052
158 V H 0.0000
159 T H -0.6032
160 V H -0.1824
161 S H -0.4196
162 W H 0.0000
163 N H -0.7985
164 S H -0.7044
165 G H -0.5381
166 A H -0.1778
167 L H 0.0088
168 T H -0.2697
169 S H -0.3284
170 G H -0.3790
171 V H 0.0537
172 H H -0.3747
173 T H 0.2434
174 F H 1.0593
175 P H 0.7723
176 A H 1.2834
177 V H 2.5395
178 L H 2.2368
179 Q H 0.7234
180 S H 0.0758
181 S H -0.2126
182 G H 0.2430
183 L H 0.4437
184 Y H 0.8951
185 S H 0.7629
186 L H 0.0000
187 S H 0.7061
188 S H 0.0000
189 V H 0.5106
190 V H 0.0000
191 T H -0.2248
192 V H 0.0000
193 P H -0.4733
194 S H -0.5508
195 S H -0.5514
196 S H -0.4530
197 L H -0.2627
198 G H -0.5881
199 T H -0.5645
200 Q H -0.7920
201 T H -0.6186
202 Y H 0.0000
203 I H -0.9387
204 C H 0.0000
205 N H -1.5711
206 V H 0.0000
207 N H -1.7572
208 H H 0.0000
209 K H -2.7775
210 P H -1.6197
211 S H -1.7181
212 N H -2.5462
213 T H -1.9810
214 K H -2.6500
215 V H -1.4153
216 D H -2.5827
217 K H -1.8519
218 K H -1.7731
219 I H -0.1402
Download PDB file
View in 3Dmol

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.2839 3.2667 View CSV PDB
4.5 -0.3217 3.2683 View CSV PDB
5.0 -0.3672 3.2731 View CSV PDB
5.5 -0.411 3.285 View CSV PDB
6.0 -0.4441 3.3068 View CSV PDB
6.5 -0.4607 3.3328 View CSV PDB
7.0 -0.4622 3.3525 View CSV PDB
7.5 -0.4552 3.3624 View CSV PDB
8.0 -0.4445 3.3662 View CSV PDB
8.5 -0.4304 3.3675 View CSV PDB
9.0 -0.4103 3.4339 View CSV PDB