Project name: 250

Status: done

Started: 2026-05-10 09:30:09
Chain sequence(s) A: SVFDTVTAAVQALLASGKAPEDISIGDVANLTGLSLYEIASSFLDQGYSSFAAFVAAVAA
input PDB
Selected Chain(s) A
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 A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:01)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:16)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/7473552a2e15030/tmp/folded.pdb                (00:00:16)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:43)
Show buried residues
Minimal score value
-2.793
Maximal score value
1.8569
Average score
-0.292
Total score value
-17.5198
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 S A -0.3003
2 V A 0.1182
3 F A -0.5509
4 D A -1.4047
5 T A -0.4409
6 V A 0.0000
7 T A -0.5698
8 A A -0.3497
9 A A 0.0000
10 V A 0.0000
11 Q A -0.5937
12 A A -0.1189
13 L A -0.3022
14 L A -0.4308
15 A A -0.2883
16 S A -0.4838
17 G A -0.6336
18 K A -1.3370
19 A A -1.4305
20 P A -1.6767
21 E A -2.7930
22 D A -2.7806
23 I A 0.0000
24 S A -0.8325
25 I A 0.1709
26 G A -0.1628
27 D A -0.7598
28 V A 0.0000
29 A A -0.1760
30 N A -0.8774
31 L A 0.4957
32 T A 0.1032
33 G A -0.3802
34 L A 0.3787
35 S A 0.5976
36 L A 1.8569
37 Y A 1.5569
38 E A 0.4272
39 I A 0.0000
40 A A 0.8499
41 S A -0.0755
42 S A 0.0000
43 F A 0.0000
44 L A -0.2623
45 D A -1.8835
46 Q A -1.7602
47 G A -1.1280
48 Y A -0.2291
49 S A -0.1989
50 S A 0.2341
51 F A 0.5419
52 A A -0.3091
53 A A 0.1966
54 F A 0.0000
55 V A 0.0000
56 A A -0.1071
57 A A 0.2496
58 V A 0.1219
59 A A 0.0634
60 A A 0.1453
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 likely a peptide. Results may be inaccurate. The input structure is globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 0.4395 2.2802 View CSV PDB
4.5 0.3488 2.2184 View CSV PDB
5.0 0.2445 2.1442 View CSV PDB
5.5 0.1368 2.0693 View CSV PDB
6.0 0.0335 2.0058 View CSV PDB
6.5 -0.0586 1.9637 View CSV PDB
7.0 -0.1374 1.9433 View CSV PDB
7.5 -0.206 1.9354 View CSV PDB
8.0 -0.2657 1.9324 View CSV PDB
8.5 -0.3126 1.9308 View CSV PDB
9.0 -0.342 1.9279 View CSV PDB