Project name: a beta 42 ph

Status: done

Started: 2026-05-30 01:42:03
Chain sequence(s) A: DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
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 partially or entirely disordered. Average 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                                          (00:00:36)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/69650dade18ba2b/tmp/folded.pdb                (00:00:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:58)
Show buried residues
Minimal score value
-3.0605
Maximal score value
3.856
Average score
0.0656
Total score value
2.754
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 D A -2.7205
2 A A -2.4196
3 E A -2.5661
4 F A -0.9892
5 R A -2.7498
6 H A -3.0605
7 D A -2.6325
8 S A -1.3739
9 G A -0.6290
10 Y A -0.2682
11 E A -1.1154
12 V A 0.4409
13 H A -1.1634
14 H A -1.1638
15 Q A -0.4199
16 K A -0.9584
17 L A 0.6238
18 V A 0.4213
19 F A 1.7515
20 F A 1.8238
21 A A 0.3837
22 E A -1.0286
23 D A -1.5678
24 V A -0.8877
25 G A -1.6018
26 S A -1.6980
27 N A -2.3388
28 K A -2.1212
29 G A -0.4553
30 A A 0.1211
31 I A 2.2515
32 I A 3.1413
33 G A 2.2908
34 L A 3.0350
35 M A 3.4122
36 V A 2.9308
37 G A 1.9830
38 G A 1.8550
39 V A 3.0365
40 V A 3.8560
41 I A 3.4881
42 A A 1.8371
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 partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 0.6298 5.9718 View CSV PDB
4.5 0.5136 5.7986 View CSV PDB
5.0 0.3787 5.5799 View CSV PDB
5.5 0.2603 5.3508 View CSV PDB
6.0 0.1746 5.1422 View CSV PDB
6.5 0.1149 4.9726 View CSV PDB
7.0 0.0732 4.8733 View CSV PDB
7.5 0.0454 4.9519 View CSV PDB
8.0 0.0276 5.048 View CSV PDB
8.5 0.0211 5.146 View CSV PDB
9.0 0.0332 5.2442 View CSV PDB