Project name: 034

Status: done

Started: 2026-10-21 11:45:14
Settings
Chain sequence(s) VHDDTLATLKEIRRRLDEEARREIEKRKAQQLGDQVLEDVDRLLQKLIQK input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
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                                          (00:03:18)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/413155301dd9f5/tmp/folded.pdb                 (00:03:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:31)
Show buried residues
Minimal score value
-5.1224
Maximal score value
1.2084
Average score
-2.2191
Total score value
-110.9546
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 V A 0.3162
2 H A -1.3695
3 D A -2.2862
4 D A -2.2739
5 T A -1.1114
6 L A -0.6817
7 A A -1.4176
8 T A -1.0624
9 L A -0.9361
10 K A -2.4334
11 E A -2.1262
12 I A -1.3292
13 R A -3.5088
14 R A -4.1874
15 R A -3.7660
16 L A -2.5974
17 D A -4.3259
18 E A -4.4914
19 E A -4.4943
20 A A -3.4625
21 R A -4.5620
22 R A -5.1224
23 E A -4.4090
24 I A -2.6461
25 E A -4.7859
26 K A -4.8584
27 R A -4.6372
28 K A -4.1917
29 A A -3.1316
30 Q A -3.4058
31 Q A -3.1145
32 L A -1.0666
33 G A -1.2215
34 D A -2.3156
35 Q A -1.6465
36 V A 0.2209
37 L A -0.0247
38 E A -2.2890
39 D A -2.2044
40 V A -0.4041
41 D A -1.9246
42 R A -2.4707
43 L A -0.0010
44 L A 0.2147
45 Q A -1.3871
46 K A -1.1168
47 L A 0.7365
48 I A 1.2084
49 Q A -1.1999
50 K A -1.6529
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.

pH
Average A3D Score
Max A3D Score
4.0 -2.5719 2.0682 View CSV PDB
4.5 -2.8252 1.6349 View CSV PDB
5.0 -3.1326 1.5647 View CSV PDB
5.5 -3.4439 1.6045 View CSV PDB
6.0 -3.7122 1.698 View CSV PDB
6.5 -3.9045 1.8632 View CSV PDB
7.0 -4.0171 2.0841 View CSV PDB
7.5 -4.0721 2.3322 View CSV PDB
8.0 -4.0912 2.5904 View CSV PDB
8.5 -4.0781 2.8513 View CSV PDB
9.0 -4.0227 3.1108 View CSV PDB