Project name: native_39aa_spsa

Status: done

Started: 2026-10-21 11:22:55
Settings
Chain sequence(s) VEEAKKKAKDQKEEDYRNYPTITYKTLELEIAESDVEVK input PDB
Selected Chain(s) S
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 S 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                                          (00:01:57)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/5c95c12dc0eeba/tmp/folded.pdb                 (00:01:57)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:03)
Show buried residues
Minimal score value
-5.3945
Maximal score value
0.9476
Average score
-1.8026
Total score value
-70.3008
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 S -1.6757
2 E S -3.4667
3 E S -3.6288
4 A S 0.0000
5 K S -5.0714
6 K S -5.2759
7 K S -5.3945
8 A S 0.0000
9 K S -5.0671
10 D S -4.9155
11 Q S -3.8697
12 K S -4.1830
13 E S -3.6593
14 E S -3.5378
15 D S 0.0000
16 Y S -0.9403
17 R S -2.4759
18 N S -1.7831
19 Y S 0.0711
20 P S -0.1434
21 T S 0.3755
22 I S 0.9476
23 T S 0.6548
24 Y S 0.8928
25 K S -0.5277
26 T S 0.0228
27 L S 0.4142
28 E S -1.4885
29 L S 0.0000
30 E S -1.2374
31 I S 0.0999
32 A S -2.3199
33 E S -2.5567
34 S S -1.6317
35 D S -2.0788
36 V S -2.6502
37 E S -2.0036
38 V S -0.3671
39 K S -1.8298
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 -1.8802 2.1423 View CSV PDB
4.5 -2.1005 1.8799 View CSV PDB
5.0 -2.3882 1.896 View CSV PDB
5.5 -2.68 1.9273 View CSV PDB
6.0 -2.902 1.9725 View CSV PDB
6.5 -2.9951 2.0253 View CSV PDB
7.0 -2.9495 2.0811 View CSV PDB
7.5 -2.804 2.1376 View CSV PDB
8.0 -2.6064 2.1936 View CSV PDB
8.5 -2.3837 2.247 View CSV PDB
9.0 -2.1442 2.2921 View CSV PDB