Project name: M13_Phe

Status: done

Started: 2025-04-03 22:00:09
Chain sequence(s) A: FFAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS
B: FFAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS
input PDB
Selected Chain(s) A,B
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average 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                                          (00:03:01)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/439268ab52f4c64/tmp/folded.pdb                (00:03:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:13)
Show buried residues
Minimal score value
-1.6712
Maximal score value
4.7656
Average score
1.6195
Total score value
139.2759
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
8 F A 3.3959
9 F A 3.3141
10 A A 2.3761
11 F A 2.8611
12 N A 0.9259
13 S A 1.1175
14 L A 1.5682
15 Q A -0.2975
16 A A -0.0625
17 S A 0.2862
18 A A 0.5355
19 T A 0.4747
20 E A 0.1479
21 Y A 2.0822
22 I A 2.9316
23 G A 1.8396
24 Y A 2.9336
25 A A 2.9038
26 W A 3.7730
27 A A 3.4740
28 M A 3.9955
29 V A 4.3244
30 V A 4.1146
31 V A 4.2303
32 I A 4.2850
33 V A 3.5903
34 G A 2.3132
35 A A 2.1046
36 T A 2.2076
37 I A 1.7739
38 G A 1.3499
39 I A 1.8311
40 K A -0.0828
41 L A 1.4869
42 F A 1.5262
43 K A -0.9016
44 K A -1.2459
45 F A 0.7674
46 T A -0.4631
47 S A -1.0585
48 K A -1.6712
49 A A -0.7806
50 S A -0.4733
8 F B 3.3997
9 F B 3.3045
10 A B 2.3451
11 F B 2.8358
12 N B 0.8633
13 S B 1.0416
14 L B 1.4831
15 Q B -0.5726
16 A B -0.2145
17 S B 0.1281
18 A B 0.3110
19 T B 0.1901
20 E B -0.1286
21 Y B 1.8655
22 I B 2.3231
23 G B 1.4599
24 Y B 2.7361
25 A B 2.7072
26 W B 3.7344
27 A B 3.5711
28 M B 4.0732
29 V B 4.5057
30 V B 4.7656
31 V B 4.5292
32 I B 4.4388
33 V B 3.7162
34 G B 2.3987
35 A B 2.0995
36 T B 2.2144
37 I B 1.7206
38 G B 1.3263
39 I B 1.7119
40 K B 0.1576
41 L B 1.6925
42 F B 1.9107
43 K B -0.7441
44 K B -1.0967
45 F B 0.9178
46 T B -0.3416
47 S B -1.0147
48 K B -1.6321
49 A B -0.7874
50 S B -0.4749
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 partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 2.5852 7.7967 View CSV PDB
4.5 2.5692 7.7967 View CSV PDB
5.0 2.5532 7.7967 View CSV PDB
5.5 2.5539 7.7967 View CSV PDB
6.0 2.5944 7.7967 View CSV PDB
6.5 2.6885 7.7967 View CSV PDB
7.0 2.8272 7.7967 View CSV PDB
7.5 2.991 7.7967 View CSV PDB
8.0 3.165 7.7967 View CSV PDB
8.5 3.3418 7.7967 View CSV PDB
9.0 3.5173 7.7967 View CSV PDB