Project name: 7aml

Status: done

Started: 2025-03-04 12:53:25
Chain sequence(s) A: KAGHGTCYCFEGKCFCERDEP
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                                          (00:00:14)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/a99272c63779c2b/tmp/folded.pdb                (00:00:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:34)
Show buried residues
Minimal score value
-4.3917
Maximal score value
2.1844
Average score
-1.0047
Total score value
-21.0984
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 K A -1.9420
2 A A -1.1927
3 G A -1.8906
4 H A -2.5968
5 G A -2.7090
6 T A -0.7904
7 C A 1.3089
8 Y A 2.1844
9 C A 1.9346
10 F A 1.3655
11 E A -1.2960
12 G A -1.0163
13 K A -1.0602
14 C A 1.3512
15 F A 1.9387
16 C A 0.3547
17 E A -2.7948
18 R A -4.3917
19 D A -4.2758
20 E A -3.7861
21 P A -1.7940
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 0.5145 4.9937 View CSV PDB
4.5 0.3477 4.9274 View CSV PDB
5.0 0.1414 4.8349 View CSV PDB
5.5 -0.0627 4.739 View CSV PDB
6.0 -0.2225 4.6708 View CSV PDB
6.5 -0.3101 4.6641 View CSV PDB
7.0 -0.3288 4.7305 View CSV PDB
7.5 -0.3062 4.8487 View CSV PDB
8.0 -0.2647 4.9911 View CSV PDB
8.5 -0.2106 5.1421 View CSV PDB
9.0 -0.142 5.2947 View CSV PDB