Project name: test

Status: done

Started: 2024-06-25 13:25:30
Settings
Chain sequence(s) A: GSAPIPDLKVFEEREGVQQLNLSFIRPPENPALLLITITATNFSEGDVTHFICQAAVPKSLQLQLQAPSGNTVPARGGLPITQLFFRRRILNPNKAPLRLKLRLTYDHFHQQSSVQEIFEVNNLPVESWQ
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:00:47)
[INFO]       Auto_mut: Residue number 739 from chain A and a score of 1.090 (leucine) selected for 
                       automated muatation                                                         (00:00:48)
[INFO]       Auto_mut: Residue number 740 from chain A and a score of 0.338 (proline) selected for 
                       automated muatation                                                         (00:00:48)
[INFO]       Auto_mut: Residue number 695 from chain A and a score of 0.294 (leucine) selected for 
                       automated muatation                                                         (00:00:48)
[INFO]       Auto_mut: Residue number 685 from chain A and a score of 0.221 (isoleucine) selected  
                       for automated muatation                                                     (00:00:48)
[INFO]       Auto_mut: Residue number 712 from chain A and a score of 0.156 (isoleucine) selected  
                       for automated muatation                                                     (00:00:48)
[INFO]       Auto_mut: Residue number 773 from chain A and a score of 0.021 (isoleucine) selected  
                       for automated muatation                                                     (00:00:48)
[INFO]       Auto_mut: Mutating residue number 739 from chain A (leucine) into glutamic acid       (00:00:48)
[INFO]       Auto_mut: Mutating residue number 739 from chain A (leucine) into aspartic acid       (00:00:48)
[INFO]       Auto_mut: Mutating residue number 740 from chain A (proline) into glutamic acid       (00:00:48)
[INFO]       Auto_mut: Mutating residue number 739 from chain A (leucine) into arginine            (00:01:13)
[INFO]       Auto_mut: Mutating residue number 740 from chain A (proline) into lysine              (00:01:14)
[INFO]       Auto_mut: Mutating residue number 739 from chain A (leucine) into lysine              (00:01:15)
[INFO]       Auto_mut: Mutating residue number 740 from chain A (proline) into aspartic acid       (00:01:45)
[INFO]       Auto_mut: Mutating residue number 695 from chain A (leucine) into glutamic acid       (00:01:50)
[INFO]       Auto_mut: Mutating residue number 695 from chain A (leucine) into aspartic acid       (00:01:50)
[INFO]       Auto_mut: Mutating residue number 740 from chain A (proline) into arginine            (00:02:12)
[INFO]       Auto_mut: Mutating residue number 695 from chain A (leucine) into arginine            (00:02:17)
[INFO]       Auto_mut: Mutating residue number 695 from chain A (leucine) into lysine              (00:02:17)
[INFO]       Auto_mut: Mutating residue number 685 from chain A (isoleucine) into glutamic acid    (00:02:42)
[INFO]       Auto_mut: Mutating residue number 685 from chain A (isoleucine) into aspartic acid    (00:02:49)
[INFO]       Auto_mut: Mutating residue number 712 from chain A (isoleucine) into glutamic acid    (00:02:50)
[INFO]       Auto_mut: Mutating residue number 685 from chain A (isoleucine) into lysine           (00:03:10)
[INFO]       Auto_mut: Mutating residue number 685 from chain A (isoleucine) into arginine         (00:03:14)
[INFO]       Auto_mut: Mutating residue number 712 from chain A (isoleucine) into lysine           (00:03:23)
[INFO]       Auto_mut: Mutating residue number 712 from chain A (isoleucine) into aspartic acid    (00:03:47)
[INFO]       Auto_mut: Mutating residue number 773 from chain A (isoleucine) into glutamic acid    (00:03:50)
[INFO]       Auto_mut: Mutating residue number 773 from chain A (isoleucine) into aspartic acid    (00:04:14)
[INFO]       Auto_mut: Mutating residue number 712 from chain A (isoleucine) into arginine         (00:04:18)
[INFO]       Auto_mut: Mutating residue number 773 from chain A (isoleucine) into lysine           (00:04:21)
[INFO]       Auto_mut: Mutating residue number 773 from chain A (isoleucine) into arginine         (00:04:44)
[INFO]       Auto_mut: Effect of mutation residue number 739 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.6011 kcal/mol, Difference in average score from 
                       the base case: -0.0928                                                      (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 739 from chain A (leucine) into lysine:   
                       Energy difference: -0.3390 kcal/mol, Difference in average score from the   
                       base case: -0.0903                                                          (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 739 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.1650 kcal/mol, Difference in average score from  
                       the base case: -0.0932                                                      (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 739 from chain A (leucine) into arginine: 
                       Energy difference: -0.0842 kcal/mol, Difference in average score from the   
                       base case: -0.0913                                                          (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 740 from chain A (proline) into glutamic  
                       acid: Energy difference: 0.7800 kcal/mol, Difference in average score from  
                       the base case: -0.0502                                                      (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 740 from chain A (proline) into lysine:   
                       Energy difference: 0.7603 kcal/mol, Difference in average score from the    
                       base case: -0.0492                                                          (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 740 from chain A (proline) into aspartic  
                       acid: Energy difference: 2.2143 kcal/mol, Difference in average score from  
                       the base case: -0.0339                                                      (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 740 from chain A (proline) into arginine: 
                       Energy difference: 0.7514 kcal/mol, Difference in average score from the    
                       base case: -0.0595                                                          (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 695 from chain A (leucine) into glutamic  
                       acid: Energy difference: 2.0599 kcal/mol, Difference in average score from  
                       the base case: -0.0164                                                      (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 695 from chain A (leucine) into lysine:   
                       Energy difference: 1.0576 kcal/mol, Difference in average score from the    
                       base case: -0.0184                                                          (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 695 from chain A (leucine) into aspartic  
                       acid: Energy difference: 3.4418 kcal/mol, Difference in average score from  
                       the base case: -0.0041                                                      (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 695 from chain A (leucine) into arginine: 
                       Energy difference: 2.0008 kcal/mol, Difference in average score from the    
                       base case: -0.0266                                                          (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 685 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.8853 kcal/mol, Difference in average    
                       score from the base case: -0.0614                                           (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 685 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.1680 kcal/mol, Difference in average score     
                       from the base case: -0.0610                                                 (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 685 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.8204 kcal/mol, Difference in average    
                       score from the base case: -0.0644                                           (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 685 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.5742 kcal/mol, Difference in average score   
                       from the base case: -0.0807                                                 (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 712 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.9113 kcal/mol, Difference in average    
                       score from the base case: -0.0687                                           (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 712 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.5435 kcal/mol, Difference in average score     
                       from the base case: -0.0621                                                 (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 712 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.4516 kcal/mol, Difference in average    
                       score from the base case: -0.0609                                           (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 712 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.2084 kcal/mol, Difference in average score   
                       from the base case: -0.0684                                                 (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 773 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.7810 kcal/mol, Difference in average    
                       score from the base case: -0.0779                                           (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 773 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.8057 kcal/mol, Difference in average score     
                       from the base case: -0.0948                                                 (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 773 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.6986 kcal/mol, Difference in average    
                       score from the base case: -0.1060                                           (00:05:26)
[INFO]       Auto_mut: Effect of mutation residue number 773 from chain A (isoleucine) into        
                       arginine: Energy difference: 1.1454 kcal/mol, Difference in average score   
                       from the base case: -0.0823                                                 (00:05:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:29)
Show buried residues
Minimal score value
-3.6318
Maximal score value
1.0897
Average score
-0.9088
Total score value
-111.7764
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
663 G A -0.7948
664 S A -0.5677
665 A A -0.4282
666 P A -0.6777
667 I A 0.0000
668 P A -1.3991
669 D A -2.1854
670 L A -1.8993
671 K A -2.4942
672 V A -1.6406
673 F A 0.0000
674 E A -3.4381
675 R A -3.6318
676 E A -3.0211
677 G A -1.9876
678 V A 0.0000
679 Q A -1.7499
680 L A 0.0000
681 N A -1.5274
682 L A 0.0000
683 S A -0.7853
684 F A 0.0000
685 I A 0.2206
686 R A -0.6482
687 P A -1.0020
688 P A -1.5499
689 E A -2.4991
690 N A -1.9335
691 P A -1.5693
692 A A -1.2992
693 L A 0.0000
694 L A 0.0000
695 L A 0.2942
696 I A 0.0000
697 T A -0.1466
698 I A 0.0000
699 T A -0.3695
700 A A 0.0000
701 T A -0.0714
702 N A 0.0000
703 F A -0.2284
704 S A 0.0000
705 E A -2.5296
706 G A -2.0276
707 D A -2.3285
708 V A 0.0000
709 T A -1.3444
710 H A -1.2400
711 F A 0.0000
712 I A 0.1562
713 C A 0.0000
714 Q A -0.7029
715 A A -0.6136
716 A A -1.3380
717 V A -1.2882
718 P A -1.6008
719 K A -1.9904
720 S A -1.7233
721 L A 0.0000
722 Q A -1.6634
723 L A -0.7831
724 Q A -1.0042
725 L A -0.2232
726 Q A -0.8897
727 A A -0.4055
728 P A -0.3144
729 S A -0.4796
730 G A -0.6075
731 N A -1.2645
732 T A -0.9622
733 V A 0.0000
734 P A -1.0741
735 A A -1.7219
736 R A -1.9820
737 G A -0.7452
738 G A -0.0692
739 L A 1.0897
740 P A 0.3380
741 I A 0.0000
742 T A -0.1741
743 Q A 0.0000
744 L A -0.0304
745 F A 0.0000
746 R A -0.6997
747 I A 0.0000
748 L A -0.8506
749 N A 0.0000
750 P A -1.7157
751 N A -2.3444
752 K A -2.7353
753 A A -2.0127
754 P A -1.2693
755 L A 0.0000
756 R A -2.5961
757 L A 0.0000
758 K A -2.0395
759 L A 0.0000
760 R A -1.0647
761 L A 0.0000
762 T A -0.7039
763 Y A 0.0000
764 D A -1.5665
765 H A 0.0000
766 F A -0.9276
767 H A -1.4626
768 Q A -1.6020
769 S A -1.3955
770 V A 0.0000
771 Q A -1.4596
772 E A -0.8908
773 I A 0.0214
774 F A -0.3808
775 E A -2.0638
776 V A 0.0000
777 N A -2.4498
778 N A -2.0574
779 L A -1.2691
780 P A -0.7531
781 V A -0.0483
782 E A -1.3055
783 S A 0.0000
784 W A -1.5152
785 Q A -2.0502
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
LE739A -0.6011 -0.0928 View CSV PDB
LK739A -0.339 -0.0903 View CSV PDB
IK685A 0.168 -0.061 View CSV PDB
IR712A 0.2084 -0.0684 View CSV PDB
IR685A 0.5742 -0.0807 View CSV PDB
IK773A 0.8057 -0.0948 View CSV PDB
IK712A 0.5435 -0.0621 View CSV PDB
IE773A 0.781 -0.0779 View CSV PDB
PR740A 0.7514 -0.0595 View CSV PDB
PK740A 0.7603 -0.0492 View CSV PDB
LK695A 1.0576 -0.0184 View CSV PDB
LR695A 2.0008 -0.0266 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018