Project name: 4bcx

Status: done

Started: 2024-06-25 13:28:01
Settings
Chain sequence(s) A: PIPDLKVFEREGVQLNLSFIRPPENPALLLITITATNFSEGDVTHFICQAAVPKSLQLQLQAPSGNTVPARGGLPITQLFRRILNPNKAPLRLKLRLTYDHFHQSVQEIFEVNNLPVESWQ
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                                          (00:00:41)
[INFO]       Auto_mut: Residue number 739 from chain A and a score of 1.087 (leucine) selected for 
                       automated muatation                                                         (00:00:42)
[INFO]       Auto_mut: Residue number 685 from chain A and a score of 0.598 (isoleucine) selected  
                       for automated muatation                                                     (00:00:42)
[INFO]       Auto_mut: Residue number 740 from chain A and a score of 0.344 (proline) selected for 
                       automated muatation                                                         (00:00:42)
[INFO]       Auto_mut: Residue number 695 from chain A and a score of 0.273 (leucine) selected for 
                       automated muatation                                                         (00:00:42)
[INFO]       Auto_mut: Residue number 773 from chain A and a score of 0.213 (isoleucine) selected  
                       for automated muatation                                                     (00:00:42)
[INFO]       Auto_mut: Residue number 781 from chain A and a score of 0.030 (valine) selected for  
                       automated muatation                                                         (00:00:42)
[INFO]       Auto_mut: Mutating residue number 739 from chain A (leucine) into glutamic acid       (00:00:42)
[INFO]       Auto_mut: Mutating residue number 739 from chain A (leucine) into aspartic acid       (00:00:42)
[INFO]       Auto_mut: Mutating residue number 685 from chain A (isoleucine) into glutamic acid    (00:00:42)
[INFO]       Auto_mut: Mutating residue number 739 from chain A (leucine) into arginine            (00:01:11)
[INFO]       Auto_mut: Mutating residue number 739 from chain A (leucine) into lysine              (00:01:13)
[INFO]       Auto_mut: Mutating residue number 685 from chain A (isoleucine) into lysine           (00:01:13)
[INFO]       Auto_mut: Mutating residue number 685 from chain A (isoleucine) into aspartic acid    (00:01:47)
[INFO]       Auto_mut: Mutating residue number 740 from chain A (proline) into glutamic acid       (00:01:49)
[INFO]       Auto_mut: Mutating residue number 740 from chain A (proline) into aspartic acid       (00:01:51)
[INFO]       Auto_mut: Mutating residue number 685 from chain A (isoleucine) into arginine         (00:02:15)
[INFO]       Auto_mut: Mutating residue number 740 from chain A (proline) into lysine              (00:02:18)
[INFO]       Auto_mut: Mutating residue number 740 from chain A (proline) into arginine            (00:02:20)
[INFO]       Auto_mut: Mutating residue number 695 from chain A (leucine) into glutamic acid       (00:02:47)
[INFO]       Auto_mut: Mutating residue number 695 from chain A (leucine) into aspartic acid       (00:02:48)
[INFO]       Auto_mut: Mutating residue number 773 from chain A (isoleucine) into glutamic acid    (00:02:49)
[INFO]       Auto_mut: Mutating residue number 695 from chain A (leucine) into arginine            (00:03:15)
[INFO]       Auto_mut: Mutating residue number 695 from chain A (leucine) into lysine              (00:03:17)
[INFO]       Auto_mut: Mutating residue number 773 from chain A (isoleucine) into lysine           (00:03:24)
[INFO]       Auto_mut: Mutating residue number 773 from chain A (isoleucine) into aspartic acid    (00:03:45)
[INFO]       Auto_mut: Mutating residue number 781 from chain A (valine) into glutamic acid        (00:03:49)
[INFO]       Auto_mut: Mutating residue number 781 from chain A (valine) into aspartic acid        (00:04:06)
[INFO]       Auto_mut: Mutating residue number 773 from chain A (isoleucine) into arginine         (00:04:19)
[INFO]       Auto_mut: Mutating residue number 781 from chain A (valine) into lysine               (00:04:20)
[INFO]       Auto_mut: Mutating residue number 781 from chain A (valine) into arginine             (00:04:34)
[INFO]       Auto_mut: Effect of mutation residue number 739 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.5612 kcal/mol, Difference in average score from 
                       the base case: -0.1302                                                      (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 739 from chain A (leucine) into lysine:   
                       Energy difference: -0.0765 kcal/mol, Difference in average score from the   
                       base case: -0.1265                                                          (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 739 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.2481 kcal/mol, Difference in average score from  
                       the base case: -0.1303                                                      (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 739 from chain A (leucine) into arginine: 
                       Energy difference: -0.1118 kcal/mol, Difference in average score from the   
                       base case: -0.1294                                                          (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 685 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.6871 kcal/mol, Difference in average    
                       score from the base case: -0.1164                                           (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 685 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.0226 kcal/mol, Difference in average score    
                       from the base case: -0.1094                                                 (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 685 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.3551 kcal/mol, Difference in average    
                       score from the base case: -0.1268                                           (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 685 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.2492 kcal/mol, Difference in average score   
                       from the base case: -0.1118                                                 (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 740 from chain A (proline) into glutamic  
                       acid: Energy difference: 0.5579 kcal/mol, Difference in average score from  
                       the base case: -0.0728                                                      (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 740 from chain A (proline) into lysine:   
                       Energy difference: 0.7534 kcal/mol, Difference in average score from the    
                       base case: -0.0766                                                          (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 740 from chain A (proline) into aspartic  
                       acid: Energy difference: 2.1640 kcal/mol, Difference in average score from  
                       the base case: -0.0604                                                      (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 740 from chain A (proline) into arginine: 
                       Energy difference: 0.9854 kcal/mol, Difference in average score from the    
                       base case: -0.0848                                                          (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 695 from chain A (leucine) into glutamic  
                       acid: Energy difference: 2.2662 kcal/mol, Difference in average score from  
                       the base case: -0.0614                                                      (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 695 from chain A (leucine) into lysine:   
                       Energy difference: 1.3771 kcal/mol, Difference in average score from the    
                       base case: -0.0608                                                          (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 695 from chain A (leucine) into aspartic  
                       acid: Energy difference: 3.2906 kcal/mol, Difference in average score from  
                       the base case: -0.0397                                                      (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 695 from chain A (leucine) into arginine: 
                       Energy difference: 2.0387 kcal/mol, Difference in average score from the    
                       base case: -0.0624                                                          (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 773 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.0159 kcal/mol, Difference in average    
                       score from the base case: -0.1254                                           (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 773 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.6891 kcal/mol, Difference in average score     
                       from the base case: -0.1197                                                 (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 773 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.8376 kcal/mol, Difference in average    
                       score from the base case: -0.1683                                           (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 773 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.9684 kcal/mol, Difference in average score   
                       from the base case: -0.1140                                                 (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 781 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.5020 kcal/mol, Difference in average score from 
                       the base case: -0.1278                                                      (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 781 from chain A (valine) into lysine:    
                       Energy difference: -0.3038 kcal/mol, Difference in average score from the   
                       base case: -0.1272                                                          (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 781 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.5928 kcal/mol, Difference in average score from  
                       the base case: -0.1179                                                      (00:05:06)
[INFO]       Auto_mut: Effect of mutation residue number 781 from chain A (valine) into arginine:  
                       Energy difference: -0.1121 kcal/mol, Difference in average score from the   
                       base case: -0.1319                                                          (00:05:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:10)
Show buried residues
Minimal score value
-3.2892
Maximal score value
1.0874
Average score
-0.9019
Total score value
-108.2246
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
666 P A -0.4225
667 I A -0.3553
668 P A -0.9264
669 D A -1.9234
670 L A -1.7498
671 K A -2.2980
672 V A -1.6299
673 F A 0.0000
674 E A -3.2866
675 R A -3.2892
676 E A -2.9140
677 G A -1.7670
678 V A 0.0000
679 Q A -1.6989
680 L A 0.0000
681 N A -1.5126
682 L A 0.0000
683 S A -0.5465
684 F A 0.0000
685 I A 0.5978
686 R A -1.1075
687 P A -1.1020
688 P A -1.5566
689 E A -2.4921
690 N A -1.9535
691 P A -1.6994
692 A A -1.3995
693 L A 0.0000
694 L A 0.0000
695 L A 0.2734
696 I A 0.0000
697 T A -0.1047
698 I A 0.0000
699 T A -0.2378
700 A A 0.0000
701 T A -0.0308
702 N A 0.0000
703 F A -0.0853
704 S A -1.5067
705 E A -2.4595
706 G A -1.9184
707 D A -2.3031
708 V A 0.0000
709 T A -1.2332
710 H A -1.1692
711 F A 0.0000
712 I A -0.0193
713 C A 0.0000
714 Q A -0.7426
715 A A -0.7326
716 A A -1.1864
717 V A -1.2416
718 P A -1.5774
719 K A -1.9785
720 S A -1.7106
721 L A 0.0000
722 Q A -1.7417
723 L A -0.9804
724 Q A -1.2658
725 L A -0.2793
726 Q A -0.8909
727 A A -0.3837
728 P A -0.2661
729 S A -0.5695
730 G A -0.6391
731 N A -0.9467
732 T A -0.8277
733 V A 0.0000
734 P A -1.0544
735 A A -1.7046
736 R A -1.9647
737 G A -0.7801
738 G A -0.0822
739 L A 1.0874
740 P A 0.3445
741 I A 0.0000
742 T A -0.1507
743 Q A 0.0000
744 L A -0.1052
745 F A 0.0000
746 R A -1.0920
747 I A 0.0000
748 L A -0.9002
749 N A 0.0000
750 P A -1.6874
751 N A -2.3420
752 K A -2.7664
753 A A -2.0053
754 P A -1.3520
755 L A 0.0000
756 R A -2.5444
757 L A 0.0000
758 K A -1.9058
759 L A 0.0000
760 R A -1.0099
761 L A 0.0000
762 T A -0.7519
763 Y A 0.0000
764 D A -1.5396
765 H A 0.0000
766 F A -0.3684
767 H A -1.3580
768 Q A -1.6560
769 S A -1.4163
770 V A 0.0000
771 Q A -1.4572
772 E A -0.7391
773 I A 0.2129
774 F A -0.2846
775 E A -2.0074
776 V A 0.0000
777 N A -2.4566
778 N A -1.9139
779 L A -1.3195
780 P A -0.6410
781 V A 0.0304
782 E A -1.0946
783 S A 0.0000
784 W A -1.5735
785 Q A -2.0868
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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 -0.5612 -0.1302 View CSV PDB
VE781A -0.502 -0.1278 View CSV PDB
VK781A -0.3038 -0.1272 View CSV PDB
LR739A -0.1118 -0.1294 View CSV PDB
IK685A -0.0226 -0.1094 View CSV PDB
IR685A 0.2492 -0.1118 View CSV PDB
IK773A 0.6891 -0.1197 View CSV PDB
PE740A 0.5579 -0.0728 View CSV PDB
IE773A 1.0159 -0.1254 View CSV PDB
PK740A 0.7534 -0.0766 View CSV PDB
LK695A 1.3771 -0.0608 View CSV PDB
LR695A 2.0387 -0.0624 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018