Project name: des17_delL

Status: done

Started: 2026-03-04 02:22:57
Settings
Chain sequence(s) A: EVQLVESGGGLEQPGGSLRLSCAGSGFDLSKGAMTWVRQAPGKGLEWVSSITRSGKGTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCALTNSLTSSGIGIGSMYGWGQGTTVTVSSAS
B: DIVMTQSPLSLPVTPGEPASISSKTSDSYGNSYVGWYLQKSGQSPQLLIYRASIRAGGVPDRFSGSGSGTDFTLKISRVEAEDVGFYYVVDTKTYPIGFGQGTKLEIKRTV
input PDB
Selected Chain(s) A,B
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]                                                (00:00:01)
[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 all chain(s) selected           (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:28)
[INFO]       Auto_mut: Residue number 111 from chain B and a score of 1.116 (valine) selected for  
                       automated muatation                                                         (00:02:30)
[INFO]       Auto_mut: Residue number 3 from chain B and a score of 0.943 (valine) selected for    
                       automated muatation                                                         (00:02:30)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 0.657 (leucine) selected for  
                       automated muatation                                                         (00:02:30)
[INFO]       Auto_mut: Residue number 29 from chain B and a score of 0.616 (tyrosine) selected for 
                       automated muatation                                                         (00:02:30)
[INFO]       Auto_mut: Residue number 107 from chain A and a score of 0.525 omitted from automated 
                       muatation (excluded by the user).                                           (00:02:30)
[INFO]       Auto_mut: Residue number 113 from chain A and a score of 0.512 omitted from automated 
                       muatation (excluded by the user).                                           (00:02:30)
[INFO]       Auto_mut: Residue number 9 from chain B and a score of 0.487 (leucine) selected for   
                       automated muatation                                                         (00:02:30)
[INFO]       Auto_mut: Residue number 5 from chain A and a score of 0.452 (valine) selected for    
                       automated muatation                                                         (00:02:30)
[INFO]       Auto_mut: Mutating residue number 111 from chain B (valine) into glutamic acid        (00:02:30)
[INFO]       Auto_mut: Mutating residue number 111 from chain B (valine) into aspartic acid        (00:02:30)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into glutamic acid          (00:02:30)
[INFO]       Auto_mut: Mutating residue number 111 from chain B (valine) into arginine             (00:03:52)
[INFO]       Auto_mut: Mutating residue number 111 from chain B (valine) into lysine               (00:03:55)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into lysine                 (00:03:56)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into aspartic acid          (00:05:14)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into glutamic acid        (00:05:15)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into aspartic acid        (00:05:50)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into lysine               (00:06:34)
[INFO]       Auto_mut: Mutating residue number 3 from chain B (valine) into arginine               (00:06:34)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (leucine) into arginine             (00:07:07)
[INFO]       Auto_mut: Mutating residue number 29 from chain B (tyrosine) into glutamic acid       (00:08:08)
[INFO]       Auto_mut: Mutating residue number 29 from chain B (tyrosine) into aspartic acid       (00:08:21)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (leucine) into glutamic acid         (00:08:32)
[INFO]       Auto_mut: Mutating residue number 29 from chain B (tyrosine) into lysine              (00:09:29)
[INFO]       Auto_mut: Mutating residue number 29 from chain B (tyrosine) into arginine            (00:09:37)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (leucine) into lysine                (00:10:08)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (leucine) into aspartic acid         (00:11:03)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into glutamic acid          (00:11:20)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into aspartic acid          (00:11:49)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (leucine) into arginine              (00:12:24)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into lysine                 (00:12:49)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into arginine               (00:13:07)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain B (valine) into glutamic   
                       acid: Energy difference: -0.2020 kcal/mol, Difference in average score from 
                       the base case: -0.0210                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain B (valine) into lysine:    
                       Energy difference: -0.1592 kcal/mol, Difference in average score from the   
                       base case: -0.0201                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain B (valine) into aspartic   
                       acid: Energy difference: -0.1212 kcal/mol, Difference in average score from 
                       the base case: -0.0198                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain B (valine) into arginine:  
                       Energy difference: -0.9006 kcal/mol, Difference in average score from the   
                       base case: -0.0212                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into glutamic     
                       acid: Energy difference: 0.0616 kcal/mol, Difference in average score from  
                       the base case: -0.0409                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into lysine:      
                       Energy difference: -0.3662 kcal/mol, Difference in average score from the   
                       base case: -0.0405                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into aspartic     
                       acid: Energy difference: 0.4104 kcal/mol, Difference in average score from  
                       the base case: -0.0413                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain B (valine) into arginine:    
                       Energy difference: -0.5036 kcal/mol, Difference in average score from the   
                       base case: -0.0405                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.8728 kcal/mol, Difference in average score from  
                       the base case: -0.0490                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into lysine:    
                       Energy difference: 0.1828 kcal/mol, Difference in average score from the    
                       base case: -0.0468                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into aspartic   
                       acid: Energy difference: 1.1071 kcal/mol, Difference in average score from  
                       the base case: -0.0495                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into arginine:  
                       Energy difference: -0.1871 kcal/mol, Difference in average score from the   
                       base case: -0.0497                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain B (tyrosine) into glutamic  
                       acid: Energy difference: 0.4392 kcal/mol, Difference in average score from  
                       the base case: -0.0452                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain B (tyrosine) into lysine:   
                       Energy difference: -0.3462 kcal/mol, Difference in average score from the   
                       base case: -0.0336                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain B (tyrosine) into aspartic  
                       acid: Energy difference: 0.6705 kcal/mol, Difference in average score from  
                       the base case: -0.0434                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain B (tyrosine) into arginine: 
                       Energy difference: -0.6421 kcal/mol, Difference in average score from the   
                       base case: -0.0374                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (leucine) into glutamic    
                       acid: Energy difference: -0.1069 kcal/mol, Difference in average score from 
                       the base case: -0.0379                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (leucine) into lysine:     
                       Energy difference: -0.2664 kcal/mol, Difference in average score from the   
                       base case: -0.0262                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (leucine) into aspartic    
                       acid: Energy difference: -0.0077 kcal/mol, Difference in average score from 
                       the base case: -0.0343                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (leucine) into arginine:   
                       Energy difference: 0.1336 kcal/mol, Difference in average score from the    
                       base case: -0.0277                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into glutamic     
                       acid: Energy difference: 0.6100 kcal/mol, Difference in average score from  
                       the base case: -0.0224                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into lysine:      
                       Energy difference: -0.3523 kcal/mol, Difference in average score from the   
                       base case: -0.0260                                                          (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into aspartic     
                       acid: Energy difference: 0.8583 kcal/mol, Difference in average score from  
                       the base case: -0.0256                                                      (00:14:43)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into arginine:    
                       Energy difference: -0.3326 kcal/mol, Difference in average score from the   
                       base case: -0.0274                                                          (00:14:43)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:49)
Show buried residues
Minimal score value
-3.4884
Maximal score value
1.1157
Average score
-0.6983
Total score value
-166.1997
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 E A -1.7831
2 V A -0.7305
3 Q A -1.2037
4 L A 0.0000
5 V A 0.4523
6 E A 0.0000
7 S A -0.5158
8 G A -0.8821
9 G A -0.4936
10 G A 0.0350
11 L A 0.6571
12 E A -0.6952
13 Q A -1.6362
14 P A -1.7034
15 G A -1.4801
16 G A -1.0899
17 S A -1.2056
18 L A -1.0749
19 R A -2.1384
20 L A 0.0000
21 S A -0.4459
22 C A 0.0000
23 A A -0.2713
24 G A -0.6255
25 S A -0.8185
26 G A -1.2178
27 F A -1.1483
28 D A -1.8905
29 L A 0.0000
30 S A -2.2088
31 K A -2.5758
32 G A 0.0000
33 A A 0.0000
34 M A 0.0000
35 T A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A 0.0000
39 Q A -0.8468
40 A A -1.2414
41 P A -1.0102
42 G A -1.4820
43 K A -2.3742
44 G A -1.4855
45 L A 0.0000
46 E A -1.1232
47 W A 0.0000
48 V A 0.0000
49 S A 0.0000
50 S A 0.0000
51 I A 0.0000
52 T A -1.5532
53 R A -2.4141
54 S A -1.8863
55 G A -1.7280
56 K A -2.1078
57 G A -1.1314
58 T A -0.4745
59 Y A -0.0733
60 Y A -0.6376
61 A A 0.0000
62 D A -2.3674
63 S A -1.6929
64 V A 0.0000
65 K A -2.4439
66 G A -1.6553
67 R A 0.0000
68 F A 0.0000
69 T A -0.7626
70 I A 0.0000
71 S A -0.6774
72 R A -1.3401
73 D A -1.5739
74 N A -2.2163
75 S A -1.6897
76 K A -2.4069
77 N A -1.9756
78 T A 0.0000
79 L A 0.0000
80 Y A -0.5767
81 L A 0.0000
82 Q A -1.2619
83 M A 0.0000
84 N A -1.4191
85 S A -1.2106
86 L A 0.0000
87 R A -2.2799
88 A A -1.7760
89 E A -2.2032
90 D A 0.0000
91 T A -0.7185
92 A A 0.0000
93 V A 0.1243
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 L A 0.0000
99 T A 0.0000
100 N A -0.9728
101 S A -0.8606
102 L A -0.2108
103 T A -0.2124
104 S A -0.2405
105 S A -0.3415
106 G A -0.0795
107 I A 0.5246
108 G A 0.0000
109 I A 0.0000
110 G A 0.0000
111 S A 0.0000
112 M A 0.0000
113 Y A 0.5118
114 G A -0.0709
115 W A -0.2503
116 G A 0.0000
117 Q A -1.3457
118 G A 0.0000
119 T A -0.2068
120 T A -0.0243
121 V A 0.0000
122 T A -0.2375
123 V A 0.0000
124 S A -0.9206
125 S A -0.6863
126 A A -0.2805
127 S A -0.2491
1 D B -1.2706
2 I B 0.0237
3 V B 0.9430
4 M B 0.0000
5 T B -0.4919
6 Q B 0.0000
7 S B -0.3901
8 P B -0.0193
9 L B 0.4873
10 S B -0.0698
11 L B -0.2304
12 P B -1.1512
13 V B 0.0000
14 T B -2.2070
15 P B -2.4175
16 G B -2.3529
17 E B -2.9721
18 P B -2.4025
19 A B 0.0000
20 S B -0.7173
21 I B 0.0000
22 S B -0.9470
23 S B 0.0000
24 K B -2.0743
25 T B 0.0000
26 S B -0.3504
27 D B -0.5518
28 S B -0.1394
29 Y B 0.6160
30 G B -0.5849
31 N B -1.1525
32 S B -1.1113
33 Y B -0.8953
34 V B 0.0000
35 G B 0.0000
36 W B 0.0000
37 Y B 0.0000
38 L B 0.0000
39 Q B 0.0000
40 K B -1.3988
41 S B -0.9165
42 G B -1.4793
43 Q B -2.0898
44 S B -1.4184
45 P B 0.0000
46 Q B -0.9603
47 L B 0.0000
48 L B 0.0000
49 I B 0.0000
50 Y B -0.4320
51 R B -1.6578
52 A B -1.0883
53 S B -0.6366
54 I B -0.1000
55 R B -1.0958
56 A B -0.8071
57 G B -0.8597
58 G B -1.0741
59 V B 0.0000
60 P B -1.4113
61 D B -2.4648
62 R B -2.2057
63 F B 0.0000
64 S B -1.1072
65 G B -0.8437
66 S B -1.0130
67 G B -1.4184
68 S B -1.3231
69 G B -1.1452
70 T B -1.5503
71 D B -2.2797
72 F B 0.0000
73 T B -1.1555
74 L B 0.0000
75 K B -1.7162
76 I B 0.0000
77 S B -2.4062
78 R B -3.4884
79 V B 0.0000
80 E B -2.4196
81 A B -1.5964
82 E B -2.0662
83 D B 0.0000
84 V B -0.4822
85 G B 0.0000
86 F B 0.2954
87 Y B 0.0000
88 Y B 0.0000
89 V B 0.0000
90 V B 0.0000
91 D B 0.0000
92 T B 0.0000
93 K B -0.5720
94 T B -0.1786
95 Y B -0.1926
96 P B -0.3715
97 I B 0.0000
98 G B -0.0880
99 F B 0.0277
100 G B 0.0000
101 Q B -1.0994
102 G B 0.0000
103 T B 0.0000
104 K B -0.4461
105 L B 0.0000
106 E B -1.3619
107 I B -1.4173
108 K B -2.2204
109 R B -2.1907
110 T B -0.4256
111 V B 1.1157
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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
YR29B -0.6421 -0.0374 View CSV PDB
VR3B -0.5036 -0.0405 View CSV PDB
VK3B -0.3662 -0.0405 View CSV PDB
LR11A -0.1871 -0.0497 View CSV PDB
VR111B -0.9006 -0.0212 View CSV PDB
YK29B -0.3462 -0.0336 View CSV PDB
LE9B -0.1069 -0.0379 View CSV PDB
VR5A -0.3326 -0.0274 View CSV PDB
VK5A -0.3523 -0.026 View CSV PDB
LK9B -0.2664 -0.0262 View CSV PDB
VE111B -0.202 -0.021 View CSV PDB
LK11A 0.1828 -0.0468 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018