Project name: BLG

Status: done

Started: 2024-01-23 09:09:31
Settings
Chain sequence(s) A: IVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI
input PDB
Selected Chain(s) A
Distance of aggregation 5 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                                          (00:01:45)
[INFO]       Auto_mut: Residue number 162 from chain A and a score of 2.013 (isoleucine) selected  
                       for automated muatation                                                     (00:01:46)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 1.920 (isoleucine) selected    
                       for automated muatation                                                     (00:01:46)
[INFO]       Auto_mut: Residue number 29 from chain A and a score of 1.381 (isoleucine) selected   
                       for automated muatation                                                     (00:01:46)
[INFO]       Auto_mut: Residue number 87 from chain A and a score of 1.338 (leucine) selected for  
                       automated muatation                                                         (00:01:46)
[INFO]       Auto_mut: Residue number 128 from chain A and a score of 1.183 (valine) selected for  
                       automated muatation                                                         (00:01:46)
[INFO]       Auto_mut: Residue number 72 from chain A and a score of 0.518 (isoleucine) selected   
                       for automated muatation                                                     (00:01:46)
[INFO]       Auto_mut: Mutating residue number 162 from chain A (isoleucine) into glutamic acid    (00:01:46)
[INFO]       Auto_mut: Mutating residue number 162 from chain A (isoleucine) into aspartic acid    (00:01:46)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (isoleucine) into glutamic acid      (00:01:46)
[INFO]       Auto_mut: Mutating residue number 162 from chain A (isoleucine) into arginine         (00:02:48)
[INFO]       Auto_mut: Mutating residue number 162 from chain A (isoleucine) into lysine           (00:02:50)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (isoleucine) into lysine             (00:02:51)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (isoleucine) into aspartic acid      (00:03:53)
[INFO]       Auto_mut: Mutating residue number 29 from chain A (isoleucine) into glutamic acid     (00:03:57)
[INFO]       Auto_mut: Mutating residue number 29 from chain A (isoleucine) into aspartic acid     (00:03:59)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (isoleucine) into arginine           (00:04:56)
[INFO]       Auto_mut: Mutating residue number 29 from chain A (isoleucine) into lysine            (00:05:01)
[INFO]       Auto_mut: Mutating residue number 29 from chain A (isoleucine) into arginine          (00:05:03)
[INFO]       Auto_mut: Mutating residue number 87 from chain A (leucine) into glutamic acid        (00:06:01)
[INFO]       Auto_mut: Mutating residue number 87 from chain A (leucine) into aspartic acid        (00:06:09)
[INFO]       Auto_mut: Mutating residue number 128 from chain A (valine) into glutamic acid        (00:06:11)
[INFO]       Auto_mut: Mutating residue number 87 from chain A (leucine) into lysine               (00:07:06)
[INFO]       Auto_mut: Mutating residue number 87 from chain A (leucine) into arginine             (00:07:11)
[INFO]       Auto_mut: Mutating residue number 128 from chain A (valine) into lysine               (00:07:17)
[INFO]       Auto_mut: Mutating residue number 128 from chain A (valine) into aspartic acid        (00:08:05)
[INFO]       Auto_mut: Mutating residue number 72 from chain A (isoleucine) into glutamic acid     (00:08:16)
[INFO]       Auto_mut: Mutating residue number 72 from chain A (isoleucine) into aspartic acid     (00:08:26)
[INFO]       Auto_mut: Mutating residue number 128 from chain A (valine) into arginine             (00:09:08)
[INFO]       Auto_mut: Mutating residue number 72 from chain A (isoleucine) into lysine            (00:09:14)
[INFO]       Auto_mut: Mutating residue number 72 from chain A (isoleucine) into arginine          (00:09:19)
[INFO]       Auto_mut: Effect of mutation residue number 162 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.0045 kcal/mol, Difference in average   
                       score from the base case: -0.0267                                           (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 162 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.5382 kcal/mol, Difference in average score    
                       from the base case: -0.0252                                                 (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 162 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.2663 kcal/mol, Difference in average    
                       score from the base case: -0.0270                                           (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 162 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.7244 kcal/mol, Difference in average score  
                       from the base case: -0.0236                                                 (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (isoleucine) into glutamic 
                       acid: Energy difference: 0.7879 kcal/mol, Difference in average score from  
                       the base case: -0.0199                                                      (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (isoleucine) into lysine:  
                       Energy difference: -0.0990 kcal/mol, Difference in average score from the   
                       base case: -0.0185                                                          (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (isoleucine) into aspartic 
                       acid: Energy difference: 1.3363 kcal/mol, Difference in average score from  
                       the base case: -0.0191                                                      (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (isoleucine) into          
                       arginine: Energy difference: -0.0456 kcal/mol, Difference in average score  
                       from the base case: -0.0178                                                 (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.4057 kcal/mol, Difference in average    
                       score from the base case: -0.0263                                           (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.5511 kcal/mol, Difference in average score from the   
                       base case: -0.0268                                                          (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.3269 kcal/mol, Difference in average    
                       score from the base case: -0.0266                                           (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.6681 kcal/mol, Difference in average score  
                       from the base case: -0.0278                                                 (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 87 from chain A (leucine) into glutamic   
                       acid: Energy difference: -0.1560 kcal/mol, Difference in average score from 
                       the base case: -0.0249                                                      (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 87 from chain A (leucine) into lysine:    
                       Energy difference: -0.0848 kcal/mol, Difference in average score from the   
                       base case: -0.0251                                                          (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 87 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.1484 kcal/mol, Difference in average score from  
                       the base case: -0.0256                                                      (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 87 from chain A (leucine) into arginine:  
                       Energy difference: -0.0799 kcal/mol, Difference in average score from the   
                       base case: -0.0269                                                          (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 128 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.5355 kcal/mol, Difference in average score from  
                       the base case: -0.0249                                                      (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 128 from chain A (valine) into lysine:    
                       Energy difference: 0.1015 kcal/mol, Difference in average score from the    
                       base case: -0.0234                                                          (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 128 from chain A (valine) into aspartic   
                       acid: Energy difference: 1.1867 kcal/mol, Difference in average score from  
                       the base case: -0.0263                                                      (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 128 from chain A (valine) into arginine:  
                       Energy difference: 0.4815 kcal/mol, Difference in average score from the    
                       base case: -0.0246                                                          (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 72 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 2.8417 kcal/mol, Difference in average    
                       score from the base case: -0.0206                                           (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 72 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.8045 kcal/mol, Difference in average score from the    
                       base case: -0.0048                                                          (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 72 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 3.2893 kcal/mol, Difference in average    
                       score from the base case: -0.0193                                           (00:10:33)
[INFO]       Auto_mut: Effect of mutation residue number 72 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.7735 kcal/mol, Difference in average score   
                       from the base case: -0.0061                                                 (00:10:33)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:37)
Show buried residues

Minimal score value
-2.3264
Maximal score value
2.0126
Average score
-0.4298
Total score value
-67.4772

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
2 I A 1.9204
3 V A 0.0000
4 T A -0.1681
5 Q A -0.5402
6 T A -0.1147
7 M A -0.2130
8 K A -1.7577
9 G A -0.7802
10 L A 0.0000
11 D A -0.6222
12 I A -0.0534
13 Q A -1.0529
14 K A -1.8400
15 V A 0.0000
16 A A 0.0080
17 G A -0.0978
18 T A -0.1084
19 W A 0.0000
20 Y A 0.1835
21 S A 0.0000
22 L A 0.0000
23 A A 0.0000
24 M A 0.0000
25 A A 0.0000
26 A A 0.0000
27 S A 0.0000
28 D A -0.9998
29 I A 1.3808
30 S A -0.0669
31 L A 0.1365
32 L A 0.0000
33 D A -1.8037
34 A A -0.4621
35 Q A -0.9956
36 S A -0.2915
37 A A 0.0000
38 P A -0.2031
39 L A 0.1900
40 R A -0.1919
41 V A 0.1235
42 Y A 0.0000
43 V A 0.0000
44 E A -0.9599
45 E A -0.5941
46 L A 0.0000
47 K A -1.1094
48 P A -0.2244
49 T A -0.0658
50 P A -0.5787
51 E A -1.8761
52 G A -0.4463
53 D A -0.6801
54 L A 0.0000
55 E A -0.8656
56 I A 0.0000
57 L A 0.0320
58 L A 0.0000
59 Q A -0.2636
60 K A 0.0000
61 W A -0.0439
62 E A -1.4667
63 N A -1.5866
64 G A -1.0244
65 E A -1.8789
66 C A -0.1702
67 A A -0.1797
68 Q A -1.3402
69 K A -1.2410
70 K A -1.7284
71 I A 0.2058
72 I A 0.5180
73 A A 0.0000
74 E A -1.5950
75 K A -1.9657
76 T A -0.6439
77 K A -1.5554
78 I A 0.4486
79 P A -0.1021
80 A A 0.0000
81 V A 0.0000
82 F A 0.0000
83 K A -0.4599
84 I A -0.1318
85 D A -1.7309
86 A A 0.0214
87 L A 1.3381
88 N A -1.3187
89 E A -2.1327
90 N A -1.0346
91 K A -0.7168
92 V A 0.0000
93 L A 0.0000
94 V A 0.0000
95 L A 0.0000
96 D A -0.5261
97 T A 0.0000
98 D A -0.4112
99 Y A -0.1653
100 K A -1.9469
101 K A -1.9290
102 Y A 0.0000
103 L A 0.0000
104 L A 0.0000
105 F A 0.0000
106 C A 0.0000
107 M A 0.0715
108 E A -0.2949
109 N A -0.9002
110 S A -0.3485
115 Q A -1.2054
116 S A -0.2493
117 L A 0.0000
118 A A 0.0000
119 C A 0.0000
120 Q A 0.0000
121 C A 0.0000
122 L A 0.0000
123 V A 0.0000
124 R A -0.3180
125 T A -0.1128
126 P A -0.4174
127 E A -1.5424
128 V A 1.1835
129 D A -0.4676
130 D A -2.1989
131 E A -2.3264
132 A A 0.0000
133 L A -0.1654
134 E A -2.1553
135 K A -1.3323
136 F A 0.0000
137 D A -1.1633
138 K A -1.8529
139 A A -0.2967
140 L A 0.0000
141 K A -1.6891
142 A A -0.2318
143 L A 0.1376
144 P A -0.1121
145 M A -0.0455
146 H A -0.9128
147 I A -0.0791
148 R A -0.8367
149 L A 0.1263
150 S A -0.0763
151 F A 0.0000
152 N A -0.9194
153 P A -0.2952
154 T A -0.1483
155 Q A -0.3221
156 L A 0.0000
157 E A -2.0677
158 E A -1.9293
159 Q A -1.4490
160 C A 0.0000
161 H A 0.0000
162 I A 2.0126
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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
IR29A -0.6681 -0.0278 View CSV PDB
IR162A -0.7244 -0.0236 View CSV PDB
IK29A -0.5511 -0.0268 View CSV PDB
IK162A -0.5382 -0.0252 View CSV PDB
LE87A -0.156 -0.0249 View CSV PDB
LR87A -0.0799 -0.0269 View CSV PDB
IK2A -0.099 -0.0185 View CSV PDB
IR2A -0.0456 -0.0178 View CSV PDB
VK128A 0.1015 -0.0234 View CSV PDB
VR128A 0.4815 -0.0246 View CSV PDB
IR72A 0.7735 -0.0061 View CSV PDB
IE72A 2.8417 -0.0206 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018