Project name: 42153bb20eebcd2

Status: done

Started: 2024-06-18 07:13:58
Settings
Chain sequence(s) A: SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFTTTVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI
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                                          (00:03:09)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 1.240 (valine) selected for   
                       automated muatation                                                         (00:03:10)
[INFO]       Auto_mut: Residue number 229 from chain A and a score of 1.194 (isoleucine) selected  
                       for automated muatation                                                     (00:03:10)
[INFO]       Auto_mut: Residue number 39 from chain A and a score of 0.940 (tyrosine) selected for 
                       automated muatation                                                         (00:03:10)
[INFO]       Auto_mut: Residue number 10 from chain A and a score of 0.451 (glycine) selected for  
                       automated muatation                                                         (00:03:10)
[INFO]       Auto_mut: Residue number 176 from chain A and a score of 0.409 (valine) selected for  
                       automated muatation                                                         (00:03:10)
[INFO]       Auto_mut: Residue number 99 from chain A and a score of 0.371 (phenylalanine)         
                       selected for automated muatation                                            (00:03:10)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into glutamic acid         (00:03:10)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into aspartic acid         (00:03:10)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (isoleucine) into glutamic acid    (00:03:10)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into arginine              (00:04:35)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (isoleucine) into lysine           (00:04:37)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (valine) into lysine                (00:04:38)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (isoleucine) into aspartic acid    (00:06:11)
[INFO]       Auto_mut: Mutating residue number 39 from chain A (tyrosine) into glutamic acid       (00:06:15)
[INFO]       Auto_mut: Mutating residue number 39 from chain A (tyrosine) into aspartic acid       (00:06:18)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (isoleucine) into arginine         (00:07:34)
[INFO]       Auto_mut: Mutating residue number 39 from chain A (tyrosine) into arginine            (00:07:36)
[INFO]       Auto_mut: Mutating residue number 39 from chain A (tyrosine) into lysine              (00:07:40)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (glycine) into glutamic acid        (00:08:59)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (glycine) into aspartic acid        (00:09:01)
[INFO]       Auto_mut: Mutating residue number 176 from chain A (valine) into glutamic acid        (00:09:12)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (glycine) into lysine               (00:10:23)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (glycine) into arginine             (00:10:23)
[INFO]       Auto_mut: Mutating residue number 176 from chain A (valine) into lysine               (00:10:37)
[INFO]       Auto_mut: Mutating residue number 176 from chain A (valine) into aspartic acid        (00:11:51)
[INFO]       Auto_mut: Mutating residue number 99 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 99 from chain A (phenylalanine) into glutamic acid  (00:11:51)
[INFO]       Auto_mut: Mutating residue number 99 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 99 from chain A (phenylalanine) into aspartic acid  (00:12:08)
[INFO]       Auto_mut: Mutating residue number 176 from chain A (valine) into arginine             (00:13:15)
[INFO]       Auto_mut: Mutating residue number 99 from chain A (phenylalanine) into lysine         (00:13:21)
[INFO]       Auto_mut: Mutating residue number 99 from chain A (phenylalanine) into arginine       (00:13:38)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.8226 kcal/mol, Difference in average score from  
                       the base case: -0.0456                                                      (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into lysine:     
                       Energy difference: -0.5527 kcal/mol, Difference in average score from the   
                       base case: -0.0314                                                          (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.9895 kcal/mol, Difference in average score from  
                       the base case: -0.0457                                                      (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (valine) into arginine:   
                       Energy difference: -0.4208 kcal/mol, Difference in average score from the   
                       base case: -0.0351                                                          (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.4456 kcal/mol, Difference in average    
                       score from the base case: -0.0312                                           (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.3903 kcal/mol, Difference in average score    
                       from the base case: -0.0266                                                 (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 2.2401 kcal/mol, Difference in average    
                       score from the base case: -0.0313                                           (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.6123 kcal/mol, Difference in average score   
                       from the base case: -0.0282                                                 (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 39 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.2602 kcal/mol, Difference in average score from  
                       the base case: -0.0250                                                      (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 39 from chain A (tyrosine) into lysine:   
                       Energy difference: -0.7179 kcal/mol, Difference in average score from the   
                       base case: -0.0227                                                          (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 39 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 0.1447 kcal/mol, Difference in average score from  
                       the base case: -0.0244                                                      (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 39 from chain A (tyrosine) into arginine: 
                       Energy difference: -0.4954 kcal/mol, Difference in average score from the   
                       base case: -0.0254                                                          (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into glutamic   
                       acid: Energy difference: 1.8000 kcal/mol, Difference in average score from  
                       the base case: -0.0218                                                      (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into lysine:    
                       Energy difference: 0.2667 kcal/mol, Difference in average score from the    
                       base case: -0.0172                                                          (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into aspartic   
                       acid: Energy difference: -0.2034 kcal/mol, Difference in average score from 
                       the base case: -0.0206                                                      (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (glycine) into arginine:  
                       Energy difference: 0.0640 kcal/mol, Difference in average score from the    
                       base case: -0.0191                                                          (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 176 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.6690 kcal/mol, Difference in average score from  
                       the base case: -0.0409                                                      (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 176 from chain A (valine) into lysine:    
                       Energy difference: -0.0001 kcal/mol, Difference in average score from the   
                       base case: -0.0395                                                          (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 176 from chain A (valine) into aspartic   
                       acid: Energy difference: 1.3387 kcal/mol, Difference in average score from  
                       the base case: -0.0451                                                      (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 176 from chain A (valine) into arginine:  
                       Energy difference: 0.0948 kcal/mol, Difference in average score from the    
                       base case: -0.0427                                                          (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 99 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 1.6068 kcal/mol, Difference in average    
                       score from the base case: -0.0313                                           (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 99 from chain A (phenylalanine) into      
                       lysine: Energy difference: 0.8000 kcal/mol, Difference in average score     
                       from the base case: -0.0277                                                 (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 99 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 2.1780 kcal/mol, Difference in average    
                       score from the base case: -0.0321                                           (00:15:13)
[INFO]       Auto_mut: Effect of mutation residue number 99 from chain A (phenylalanine) into      
                       arginine: Energy difference: 1.4532 kcal/mol, Difference in average score   
                       from the base case: -0.0252                                                 (00:15:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:19)
Show buried residues
Minimal score value
-3.9904
Maximal score value
1.2396
Average score
-0.9342
Total score value
-210.204
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
2 S A -1.7480
3 K A -1.9266
4 G A 0.0000
5 E A -2.6551
6 E A -2.5822
7 L A -1.1964
8 F A 0.0000
9 T A -0.6278
10 G A 0.4512
11 V A 1.2396
12 V A 0.0000
13 P A -0.9752
14 I A 0.0000
15 L A -0.9862
16 V A 0.0000
17 E A -1.9305
18 L A 0.0000
19 D A -3.3361
20 G A 0.0000
21 D A -2.4363
22 V A 0.0000
23 N A -2.0751
24 G A -1.6314
25 H A -2.1611
26 K A -2.8459
27 F A 0.0000
28 S A -1.6658
29 V A 0.0000
30 S A -0.9663
31 G A 0.0000
32 E A -2.1402
33 G A -1.4854
34 E A -1.5504
35 G A 0.0000
36 D A 0.0545
37 A A 0.0000
38 T A 0.2714
39 Y A 0.9402
40 G A 0.0000
41 K A -0.3884
42 L A 0.0000
43 T A -0.7581
44 L A 0.0000
45 K A -0.9364
46 F A 0.0000
47 I A -1.0400
48 C A 0.0000
49 T A -0.7814
50 T A -1.2946
51 G A -1.6006
52 K A -2.2497
53 L A 0.0000
54 P A -1.1990
55 V A 0.0000
56 P A 0.0000
57 W A 0.0000
58 P A 0.0000
59 T A 0.0000
60 L A 0.0000
61 V A 0.0000
62 T A -0.0037
63 T A 0.0000
64 F A 0.0000
68 V A -0.0527
69 Q A -0.2169
70 C A 0.0000
71 F A 0.0000
72 S A 0.0000
73 R A -1.1774
74 Y A 0.0000
75 P A -1.8004
76 D A -3.0657
77 H A -2.2846
78 M A 0.0000
79 K A -3.3140
80 R A -3.0544
81 H A -1.7645
82 D A 0.0000
83 F A 0.0000
84 F A 0.0000
85 K A -1.1575
86 S A 0.0000
87 A A 0.0000
88 M A 0.0000
89 P A -1.8367
90 E A -2.5061
91 G A 0.0000
92 Y A 0.0000
93 V A -0.9173
94 Q A 0.0000
95 E A -2.5636
96 R A 0.0000
97 T A -0.5103
98 I A 0.0000
99 F A 0.3706
100 F A 0.0000
101 K A -1.5851
102 D A -2.5554
103 D A -2.4961
104 G A 0.0000
105 N A -0.7386
106 Y A 0.0000
107 K A -1.8764
108 T A 0.0000
109 R A -3.1202
110 A A 0.0000
111 E A -2.2195
112 V A 0.0000
113 K A -1.9659
114 F A -2.0041
115 E A -2.7630
116 G A -2.2840
117 D A -2.5449
118 T A -1.7283
119 L A 0.0000
120 V A 0.0000
121 N A 0.0000
122 R A -2.8747
123 I A 0.0000
124 E A -3.9529
125 L A 0.0000
126 K A -2.7094
127 G A 0.0000
128 I A -1.1789
129 D A -2.3003
130 F A 0.0000
131 K A -3.9622
132 E A -3.9904
133 D A -3.6067
134 G A -2.8039
135 N A -2.1472
136 I A 0.0000
137 L A -1.9260
138 G A -2.2856
139 H A -2.2238
140 K A -2.5262
141 L A 0.0000
142 E A -1.8498
143 Y A -0.6819
144 N A -0.6203
145 Y A -0.7041
146 N A -0.9709
147 S A -1.0619
148 H A 0.0000
149 N A -1.0828
150 V A 0.0000
151 Y A 0.0634
152 I A 0.0000
153 M A -0.9507
154 A A -1.7151
155 D A 0.0000
156 K A -3.1149
157 Q A -3.1357
158 K A -3.4573
159 N A -2.6641
160 G A 0.0000
161 I A 0.0000
162 K A -1.5315
163 V A 0.0000
164 N A -0.3613
165 F A 0.0000
166 K A -1.1632
167 I A 0.0000
168 R A -0.8515
169 H A 0.0000
170 N A -1.1601
171 I A 0.0000
172 E A -3.2753
173 D A -2.9818
174 G A -1.8027
175 S A -0.7058
176 V A 0.4094
177 Q A 0.0000
178 L A -0.4014
179 A A 0.0000
180 D A 0.0000
181 H A 0.0000
182 Y A 0.1868
183 Q A 0.0000
184 Q A -1.7438
185 N A 0.0000
186 T A -0.9755
187 P A -0.8470
188 I A -0.4057
189 G A -1.3325
190 D A -2.0301
191 G A -1.3720
192 P A -0.8415
193 V A -0.5890
194 L A -0.6668
195 L A -0.7930
196 P A 0.0000
197 D A -2.2076
198 N A -1.6201
199 H A 0.0000
200 Y A 0.1242
201 L A 0.0000
202 S A -0.6276
203 T A -0.8347
204 Q A -1.3131
205 S A -0.5628
206 A A -0.0198
207 L A -0.0167
208 S A -0.6496
209 K A -1.7214
210 D A -2.1751
211 P A -1.8352
212 N A -2.4809
213 E A -2.7245
214 K A -3.1977
215 R A -3.4038
216 D A -2.3139
217 H A 0.0000
218 M A 0.0000
219 V A -0.1304
220 L A 0.0000
221 L A 0.2860
222 E A -0.2495
223 F A -0.0424
224 V A 0.0000
225 T A -0.4465
226 A A 0.0000
227 A A 0.0830
228 G A 0.3013
229 I A 1.1944
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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
VK11A -0.5527 -0.0314 View CSV PDB
VR11A -0.4208 -0.0351 View CSV PDB
YK39A -0.7179 -0.0227 View CSV PDB
YR39A -0.4954 -0.0254 View CSV PDB
IK229A -0.3903 -0.0266 View CSV PDB
VK176A -0.0001 -0.0395 View CSV PDB
GD10A -0.2034 -0.0206 View CSV PDB
VR176A 0.0948 -0.0427 View CSV PDB
GR10A 0.064 -0.0191 View CSV PDB
IR229A 0.6123 -0.0282 View CSV PDB
FK99A 0.8 -0.0277 View CSV PDB
FE99A 1.6068 -0.0313 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018