Project name: b782c78ade6a767

Status: done

Started: 2025-02-17 11:19:24
Settings
Chain sequence(s) A: EFKPTYQDRVAPPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDDMIFEDCGDVPSEPKERGDFNHERGERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKLNRVLGFKPKPPKNESLETYPVMKYNPNVLPVQCTGKRDEDKDKVGNVEYFGLGNSPGFPLQYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRIECKAYGENIGYSEKDRFQGRFDVKIEVKS
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                                          (00:05:08)
[INFO]       Auto_mut: Residue number 139 from chain A and a score of 1.180 (valine) selected for  
                       automated muatation                                                         (00:05:09)
[INFO]       Auto_mut: Residue number 67 from chain A and a score of 0.444 (valine) selected for   
                       automated muatation                                                         (00:05:09)
[INFO]       Auto_mut: Residue number 150 from chain A and a score of 0.045 (glutamine) selected   
                       for automated muatation                                                     (00:05:09)
[INFO]       Auto_mut: Residue number 138 from chain A and a score of 0.020 (proline) selected for 
                       automated muatation                                                         (00:05:09)
[INFO]       Auto_mut: Residue number 137 from chain A and a score of -0.014 (tyrosine) selected   
                       for automated muatation                                                     (00:05:09)
[INFO]       Auto_mut: Residue number 6 from chain A and a score of -0.140 (tyrosine) selected for 
                       automated muatation                                                         (00:05:09)
[INFO]       Auto_mut: Mutating residue number 139 from chain A (valine) into glutamic acid        (00:05:09)
[INFO]       Auto_mut: Mutating residue number 139 from chain A (valine) into aspartic acid        (00:05:09)
[INFO]       Auto_mut: Mutating residue number 67 from chain A (valine) into glutamic acid         (00:05:09)
[INFO]       Auto_mut: Mutating residue number 139 from chain A (valine) into arginine             (00:07:20)
[INFO]       Auto_mut: Mutating residue number 67 from chain A (valine) into lysine                (00:07:21)
[INFO]       Auto_mut: Mutating residue number 139 from chain A (valine) into lysine               (00:07:21)
[INFO]       Auto_mut: Mutating residue number 67 from chain A (valine) into aspartic acid         (00:09:36)
[INFO]       Auto_mut: Mutating residue number 150 from chain A (glutamine) into glutamic acid     (00:09:37)
[INFO]       Auto_mut: Mutating residue number 150 from chain A (glutamine) into aspartic acid     (00:09:47)
[INFO]       Auto_mut: Mutating residue number 67 from chain A (valine) into arginine              (00:11:45)
[INFO]       Auto_mut: Mutating residue number 150 from chain A (glutamine) into lysine            (00:11:56)
[INFO]       Auto_mut: Mutating residue number 150 from chain A (glutamine) into arginine          (00:11:59)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (proline) into glutamic acid       (00:13:59)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (proline) into aspartic acid       (00:14:12)
[INFO]       Auto_mut: Mutating residue number 137 from chain A (tyrosine) into glutamic acid      (00:14:15)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (proline) into lysine              (00:16:13)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (proline) into arginine            (00:16:23)
[INFO]       Auto_mut: Mutating residue number 137 from chain A (tyrosine) into lysine             (00:16:31)
[INFO]       Auto_mut: Mutating residue number 137 from chain A (tyrosine) into aspartic acid      (00:18:34)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (tyrosine) into glutamic acid        (00:18:39)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (tyrosine) into aspartic acid        (00:19:10)
[INFO]       Auto_mut: Mutating residue number 137 from chain A (tyrosine) into arginine           (00:20:46)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (tyrosine) into lysine               (00:21:00)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (tyrosine) into arginine             (00:21:30)
[INFO]       Auto_mut: Effect of mutation residue number 139 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.5451 kcal/mol, Difference in average score from  
                       the base case: -0.0586                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 139 from chain A (valine) into lysine:    
                       Energy difference: 0.4203 kcal/mol, Difference in average score from the    
                       base case: -0.0533                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 139 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.7075 kcal/mol, Difference in average score from  
                       the base case: -0.0584                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 139 from chain A (valine) into arginine:  
                       Energy difference: -0.1084 kcal/mol, Difference in average score from the   
                       base case: -0.0497                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 67 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.3988 kcal/mol, Difference in average score from 
                       the base case: -0.0694                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 67 from chain A (valine) into lysine:     
                       Energy difference: -0.7252 kcal/mol, Difference in average score from the   
                       base case: -0.0589                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 67 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.4701 kcal/mol, Difference in average score from  
                       the base case: -0.0684                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 67 from chain A (valine) into arginine:   
                       Energy difference: -0.6943 kcal/mol, Difference in average score from the   
                       base case: -0.0601                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 150 from chain A (glutamine) into         
                       glutamic acid: Energy difference: 0.7835 kcal/mol, Difference in average    
                       score from the base case: -0.0191                                           (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 150 from chain A (glutamine) into lysine: 
                       Energy difference: -0.7117 kcal/mol, Difference in average score from the   
                       base case: -0.0203                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 150 from chain A (glutamine) into         
                       aspartic acid: Energy difference: 1.4887 kcal/mol, Difference in average    
                       score from the base case: -0.0176                                           (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 150 from chain A (glutamine) into         
                       arginine: Energy difference: -0.3738 kcal/mol, Difference in average score  
                       from the base case: -0.0175                                                 (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (proline) into glutamic  
                       acid: Energy difference: 1.1193 kcal/mol, Difference in average score from  
                       the base case: -0.0401                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (proline) into lysine:   
                       Energy difference: 0.9180 kcal/mol, Difference in average score from the    
                       base case: -0.0357                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (proline) into aspartic  
                       acid: Energy difference: 1.1865 kcal/mol, Difference in average score from  
                       the base case: -0.0369                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (proline) into arginine: 
                       Energy difference: 0.8691 kcal/mol, Difference in average score from the    
                       base case: -0.0375                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 137 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 2.1709 kcal/mol, Difference in average score from  
                       the base case: -0.0277                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 137 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.6142 kcal/mol, Difference in average score from the    
                       base case: -0.0196                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 137 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 1.6453 kcal/mol, Difference in average score from  
                       the base case: -0.0255                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 137 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.3040 kcal/mol, Difference in average score  
                       from the base case: -0.0082                                                 (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (tyrosine) into glutamic   
                       acid: Energy difference: 2.1370 kcal/mol, Difference in average score from  
                       the base case: -0.0452                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (tyrosine) into lysine:    
                       Energy difference: 2.0023 kcal/mol, Difference in average score from the    
                       base case: -0.0344                                                          (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (tyrosine) into aspartic   
                       acid: Energy difference: 2.0332 kcal/mol, Difference in average score from  
                       the base case: -0.0371                                                      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (tyrosine) into arginine:  
                       Energy difference: 1.0020 kcal/mol, Difference in average score from the    
                       base case: -0.0485                                                          (00:23:44)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:50)
Show buried residues
Minimal score value
-4.2212
Maximal score value
1.1801
Average score
-1.2307
Total score value
-296.6105
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 -2.1566
2 F A -1.8622
3 K A -2.1340
4 P A -1.2787
5 T A -0.7589
6 Y A -0.1397
7 Q A -1.0980
8 D A -2.0645
9 R A -1.8620
10 V A -0.3830
11 A A -0.8049
12 P A -0.3936
13 P A 0.0000
14 G A -0.5425
15 L A 0.0000
16 T A -0.3257
17 Q A 0.0000
18 I A 0.0000
19 P A 0.0000
20 Q A -1.6858
21 I A -1.6551
22 Q A -2.3841
23 K A -2.7023
24 T A -1.9808
25 E A -2.3101
26 I A 0.0000
27 S A -1.1915
28 F A 0.0000
29 R A -2.7271
30 P A -2.8605
31 N A -2.8271
32 D A -2.6232
33 P A -2.6256
34 K A -2.8998
35 S A -2.0937
36 Y A 0.0000
37 E A -2.3908
38 A A -1.0573
39 Y A -0.6493
40 V A 0.0000
41 L A -0.5994
42 N A -1.0438
43 I A 0.0000
44 V A -1.2383
45 R A -2.3934
46 F A 0.0000
47 L A 0.0000
48 E A -3.3887
49 K A -3.0000
50 Y A 0.0000
51 K A -3.3517
52 D A -3.5207
53 S A -2.4696
54 A A -2.5100
55 Q A 0.0000
56 R A -3.3930
57 D A -2.5531
58 D A -2.6938
59 M A -0.6914
60 I A -1.2587
61 F A 0.0000
62 E A -2.1937
63 D A -2.6906
64 C A -1.2878
65 G A -1.1469
66 D A -1.6055
67 V A 0.4440
68 P A -0.4263
69 S A -1.1300
70 E A -2.6184
71 P A -2.2614
72 K A -2.6722
73 E A -3.0195
74 R A -2.4175
75 G A -2.4364
76 D A -2.9473
77 F A -2.0405
78 N A -3.0254
79 H A -3.2279
80 E A -3.9587
81 R A -4.0125
82 G A -3.0129
83 E A -2.8689
84 R A 0.0000
85 K A -1.7070
86 V A 0.0000
87 C A 0.0000
88 R A -1.8824
89 F A 0.0000
90 K A -1.9503
91 L A 0.0000
92 E A -2.2339
93 W A -1.5897
94 L A 0.0000
95 G A -1.5122
96 N A -2.0457
97 C A 0.0000
98 S A 0.0000
99 G A -1.0890
100 L A -0.3006
101 N A -1.6868
102 D A -1.9332
103 E A -2.1659
104 T A -2.0320
105 Y A 0.0000
106 G A 0.0000
107 Y A 0.0000
108 K A -3.3490
109 E A -3.2156
110 G A -2.3307
111 K A -1.9435
112 P A 0.0000
113 C A 0.0000
114 I A 0.0000
115 I A 0.0000
116 I A 0.0000
117 K A -0.6367
118 L A 0.0000
119 N A -1.2779
120 R A -1.8916
121 V A 0.0000
122 L A -0.9272
123 G A -1.0547
124 F A -0.8301
125 K A -1.6717
126 P A 0.0000
127 K A -2.1365
128 P A -1.8054
129 P A -2.3200
130 K A -3.5381
131 N A -3.5534
132 E A -3.4668
133 S A -2.4017
134 L A 0.0000
135 E A -2.6694
136 T A -0.8460
137 Y A -0.0141
138 P A 0.0203
139 V A 1.1801
140 M A 0.0000
141 K A -1.5490
142 Y A -1.5477
143 N A -1.2177
144 P A -1.5217
145 N A -0.9105
146 V A 0.0000
147 L A 0.0000
148 P A 0.0000
149 V A 0.0000
150 Q A 0.0451
151 C A 0.0000
152 T A -1.4054
153 G A 0.0000
154 K A -2.2562
155 R A -3.1381
156 D A -4.0635
157 E A -4.0826
158 D A 0.0000
159 K A -4.2212
160 D A -3.8743
161 K A -3.1028
162 V A 0.0000
163 G A -2.0620
164 N A -1.6136
165 V A -0.8699
166 E A -0.9860
167 Y A -0.5874
168 F A -0.8503
169 G A 0.0000
170 L A 0.0000
171 G A -0.8504
172 N A -1.3419
173 S A -0.7249
174 P A -0.4460
175 G A 0.0000
176 F A 0.0000
177 P A 0.0000
178 L A 0.0000
179 Q A 0.0000
180 Y A 0.0000
181 Y A 0.0000
182 P A 0.0000
183 Y A 0.0000
184 Y A 0.0000
185 G A 0.0000
186 K A -1.4492
187 L A -0.3956
188 L A 0.0000
189 Q A 0.0000
190 P A -1.3172
191 K A -1.6859
192 Y A -1.2748
193 L A 0.0000
194 Q A 0.0000
195 P A 0.0000
196 L A 0.0000
197 L A 0.0000
198 A A 0.0000
199 V A 0.0000
200 Q A 0.0000
201 F A 0.0000
202 T A -1.5330
203 N A -1.9134
204 L A 0.0000
205 T A -1.3541
206 M A -1.2127
207 D A -2.3291
208 T A -1.8466
209 E A -2.3788
210 I A 0.0000
211 R A -2.0610
212 I A 0.0000
213 E A 0.0000
214 C A 0.0000
215 K A -0.3596
216 A A 0.0000
217 Y A -0.5478
218 G A -1.6658
219 E A -2.6076
220 N A -1.7571
221 I A 0.0000
222 G A -0.2286
223 Y A -0.3688
224 S A -1.8831
225 E A -3.1737
226 K A -3.4215
227 D A -3.0917
228 R A -2.9018
229 F A -1.0539
230 Q A -0.9531
231 G A 0.0000
232 R A -0.7012
233 F A 0.0000
234 D A -0.9614
235 V A 0.0000
236 K A -1.7058
237 I A 0.0000
238 E A -1.9156
239 V A 0.0000
240 K A -2.0697
241 S A -1.3746
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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
VK67A -0.7252 -0.0589 View CSV PDB
VR67A -0.6943 -0.0601 View CSV PDB
VR139A -0.1084 -0.0497 View CSV PDB
QK150A -0.7117 -0.0203 View CSV PDB
QR150A -0.3738 -0.0175 View CSV PDB
YR137A -0.304 -0.0082 View CSV PDB
VK139A 0.4203 -0.0533 View CSV PDB
YR6A 1.002 -0.0485 View CSV PDB
PR138A 0.8691 -0.0375 View CSV PDB
PK138A 0.918 -0.0357 View CSV PDB
YK137A 0.6142 -0.0196 View CSV PDB
YE6A 2.137 -0.0452 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018