Project name: Lip1_test2

Status: done

Started: 2023-09-26 06:22:04
Settings
Chain sequence(s) A: TLLYRDMNQAQLDAAYNNTQAVPDFPGIYAALQARSASSFYASAAGRLNLPYGTAPRQRYDWLPCGKADAPTLIFIHGGYWQNNCSKEDFAFIAAGPLAAGFNIVLAEYTLAPQASMTQIVSEIGSLLEHLQADADQLGIAGHKVVLSGHSAGGHLALQFRSHPWVTDVLAISALVDLEPISLSWLNEKLSLSEAEIDAYSPLYHIDKGANTWVAVGADELSELVRQSDEYAKQALARGESVQLIHVPGCTHFSVLDEMAKPQGALLQALSSIRLEHHH
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                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:18)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:02:18)
[INFO]       Auto_mut: Residue number 5 from chain A and a score of 0.523 (leucine) selected for   
                       automated muatation                                                         (00:02:20)
[INFO]       Auto_mut: Residue number 6 from chain A and a score of 0.444 (leucine) selected for   
                       automated muatation                                                         (00:02:20)
[INFO]       Auto_mut: Residue number 4 from chain A and a score of 0.392 (threonine) selected for 
                       automated muatation                                                         (00:02:20)
[INFO]       Auto_mut: Residue number 246 from chain A and a score of 0.237 (isoleucine) selected  
                       for automated muatation                                                     (00:02:20)
[INFO]       Auto_mut: Residue number 184 from chain A and a score of 0.152 (leucine) selected for 
                       automated muatation                                                         (00:02:20)
[INFO]       Auto_mut: Residue number 31 from chain A and a score of 0.132 (isoleucine) selected   
                       for automated muatation                                                     (00:02:20)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (leucine) into glutamic acid         (00:02:20)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into glutamic acid         (00:02:20)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (leucine) into aspartic acid         (00:02:20)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (leucine) into arginine              (00:03:35)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (leucine) into lysine                (00:03:36)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into lysine                (00:03:36)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into aspartic acid         (00:04:55)
[INFO]       Auto_mut: Mutating residue number 4 from chain A (threonine) into glutamic acid       (00:04:56)
[INFO]       Auto_mut: Mutating residue number 4 from chain A (threonine) into aspartic acid       (00:05:02)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into arginine              (00:06:03)
[INFO]       Auto_mut: Mutating residue number 4 from chain A (threonine) into lysine              (00:06:07)
[INFO]       Auto_mut: Mutating residue number 4 from chain A (threonine) into arginine            (00:06:14)
[INFO]       Auto_mut: Mutating residue number 246 from chain A (isoleucine) into glutamic acid    (00:07:16)
[INFO]       Auto_mut: Mutating residue number 246 from chain A (isoleucine) into aspartic acid    (00:07:24)
[INFO]       Auto_mut: Mutating residue number 184 from chain A (leucine) into glutamic acid       (00:07:32)
[INFO]       Auto_mut: Mutating residue number 246 from chain A (isoleucine) into lysine           (00:08:31)
[INFO]       Auto_mut: Mutating residue number 246 from chain A (isoleucine) into arginine         (00:08:38)
[INFO]       Auto_mut: Mutating residue number 184 from chain A (leucine) into lysine              (00:08:50)
[INFO]       Auto_mut: Mutating residue number 184 from chain A (leucine) into aspartic acid       (00:09:59)
[INFO]       Auto_mut: Mutating residue number 31 from chain A (isoleucine) into glutamic acid     (00:10:07)
[INFO]       Auto_mut: Mutating residue number 31 from chain A (isoleucine) into aspartic acid     (00:10:56)
[INFO]       Auto_mut: Mutating residue number 184 from chain A (leucine) into arginine            (00:11:15)
[INFO]       Auto_mut: Mutating residue number 31 from chain A (isoleucine) into lysine            (00:11:34)
[INFO]       Auto_mut: Mutating residue number 31 from chain A (isoleucine) into arginine          (00:12:13)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (leucine) into glutamic    
                       acid: Energy difference: 0.0363 kcal/mol, Difference in average score from  
                       the base case: -0.0709                                                      (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (leucine) into lysine:     
                       Energy difference: 0.3037 kcal/mol, Difference in average score from the    
                       base case: -0.0687                                                          (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (leucine) into aspartic    
                       acid: Energy difference: 0.6368 kcal/mol, Difference in average score from  
                       the base case: -0.0721                                                      (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (leucine) into arginine:   
                       Energy difference: 0.6023 kcal/mol, Difference in average score from the    
                       base case: -0.0714                                                          (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into glutamic    
                       acid: Energy difference: 1.6863 kcal/mol, Difference in average score from  
                       the base case: -0.0526                                                      (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into lysine:     
                       Energy difference: 0.0662 kcal/mol, Difference in average score from the    
                       base case: -0.0448                                                          (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into aspartic    
                       acid: Energy difference: 2.7206 kcal/mol, Difference in average score from  
                       the base case: -0.0517                                                      (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into arginine:   
                       Energy difference: 1.1458 kcal/mol, Difference in average score from the    
                       base case: -0.0614                                                          (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 4 from chain A (threonine) into glutamic  
                       acid: Energy difference: -0.5718 kcal/mol, Difference in average score from 
                       the base case: -0.0434                                                      (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 4 from chain A (threonine) into lysine:   
                       Energy difference: -0.5194 kcal/mol, Difference in average score from the   
                       base case: -0.0466                                                          (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 4 from chain A (threonine) into aspartic  
                       acid: Energy difference: -0.0982 kcal/mol, Difference in average score from 
                       the base case: -0.0382                                                      (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 4 from chain A (threonine) into arginine: 
                       Energy difference: -0.4726 kcal/mol, Difference in average score from the   
                       base case: -0.0480                                                          (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 246 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 2.5843 kcal/mol, Difference in average    
                       score from the base case: -0.0284                                           (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 246 from chain A (isoleucine) into        
                       lysine: Energy difference: 1.5636 kcal/mol, Difference in average score     
                       from the base case: -0.0240                                                 (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 246 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 3.1178 kcal/mol, Difference in average    
                       score from the base case: -0.0325                                           (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 246 from chain A (isoleucine) into        
                       arginine: Energy difference: 1.9172 kcal/mol, Difference in average score   
                       from the base case: -0.0246                                                 (00:13:41)
[INFO]       Auto_mut: Effect of mutation residue number 184 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.7445 kcal/mol, Difference in average score from  
                       the base case: -0.0359                                                      (00:13:42)
[INFO]       Auto_mut: Effect of mutation residue number 184 from chain A (leucine) into lysine:   
                       Energy difference: 1.5431 kcal/mol, Difference in average score from the    
                       base case: -0.0354                                                          (00:13:42)
[INFO]       Auto_mut: Effect of mutation residue number 184 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.0945 kcal/mol, Difference in average score from  
                       the base case: -0.0369                                                      (00:13:42)
[INFO]       Auto_mut: Effect of mutation residue number 184 from chain A (leucine) into arginine: 
                       Energy difference: 0.8998 kcal/mol, Difference in average score from the    
                       base case: -0.0384                                                          (00:13:42)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 1.7783 kcal/mol, Difference in average    
                       score from the base case: -0.0418                                           (00:13:42)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain A (isoleucine) into lysine: 
                       Energy difference: 1.1079 kcal/mol, Difference in average score from the    
                       base case: -0.0394                                                          (00:13:42)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 2.4589 kcal/mol, Difference in average    
                       score from the base case: -0.0453                                           (00:13:42)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain A (isoleucine) into         
                       arginine: Energy difference: 1.7032 kcal/mol, Difference in average score   
                       from the base case: -0.0280                                                 (00:13:42)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:50)
Show buried residues
Minimal score value
-3.1223
Maximal score value
0.5234
Average score
-0.5884
Total score value
-162.3851
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
4 T A 0.3916
5 L A 0.5234
6 L A 0.4441
7 Y A -0.8262
8 R A -2.2099
9 D A -2.2999
10 M A -1.3528
11 N A -0.9943
12 Q A -0.6303
13 A A -0.7138
14 Q A -1.3519
15 L A 0.0000
16 D A -0.8275
17 A A -0.8148
18 A A -0.5614
19 Y A 0.0000
20 N A -0.6510
21 N A 0.0000
22 T A -0.7469
23 Q A -1.4704
24 A A -0.6851
25 V A -0.6468
26 P A -1.1705
27 D A -1.8391
28 F A -0.6906
29 P A -0.4394
30 G A -0.5027
31 I A 0.1318
32 Y A -0.0206
33 A A -0.1396
34 A A -0.3605
35 L A 0.0000
36 Q A -1.1202
37 A A -1.0618
38 R A -2.0151
39 S A 0.0000
40 A A -0.8366
41 S A -0.8229
42 F A 0.0000
43 Y A -0.1305
44 A A -0.1578
45 S A -0.1597
46 A A -0.0368
47 A A -0.2965
48 G A -0.8234
49 R A -1.3627
50 L A -0.4952
51 N A -1.2368
52 L A -0.6834
53 P A -0.6506
54 Y A 0.0000
55 G A -0.4269
56 T A -0.3617
57 A A -0.4048
58 P A -0.5864
59 R A -0.8311
60 Q A -0.8107
61 R A -0.8198
62 Y A 0.0000
63 D A 0.0000
64 W A 0.0000
65 L A 0.0000
66 P A -0.7106
67 C A -0.5403
68 G A -1.4000
69 K A -2.2931
70 A A -1.7933
71 D A -2.6189
72 A A 0.0000
73 P A 0.0000
74 T A 0.0000
75 L A 0.0000
76 I A 0.0000
77 F A 0.0000
78 I A 0.0000
79 H A 0.0000
80 G A 0.0000
81 G A -0.4755
82 Y A -0.2375
83 W A 0.0000
84 Q A 0.0000
85 N A -1.2030
86 C A -0.6771
87 S A -0.6722
88 K A 0.0000
89 E A -1.1930
90 D A 0.0000
91 F A 0.0000
92 A A 0.0000
93 F A 0.0000
94 I A 0.0000
95 A A 0.0000
96 A A -0.3269
97 G A 0.0000
98 P A 0.0000
99 L A 0.0213
100 A A -0.2367
101 A A -0.2266
102 G A 0.0000
103 F A 0.0000
104 N A 0.0000
105 I A 0.0000
106 V A 0.0000
107 L A 0.0000
108 A A 0.0000
109 E A 0.0000
110 Y A 0.0000
111 T A 0.0000
112 L A -0.8867
113 A A 0.0000
114 P A -1.5565
115 Q A -1.5803
116 A A 0.0000
117 S A -0.9227
118 M A 0.0000
119 T A -0.5519
120 Q A -1.3141
121 I A 0.0000
122 V A -0.3189
123 S A -0.6073
124 E A 0.0000
125 I A 0.0000
126 G A -0.7579
127 S A -1.0047
128 L A 0.0000
129 L A 0.0000
130 E A -2.3878
131 H A -1.6014
132 L A 0.0000
133 Q A -1.9889
134 A A -1.4049
135 D A -1.5313
136 A A -1.1521
137 D A -1.1737
138 Q A -1.4702
139 L A -0.9653
140 G A -1.1048
141 I A -1.0163
142 A A -1.2674
143 G A -1.4795
144 H A -1.8584
145 K A -1.0720
146 V A 0.0000
147 V A 0.0000
148 L A 0.0000
149 S A 0.0000
150 G A 0.0000
151 H A 0.0000
152 S A 0.0000
153 A A 0.0000
154 G A 0.0000
155 G A 0.0000
156 H A 0.0000
157 L A 0.0000
158 A A 0.0000
159 L A 0.0000
160 Q A -0.2305
161 F A -0.0342
162 R A 0.0000
163 S A -1.1547
164 H A -0.4791
165 P A -0.2943
166 W A -0.7632
167 V A 0.0000
168 T A -0.4901
169 D A 0.0000
170 V A 0.0000
171 L A 0.0000
172 A A 0.0000
173 I A 0.0000
174 S A 0.0000
175 A A 0.0000
176 L A 0.0000
177 V A 0.0000
178 D A -0.5512
179 L A 0.0000
180 E A -1.3323
181 P A 0.0000
182 I A 0.0000
183 S A -0.6011
184 L A 0.1525
185 S A 0.0000
186 W A -0.5290
187 L A 0.0000
188 N A -1.3318
189 E A -2.4007
190 K A -2.3491
191 L A 0.0000
192 S A -1.3320
193 L A -1.0456
194 S A -1.1432
195 E A -2.2988
196 A A -1.3114
197 E A 0.0000
198 I A -1.3437
199 D A -2.1764
200 A A -1.0098
201 Y A -0.3093
202 S A 0.0000
203 P A 0.0000
204 L A -0.5303
205 Y A -0.3079
206 H A -1.4453
207 I A -1.6401
208 D A -3.0795
209 K A -3.1223
210 G A -1.6783
211 A A -0.9375
212 N A -0.9275
213 T A 0.0000
214 W A 0.0303
215 V A 0.0000
216 A A 0.0000
217 V A 0.0000
218 G A 0.0000
219 A A -1.1041
220 D A -1.9849
221 E A 0.0000
222 L A -0.2824
223 S A -0.3749
224 E A 0.0000
225 L A 0.0000
226 V A -0.4361
227 R A -0.4851
228 Q A 0.0000
229 S A 0.0000
230 D A -1.1765
231 E A -1.4576
232 Y A 0.0000
233 A A 0.0000
234 K A -2.1141
235 Q A -1.4206
236 A A 0.0000
237 L A -0.5924
238 A A -1.0880
239 R A -2.4883
240 G A -1.4939
241 E A 0.0000
242 S A -0.9257
243 V A 0.0000
244 Q A -0.6440
245 L A -0.0015
246 I A 0.2367
247 H A -0.5263
248 V A 0.0000
249 P A -0.8964
250 G A -1.1588
251 C A 0.0000
252 T A -0.7189
253 H A 0.0000
254 F A 0.0000
255 S A -0.6292
256 V A 0.0000
257 L A 0.0000
258 D A -1.7562
259 E A -1.7086
260 M A 0.0000
261 A A 0.0000
262 K A -2.5312
263 P A -1.8363
264 Q A -2.1756
265 G A 0.0000
266 A A -1.0693
267 L A 0.0000
268 L A 0.0000
269 Q A -1.5466
270 A A -0.6548
271 L A 0.0000
272 S A -0.5919
273 S A -0.5329
274 I A 0.0000
276 L A -0.2776
277 E A -2.0459
278 H A 0.0000
279 H A -2.0253
280 H A -1.7276
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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
TK4A -0.5194 -0.0466 View CSV PDB
TR4A -0.4726 -0.048 View CSV PDB
LE5A 0.0363 -0.0709 View CSV PDB
LK6A 0.0662 -0.0448 View CSV PDB
LK5A 0.3037 -0.0687 View CSV PDB
LR6A 1.1458 -0.0614 View CSV PDB
LR184A 0.8998 -0.0384 View CSV PDB
IK31A 1.1079 -0.0394 View CSV PDB
IE31A 1.7783 -0.0418 View CSV PDB
LK184A 1.5431 -0.0354 View CSV PDB
IK246A 1.5636 -0.024 View CSV PDB
IR246A 1.9172 -0.0246 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018