Project name: Bf13FT

Status: done

Started: 2024-07-08 13:14:42
Settings
Chain sequence(s) A: MKKIYLKFVDFWDGFDTISNFIVDALSIQYEVVLSNEPDYLFYSCFGTSHLEYDCIKIMFIGENIVPDFNVCDYAIGFNYIDFGDRYLRLPLYAIYDGFSNLQNKKIDVNKALDRKFCSIVVSNNKWADPIRETFFKLLSSYKKVDSGGRAWNNIGGPVDNKLDFISQYKFNIAFENSRVLGYTTEKIMEPMQVNSIPVYWGNPLVGKDFNVDSFVNAHDFDSLERLVEYIIELDSSKDKYLEMLEKPWLLDKTYLDWKQLLLNFINNIMMKSYKDAKYLVNYGHAGKYRNEQRFWGRCERKFKLQRIIEYYSQLFDRK
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                                          (00:04:21)
[INFO]       Auto_mut: Residue number 66 from chain A and a score of 1.996 (valine) selected for   
                       automated muatation                                                         (00:04:22)
[INFO]       Auto_mut: Residue number 312 from chain A and a score of 1.716 (tyrosine) selected    
                       for automated muatation                                                     (00:04:22)
[INFO]       Auto_mut: Residue number 18 from chain A and a score of 1.542 (isoleucine) selected   
                       for automated muatation                                                     (00:04:23)
[INFO]       Auto_mut: Residue number 311 from chain A and a score of 1.518 (tyrosine) selected    
                       for automated muatation                                                     (00:04:23)
[INFO]       Auto_mut: Residue number 65 from chain A and a score of 1.391 (isoleucine) selected   
                       for automated muatation                                                     (00:04:23)
[INFO]       Auto_mut: Residue number 309 from chain A and a score of 1.275 (isoleucine) selected  
                       for automated muatation                                                     (00:04:23)
[INFO]       Auto_mut: Mutating residue number 66 from chain A (valine) into glutamic acid         (00:04:23)
[INFO]       Auto_mut: Mutating residue number 66 from chain A (valine) into aspartic acid         (00:04:23)
[INFO]       Auto_mut: Mutating residue number 312 from chain A (tyrosine) into glutamic acid      (00:04:23)
[INFO]       Auto_mut: Mutating residue number 66 from chain A (valine) into lysine                (00:06:09)
[INFO]       Auto_mut: Mutating residue number 66 from chain A (valine) into arginine              (00:06:19)
[INFO]       Auto_mut: Mutating residue number 312 from chain A (tyrosine) into lysine             (00:06:25)
[INFO]       Auto_mut: Mutating residue number 312 from chain A (tyrosine) into aspartic acid      (00:08:12)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (isoleucine) into glutamic acid     (00:08:18)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (isoleucine) into aspartic acid     (00:08:28)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (isoleucine) into lysine            (00:10:07)
[INFO]       Auto_mut: Mutating residue number 312 from chain A (tyrosine) into arginine           (00:10:12)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (isoleucine) into arginine          (00:10:22)
[INFO]       Auto_mut: Mutating residue number 311 from chain A (tyrosine) into glutamic acid      (00:12:17)
[INFO]       Auto_mut: Mutating residue number 311 from chain A (tyrosine) into aspartic acid      (00:12:21)
[INFO]       Auto_mut: Mutating residue number 65 from chain A (isoleucine) into glutamic acid     (00:12:27)
[INFO]       Auto_mut: Mutating residue number 311 from chain A (tyrosine) into lysine             (00:14:21)
[INFO]       Auto_mut: Mutating residue number 311 from chain A (tyrosine) into arginine           (00:14:22)
[INFO]       Auto_mut: Mutating residue number 65 from chain A (isoleucine) into lysine            (00:14:28)
[INFO]       Auto_mut: Mutating residue number 65 from chain A (isoleucine) into aspartic acid     (00:16:29)
[INFO]       Auto_mut: Mutating residue number 309 from chain A (isoleucine) into glutamic acid    (00:16:30)
[INFO]       Auto_mut: Mutating residue number 309 from chain A (isoleucine) into aspartic acid    (00:16:47)
[INFO]       Auto_mut: Mutating residue number 65 from chain A (isoleucine) into arginine          (00:18:22)
[INFO]       Auto_mut: Mutating residue number 309 from chain A (isoleucine) into lysine           (00:18:33)
[INFO]       Auto_mut: Mutating residue number 309 from chain A (isoleucine) into arginine         (00:18:56)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.0928 kcal/mol, Difference in average score from 
                       the base case: -0.0220                                                      (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain A (valine) into lysine:     
                       Energy difference: -0.4790 kcal/mol, Difference in average score from the   
                       base case: -0.0116                                                          (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.5405 kcal/mol, Difference in average score from  
                       the base case: -0.0134                                                      (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain A (valine) into arginine:   
                       Energy difference: -0.4649 kcal/mol, Difference in average score from the   
                       base case: -0.0186                                                          (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 312 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.6852 kcal/mol, Difference in average score from  
                       the base case: -0.0086                                                      (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 312 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.1694 kcal/mol, Difference in average score from the    
                       base case: -0.0051                                                          (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 312 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 1.8572 kcal/mol, Difference in average score from  
                       the base case: -0.0000                                                      (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 312 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.7660 kcal/mol, Difference in average score   
                       from the base case: -0.0326                                                 (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.1252 kcal/mol, Difference in average   
                       score from the base case: -0.0314                                           (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.3716 kcal/mol, Difference in average score from the   
                       base case: -0.0222                                                          (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: -0.0780 kcal/mol, Difference in average   
                       score from the base case: -0.0237                                           (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (isoleucine) into         
                       arginine: Energy difference: -1.0783 kcal/mol, Difference in average score  
                       from the base case: -0.0198                                                 (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 311 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.8204 kcal/mol, Difference in average score from  
                       the base case: -0.0317                                                      (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 311 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.5187 kcal/mol, Difference in average score from the    
                       base case: -0.0221                                                          (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 311 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 1.2897 kcal/mol, Difference in average score from  
                       the base case: -0.0253                                                      (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 311 from chain A (tyrosine) into          
                       arginine: Energy difference: 1.0241 kcal/mol, Difference in average score   
                       from the base case: -0.0343                                                 (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 65 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 1.1500 kcal/mol, Difference in average    
                       score from the base case: -0.0242                                           (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 65 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.0858 kcal/mol, Difference in average score from the    
                       base case: -0.0081                                                          (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 65 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.6498 kcal/mol, Difference in average    
                       score from the base case: -0.0126                                           (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 65 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.4524 kcal/mol, Difference in average score   
                       from the base case: -0.0182                                                 (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 309 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.5811 kcal/mol, Difference in average    
                       score from the base case: -0.0376                                           (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 309 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.1681 kcal/mol, Difference in average score     
                       from the base case: -0.0340                                                 (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 309 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.0387 kcal/mol, Difference in average    
                       score from the base case: -0.0360                                           (00:21:07)
[INFO]       Auto_mut: Effect of mutation residue number 309 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.4109 kcal/mol, Difference in average score   
                       from the base case: -0.0476                                                 (00:21:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:13)
Show buried residues
Minimal score value
-3.7604
Maximal score value
1.9957
Average score
-0.7706
Total score value
-245.8329
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 M A -0.4873
2 K A -2.3293
3 K A -2.2606
4 I A 0.0000
5 Y A -0.4068
6 L A 0.0000
7 K A -0.5231
8 F A 0.0000
9 V A 0.2629
10 D A 0.1796
11 F A 0.0531
12 W A -0.2988
13 D A -1.7367
14 G A -1.4410
15 F A -0.8005
16 D A -0.9448
17 T A 0.3857
18 I A 1.5425
19 S A 0.0237
20 N A -0.3616
21 F A -0.4781
22 I A 0.0000
23 V A -0.2465
24 D A -1.3164
25 A A 0.0000
26 L A 0.0000
27 S A -0.2963
28 I A 0.7677
29 Q A -0.5890
30 Y A -1.1202
31 E A -1.6839
32 V A -0.1611
33 V A 0.6039
34 L A 0.8331
35 S A -0.8070
36 N A -2.0677
37 E A -2.7076
38 P A 0.0000
39 D A -1.3127
40 Y A -0.6081
41 L A 0.0000
42 F A 0.0000
43 Y A 0.0000
44 S A 0.0000
45 C A 0.6150
46 F A 0.7169
47 G A 0.0750
48 T A -0.6717
49 S A -1.0353
50 H A 0.0000
51 L A 0.0000
52 E A -2.2665
53 Y A -2.1074
54 D A -2.4528
55 C A 0.0000
56 I A 0.0000
57 K A 0.0000
58 I A 0.0000
59 M A 0.0000
60 F A 0.0000
61 I A 0.0000
62 G A -0.1533
63 E A -0.5938
64 N A -0.2899
65 I A 1.3913
66 V A 1.9957
67 P A 0.0000
68 D A -0.0650
69 F A -0.0359
70 N A -0.7694
71 V A 0.0000
72 C A 0.0000
73 D A 0.0000
74 Y A 0.0000
75 A A 0.0000
76 I A 0.0000
77 G A 0.0000
78 F A 0.0000
79 N A 0.7703
80 Y A 0.5754
81 I A 0.1427
82 D A -1.3264
83 F A -0.2734
84 G A -0.9596
85 D A -1.4271
86 R A -0.6596
87 Y A 0.0000
88 L A 0.0000
89 R A -0.2572
90 L A 0.0000
91 P A 0.0000
92 L A 0.1020
93 Y A 0.0000
94 A A 0.0000
95 I A -0.1830
96 Y A -0.2736
97 D A -1.7985
98 G A -1.5069
99 F A 0.0000
100 S A -1.9515
101 N A -2.5210
102 L A 0.0000
103 Q A -2.5660
104 N A -2.8676
105 K A -2.7175
106 K A -2.6019
107 I A -1.7989
108 D A -1.7025
109 V A -1.4962
110 N A -2.3834
111 K A -3.1212
112 A A 0.0000
113 L A -2.0789
114 D A -3.1262
115 R A -2.8255
116 K A -2.6570
117 F A -1.7243
118 C A 0.0000
119 S A 0.0000
120 I A 0.0000
121 V A -0.3536
122 V A 0.0000
123 S A -1.6619
124 N A -1.9137
125 N A -2.0364
126 K A -1.8268
127 W A -0.2512
128 A A -1.0563
129 D A -1.2025
130 P A -0.7981
131 I A -0.3691
132 R A 0.0000
133 E A -1.3037
134 T A -0.8134
135 F A 0.0000
136 F A 0.0000
137 K A -1.7843
138 L A -0.9377
139 L A 0.0000
140 S A -1.5272
141 S A -1.0000
142 Y A -0.8799
143 K A -1.7165
144 K A -2.6568
145 V A 0.0000
146 D A 0.0000
147 S A 0.0000
148 G A 0.0000
149 G A 0.0000
150 R A -2.3823
151 A A 0.0000
152 W A -0.9925
153 N A -1.0928
154 N A -1.0357
155 I A 0.0698
156 G A -0.6306
157 G A -1.0102
158 P A -1.4758
159 V A -1.5558
160 D A -2.5470
161 N A -2.5703
162 K A -2.1228
163 L A -1.5378
164 D A -2.5787
165 F A 0.0000
166 I A 0.0000
167 S A -1.7297
168 Q A -2.5164
169 Y A 0.0000
170 K A -1.3874
171 F A 0.0000
172 N A 0.0000
173 I A 0.0000
174 A A 0.0000
175 F A 0.0000
176 E A 0.0000
177 N A -1.3218
178 S A -1.0567
179 R A -1.7178
180 V A 0.0115
181 L A 1.0038
182 G A 0.0000
183 Y A 0.0000
184 T A 0.0000
185 T A 0.0000
186 E A -0.6850
187 K A -0.6900
188 I A 0.0000
189 M A 0.0000
190 E A -0.7936
191 P A 0.0000
192 M A 0.0000
193 Q A -1.2236
194 V A -0.6419
195 N A -1.1372
196 S A 0.0000
197 I A 0.0000
198 P A 0.0000
199 V A 0.0000
200 Y A 0.0000
201 W A 0.0000
202 G A 0.0000
203 N A 0.0000
204 P A -0.3442
205 L A 0.4435
206 V A 0.0000
207 G A -0.4963
208 K A -1.3802
209 D A 0.0000
210 F A 0.0000
211 N A 0.0000
212 V A 0.4116
213 D A -1.6660
214 S A 0.0000
215 F A 0.0000
216 V A 0.0000
217 N A -0.6857
218 A A 0.0000
219 H A -1.4125
220 D A -2.3253
221 F A -2.3402
222 D A -2.7951
223 S A -2.4558
224 L A -1.7478
225 E A -3.2364
226 R A -3.7604
227 L A 0.0000
228 V A 0.0000
229 E A -2.9624
230 Y A -1.6687
231 I A 0.0000
232 I A -1.1401
233 E A -2.0099
234 L A 0.0000
235 D A -1.6207
236 S A -1.4458
237 S A -2.3755
238 K A -3.2095
239 D A -3.5574
240 K A -3.1581
241 Y A 0.0000
242 L A -2.4495
243 E A -3.7570
244 M A 0.0000
245 L A 0.0000
246 E A -3.1275
247 K A -2.1742
248 P A -1.3453
249 W A 0.0000
250 L A 0.0000
251 L A 0.3579
252 D A -1.2880
253 K A -2.2039
254 T A -1.2643
255 Y A 0.0000
256 L A -1.8095
257 D A -2.3319
258 W A -1.4424
259 K A -1.8084
260 Q A -1.3999
261 L A -0.8860
262 L A 0.0000
263 L A 0.0000
264 N A -1.3133
265 F A -0.9307
266 I A 0.0000
267 N A -0.7657
268 N A -1.2066
269 I A 0.0000
270 M A -0.1156
271 M A 0.4272
272 K A -0.7076
273 S A -0.7866
274 Y A -0.5458
275 K A -2.1694
276 D A -2.2498
277 A A 0.0000
278 K A -0.7308
279 Y A 0.2626
280 L A 0.4923
281 V A 0.7791
282 N A -0.4746
283 Y A 0.2970
284 G A -0.7089
285 H A -1.5775
286 A A -0.9717
287 G A 0.0000
288 K A -2.6097
289 Y A -1.7929
290 R A 0.0000
291 N A -1.7573
292 E A -1.9528
293 Q A -1.1089
294 R A -1.2802
295 F A 0.5721
296 W A 0.0105
297 G A 0.0000
298 R A -2.1839
299 C A -1.0661
300 E A -1.8987
301 R A -3.1906
302 K A -2.5240
303 F A -0.8417
304 K A -1.8219
305 L A -0.3894
306 Q A -1.0488
307 R A -1.1943
308 I A 0.9552
309 I A 1.2748
310 E A -0.1194
311 Y A 1.5176
312 Y A 1.7155
313 S A 0.4183
314 Q A -0.4724
315 L A 0.1480
316 F A 0.2400
317 D A -2.3316
318 R A -2.9745
319 K A -2.6287
Download PDB file
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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
IR18A -1.0783 -0.0198 View CSV PDB
IE18A -0.1252 -0.0314 View CSV PDB
VR66A -0.4649 -0.0186 View CSV PDB
VE66A -0.0928 -0.022 View CSV PDB
IK309A 0.1681 -0.034 View CSV PDB
IR309A 0.4109 -0.0476 View CSV PDB
IK65A 0.0858 -0.0081 View CSV PDB
YK311A 0.5187 -0.0221 View CSV PDB
YR312A 0.766 -0.0326 View CSV PDB
IR65A 0.4524 -0.0182 View CSV PDB
YE311A 0.8204 -0.0317 View CSV PDB
YK312A 0.1694 -0.0051 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018