Project name: YfjR_mut2

Status: done

Started: 2025-08-08 10:38:53
Settings
Chain sequence(s) A: MTQAERRHDRLAVRLSLIISRLVAGETLSVRKLAAEFGVSVRTLRRDFRERLMYLDLEYQSGYCRLRTAGSEMQMVPDVLIFAHRSGLAGLFPGLDRRLVNALLMCDESPCVIAPANPRPSPSGALSFWRLIQAITGRRRVTLIAEGRRCERLAPCRLLIHQQTWYLVAEHEGHIAVFTLDEIHLIQPLQETFRRNDSLCRLVEDPRFIQALPHRRFIQHSRKTRVPADSPPE
B: MTQAERRHDRLAVRLSLIISRLVAGETLSVRKLAAEFGVSVRTLRRDFRERLMYLDLEYQSGYCRLRTAGSEMQMVPDVLIFAHRSGLAGLFPGLDRRLVNALLMCDESPCVIAPANPRPSPSGALSFWRLIQAITGRRRVTLIAEGRRCERLAPCRLLIHQQTWYLVAEHEGHIAVFTLDEIHLIQPLQETFRRNDSLCRLVEDPRFIQALPHRRFIQHSRKTRVPADSPPE
input PDB
Selected Chain(s) A,B
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 all 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                                          (00:09:00)
[INFO]       Auto_mut: Residue number 17 from chain A and a score of 1.573 (leucine) selected for  
                       automated muatation                                                         (00:09:04)
[INFO]       Auto_mut: Residue number 23 from chain A and a score of 1.427 (valine) selected for   
                       automated muatation                                                         (00:09:04)
[INFO]       Auto_mut: Residue number 17 from chain B and a score of 1.411 (leucine) selected for  
                       automated muatation                                                         (00:09:04)
[INFO]       Auto_mut: Residue number 23 from chain B and a score of 1.389 (valine) selected for   
                       automated muatation                                                         (00:09:04)
[INFO]       Auto_mut: Residue number 19 from chain A and a score of 1.157 (isoleucine) selected   
                       for automated muatation                                                     (00:09:04)
[INFO]       Auto_mut: Residue number 19 from chain B and a score of 1.135 (isoleucine) selected   
                       for automated muatation                                                     (00:09:04)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (leucine) into glutamic acid        (00:09:04)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (leucine) into aspartic acid        (00:09:04)
[INFO]       Auto_mut: Mutating residue number 23 from chain A (valine) into glutamic acid         (00:09:04)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (leucine) into arginine             (00:12:41)
[INFO]       Auto_mut: Mutating residue number 23 from chain A (valine) into lysine                (00:12:47)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (leucine) into lysine               (00:12:53)
[INFO]       Auto_mut: Mutating residue number 23 from chain A (valine) into aspartic acid         (00:16:22)
[INFO]       Auto_mut: Mutating residue number 17 from chain B (leucine) into glutamic acid        (00:16:31)
[INFO]       Auto_mut: Mutating residue number 17 from chain B (leucine) into aspartic acid        (00:17:12)
[INFO]       Auto_mut: Mutating residue number 23 from chain A (valine) into arginine              (00:19:59)
[INFO]       Auto_mut: Mutating residue number 17 from chain B (leucine) into lysine               (00:20:08)
[INFO]       Auto_mut: Mutating residue number 17 from chain B (leucine) into arginine             (00:20:52)
[INFO]       Auto_mut: Mutating residue number 23 from chain B (valine) into glutamic acid         (00:23:46)
[INFO]       Auto_mut: Mutating residue number 23 from chain B (valine) into aspartic acid         (00:24:05)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into glutamic acid     (00:24:33)
[INFO]       Auto_mut: Mutating residue number 23 from chain B (valine) into lysine                (00:27:15)
[INFO]       Auto_mut: Mutating residue number 23 from chain B (valine) into arginine              (00:27:42)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into lysine            (00:28:04)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into aspartic acid     (00:30:46)
[INFO]       Auto_mut: Mutating residue number 19 from chain B (isoleucine) into glutamic acid     (00:31:37)
[INFO]       Auto_mut: Mutating residue number 19 from chain B (isoleucine) into aspartic acid     (00:31:47)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into arginine          (00:34:22)
[INFO]       Auto_mut: Mutating residue number 19 from chain B (isoleucine) into arginine          (00:35:11)
[INFO]       Auto_mut: Mutating residue number 19 from chain B (isoleucine) into lysine            (00:35:12)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.4039 kcal/mol, Difference in average score from  
                       the base case: -0.0201                                                      (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (leucine) into lysine:    
                       Energy difference: 0.2436 kcal/mol, Difference in average score from the    
                       base case: -0.0181                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.9707 kcal/mol, Difference in average score from  
                       the base case: -0.0201                                                      (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (leucine) into arginine:  
                       Energy difference: -0.3181 kcal/mol, Difference in average score from the   
                       base case: -0.0253                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.1597 kcal/mol, Difference in average score from 
                       the base case: -0.0391                                                      (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain A (valine) into lysine:     
                       Energy difference: -0.5823 kcal/mol, Difference in average score from the   
                       base case: -0.0402                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.4002 kcal/mol, Difference in average score from  
                       the base case: -0.0287                                                      (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain A (valine) into arginine:   
                       Energy difference: -0.5725 kcal/mol, Difference in average score from the   
                       base case: -0.0415                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain B (leucine) into glutamic   
                       acid: Energy difference: 0.4091 kcal/mol, Difference in average score from  
                       the base case: -0.0259                                                      (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain B (leucine) into lysine:    
                       Energy difference: 0.4540 kcal/mol, Difference in average score from the    
                       base case: -0.0184                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain B (leucine) into aspartic   
                       acid: Energy difference: 0.9906 kcal/mol, Difference in average score from  
                       the base case: -0.0270                                                      (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain B (leucine) into arginine:  
                       Energy difference: -0.1391 kcal/mol, Difference in average score from the   
                       base case: -0.0240                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain B (valine) into glutamic    
                       acid: Energy difference: -0.1886 kcal/mol, Difference in average score from 
                       the base case: -0.0380                                                      (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain B (valine) into lysine:     
                       Energy difference: -0.5782 kcal/mol, Difference in average score from the   
                       base case: -0.0375                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain B (valine) into aspartic    
                       acid: Energy difference: 0.3574 kcal/mol, Difference in average score from  
                       the base case: -0.0377                                                      (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 23 from chain B (valine) into arginine:   
                       Energy difference: -0.5472 kcal/mol, Difference in average score from the   
                       base case: -0.0398                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 1.5137 kcal/mol, Difference in average    
                       score from the base case: -0.0186                                           (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.5742 kcal/mol, Difference in average score from the    
                       base case: -0.0203                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 2.5409 kcal/mol, Difference in average    
                       score from the base case: -0.0131                                           (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       arginine: Energy difference: 1.1491 kcal/mol, Difference in average score   
                       from the base case: -0.0228                                                 (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain B (isoleucine) into         
                       glutamic acid: Energy difference: 1.4748 kcal/mol, Difference in average    
                       score from the base case: -0.0168                                           (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain B (isoleucine) into lysine: 
                       Energy difference: 0.5378 kcal/mol, Difference in average score from the    
                       base case: -0.0192                                                          (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain B (isoleucine) into         
                       aspartic acid: Energy difference: 2.4580 kcal/mol, Difference in average    
                       score from the base case: -0.0161                                           (00:39:18)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain B (isoleucine) into         
                       arginine: Energy difference: 1.0099 kcal/mol, Difference in average score   
                       from the base case: -0.0207                                                 (00:39:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:39:28)
Show buried residues
Minimal score value
-4.8865
Maximal score value
1.5734
Average score
-0.9434
Total score value
-439.606
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 -0.3748
2 T A -1.2922
3 Q A -2.4368
4 A A -2.7752
5 E A -3.7489
6 R A -4.3731
7 R A -4.6966
8 H A -4.0240
9 D A -3.7870
10 R A -3.3735
11 L A -1.7834
12 A A -0.6951
13 V A 0.9898
14 R A 0.0000
15 L A 0.5207
16 S A 0.8935
17 L A 1.5734
18 I A 0.0000
19 I A 1.1565
20 S A 0.5784
21 R A -0.0597
22 L A 0.0000
23 V A 1.4270
24 A A 0.2429
25 G A -0.5060
26 E A -0.9363
27 T A -0.9136
28 L A 0.0000
29 S A -1.3486
30 V A 0.0000
31 R A -2.7891
32 K A -2.7767
33 L A 0.0000
34 A A 0.0000
35 A A -1.4165
36 E A -1.7093
37 F A -0.3336
38 G A -0.5451
39 V A -0.2792
40 S A -0.6355
41 V A -1.1200
42 R A -1.8606
43 T A -0.9620
44 L A 0.0000
45 R A -1.5152
46 R A -1.7859
47 D A 0.0000
48 F A 0.0000
49 R A 0.0000
50 E A -1.1512
51 R A -0.8854
52 L A 0.0000
53 M A -0.1266
54 Y A 0.7583
55 L A 0.1306
56 D A -1.9400
57 L A 0.0000
58 E A -1.2127
59 Y A 0.0000
60 Q A -0.3430
61 S A 0.1575
62 G A -0.4150
63 Y A -0.5788
64 C A 0.0000
65 R A -1.3090
66 L A -0.6584
67 R A -1.0328
68 T A -0.9082
69 A A -0.9334
70 G A -1.1478
71 S A -1.2558
72 E A -1.8178
73 M A -0.2251
74 Q A -0.7118
75 M A 0.1659
76 V A 0.6250
77 P A -0.2376
78 D A -0.1303
79 V A 0.0000
80 L A 0.0000
81 I A -0.0854
82 F A 0.0000
83 A A 0.0000
84 H A -1.3981
85 R A -1.6716
86 S A 0.0000
87 G A -1.0089
88 L A 0.0000
89 A A -0.6739
90 G A -0.9189
91 L A 0.0000
92 F A 0.0000
93 P A 0.0000
94 G A -0.7821
95 L A -1.1189
96 D A -1.9882
97 R A -2.9773
98 R A -2.5898
99 L A 0.0000
100 V A 0.0000
101 N A -1.4918
102 A A 0.0000
103 L A 0.0000
104 L A 0.0000
105 M A 0.0000
106 C A 0.0000
107 D A -1.1651
108 E A -0.8024
109 S A -0.6192
110 P A 0.0000
111 C A 0.0000
112 V A 0.0000
113 I A 0.0000
114 A A 0.0000
115 P A -1.2398
116 A A 0.0000
117 N A -2.4661
118 P A -2.2981
119 R A -2.8085
120 P A -1.7517
121 S A -1.0026
122 P A -0.3834
123 S A -0.2449
124 G A 0.0000
125 A A -0.2206
126 L A 0.7478
127 S A 0.0000
128 F A 0.0000
129 W A -0.0785
130 R A -0.3596
131 L A 0.0000
132 I A 0.0000
133 Q A -0.6487
134 A A 0.0000
135 I A 0.0000
136 T A -1.0105
137 G A 0.0000
138 R A -1.5910
139 R A -1.8984
140 R A -2.2779
141 V A 0.0000
142 T A 0.0000
143 L A 0.0000
144 I A -1.6542
145 A A 0.0000
146 E A -3.0530
147 G A -2.3314
148 R A -3.2366
149 R A -3.2461
150 C A 0.0000
151 E A -3.4441
152 R A -3.3296
153 L A 0.0000
154 A A 0.0000
155 P A 0.0000
156 C A 0.0000
157 R A 0.0000
158 L A 0.0000
159 L A 0.0000
160 I A 0.0000
161 H A 0.0000
162 Q A -1.0062
163 Q A 0.0000
164 T A -1.1542
165 W A 0.0000
166 Y A 0.0000
167 L A 0.0000
168 V A 0.0000
169 A A 0.0000
170 E A -1.5910
171 H A -2.1070
172 E A -2.9116
173 G A -2.1655
174 H A -1.6459
175 I A 0.0000
176 A A 0.0000
177 V A 0.0000
178 F A 0.0000
179 T A -0.9421
180 L A 0.0000
181 D A -2.7791
182 E A -1.9025
183 I A 0.0000
184 H A -1.2668
185 L A -0.1468
186 I A 0.0000
187 Q A -1.1536
188 P A -1.2283
189 L A -1.5568
190 Q A -1.8060
191 E A -1.6519
192 T A -1.6598
193 F A -1.6462
194 R A -2.4915
195 R A -2.0893
196 N A -1.9033
197 D A -2.3402
198 S A -1.3829
199 L A 0.0000
200 C A 0.0000
201 R A -2.7330
202 L A -1.7283
203 V A 0.0000
204 E A -2.7799
205 D A -2.3269
206 P A -2.1687
207 R A -2.6468
208 F A 0.0000
209 I A 0.0000
210 Q A -2.2551
211 A A -1.8889
212 L A 0.0000
213 P A -1.5980
214 H A -2.0802
215 R A -2.2722
216 R A -2.1128
217 F A -0.7433
218 I A -0.7767
219 Q A -1.7200
220 H A -1.7807
221 S A -2.1238
222 R A -3.3716
223 K A -2.9455
224 T A -1.9206
225 R A -1.8216
226 V A 0.1661
227 P A -0.5033
228 A A -0.8669
229 D A -1.7597
230 S A -1.5821
231 P A -1.4229
232 P A -1.6057
233 E A -2.0425
1 M B -0.5374
2 T B -1.4385
3 Q B -2.6345
4 A B -2.7954
5 E B -4.0281
6 R B -4.8865
7 R B -4.8808
8 H B -4.1475
9 D B -3.9030
10 R B -3.2567
11 L B -1.7879
12 A B -0.6937
13 V B 1.0016
14 R B 0.0000
15 L B 0.5113
16 S B 0.8570
17 L B 1.4113
18 I B 0.0000
19 I B 1.1346
20 S B 0.5714
21 R B 0.0169
22 L B 0.0000
23 V B 1.3887
24 A B 0.2616
25 G B -0.5857
26 E B -1.0004
27 T B -0.9496
28 L B 0.0000
29 S B -1.3358
30 V B 0.0000
31 R B -2.8269
32 K B -2.8150
33 L B 0.0000
34 A B 0.0000
35 A B -1.5297
36 E B -1.8475
37 F B 0.0000
38 G B -0.7494
39 V B -0.4938
40 S B -0.8250
41 V B -1.5638
42 R B -2.5418
43 T B -1.2441
44 L B 0.0000
45 R B -1.8235
46 R B -1.8775
47 D B 0.0000
48 F B 0.0000
49 R B 0.0000
50 E B -0.9032
51 R B -0.8120
52 L B 0.0000
53 M B 0.1553
54 Y B 1.0307
55 L B 0.2003
56 D B -1.6967
57 L B -1.1965
58 E B -1.2935
59 Y B 0.0000
60 Q B -0.5163
61 S B 0.1409
62 G B -0.4495
63 Y B -0.6263
64 C B 0.0000
65 R B -1.3587
66 L B -0.7853
67 R B -1.4447
68 T B -1.1141
69 A B -1.0371
70 G B -1.2155
71 S B -1.3376
72 E B -1.8136
73 M B -0.2540
74 Q B -0.9334
75 M B 0.0016
76 V B 0.4750
77 P B -0.2313
78 D B -0.2457
79 V B 0.0000
80 L B 0.0000
81 I B -0.1240
82 F B 0.0000
83 A B 0.0000
84 H B -1.1686
85 R B -0.9634
86 S B 0.0000
87 G B -0.8471
88 L B 0.0000
89 A B -0.6385
90 G B -0.9299
91 L B 0.0000
92 F B 0.0000
93 P B 0.0000
94 G B -0.7598
95 L B -0.9768
96 D B -1.6307
97 R B -1.8832
98 R B -2.2888
99 L B 0.0000
100 V B 0.0000
101 N B -1.0957
102 A B 0.0000
103 L B 0.0000
104 L B 0.0000
105 M B 0.0000
106 C B 0.0000
107 D B -2.3728
108 E B -1.5510
109 S B -1.0938
110 P B 0.0000
111 C B 0.0000
112 V B 0.0000
113 I B 0.0000
114 A B 0.0000
115 P B -1.2332
116 A B 0.0000
117 N B -2.4660
118 P B -2.3046
119 R B -2.8163
120 P B -1.7490
121 S B -1.0214
122 P B -0.3668
123 S B -0.2149
124 G B 0.0000
125 A B -0.1785
126 L B 0.8378
127 S B 0.0000
128 F B 0.0000
129 W B -0.1341
130 R B -0.5254
131 L B 0.0000
132 I B 0.0000
133 Q B -0.9902
134 A B 0.0000
135 I B 0.0000
136 T B -0.9733
137 G B 0.0000
138 R B -1.7087
139 R B -2.1438
140 R B -2.4038
141 V B 0.0000
142 T B 0.0000
143 L B 0.0000
144 I B -1.4520
145 A B 0.0000
146 E B -2.9441
147 G B -2.1898
148 R B -2.9145
149 R B -3.0547
150 C B 0.0000
151 E B -3.2912
152 R B -3.5680
153 L B 0.0000
154 A B 0.0000
155 P B 0.0000
156 C B 0.0000
157 R B -0.3887
158 L B 0.0000
159 L B 0.0000
160 I B 0.0000
161 H B 0.0000
162 Q B -1.0111
163 Q B 0.0000
164 T B -1.1556
165 W B 0.0000
166 Y B 0.0000
167 L B 0.0000
168 V B 0.0000
169 A B 0.0000
170 E B -1.4610
171 H B -2.1715
172 E B -2.9115
173 G B -2.2306
174 H B -1.9556
175 I B 0.0000
176 A B 0.0000
177 V B 0.0000
178 F B 0.0000
179 T B -0.9464
180 L B 0.0000
181 D B -2.7783
182 E B -1.8475
183 I B 0.0000
184 H B -1.1773
185 L B -0.0975
186 I B 0.0000
187 Q B -1.1369
188 P B -1.3469
189 L B -1.6092
190 Q B -1.8700
191 E B -1.7455
192 T B -1.7695
193 F B -1.7380
194 R B -2.5076
195 R B -2.0020
196 N B -1.8111
197 D B -2.0378
198 S B -1.2509
199 L B 0.0000
200 C B -1.7594
201 R B -2.6181
202 L B -1.6361
203 V B 0.0000
204 E B -2.7849
205 D B -2.3355
206 P B -2.1781
207 R B -2.6502
208 F B 0.0000
209 I B 0.0000
210 Q B -2.2562
211 A B -1.8785
212 L B 0.0000
213 P B -1.5927
214 H B -2.0796
215 R B -2.2800
216 R B -2.1657
217 F B -0.8870
218 I B -0.8898
219 Q B -1.8516
220 H B -1.9254
221 S B -2.1780
222 R B -3.4558
223 K B -2.9703
224 T B -1.9176
225 R B -1.8239
226 V B 0.1797
227 P B -0.4918
228 A B -0.8639
229 D B -1.7631
230 S B -1.5800
231 P B -1.4220
232 P B -1.5997
233 E B -2.0420
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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
VR23A -0.5725 -0.0415 View CSV PDB
VK23A -0.5823 -0.0402 View CSV PDB
VR23B -0.5472 -0.0398 View CSV PDB
VK23B -0.5782 -0.0375 View CSV PDB
LR17A -0.3181 -0.0253 View CSV PDB
LR17B -0.1391 -0.024 View CSV PDB
LK17A 0.2436 -0.0181 View CSV PDB
LE17B 0.4091 -0.0259 View CSV PDB
IK19B 0.5378 -0.0192 View CSV PDB
IK19A 0.5742 -0.0203 View CSV PDB
IR19B 1.0099 -0.0207 View CSV PDB
IR19A 1.1491 -0.0228 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018