Project name: MUT_N403-660-TSA1

Status: done

Started: 2025-02-10 19:12:51
Settings
Chain sequence(s) A: MANSVLSTWRQLDASFSESSIPTAGLVGFLSNTTSSGDTWIDGYRSMNATVTKAAKVENGFKFTGPGSRATWPVNSRWDIKQYGFVDYNFTIVAMATIHQVPSESTPLLGASLRGNKRTKLIGLSYGAGGKWETVYDGTKTVQGGTWEPGREYQVALMLQDGNKGFVYVDGVLVGNPAMLPTPEERWTEFSHFYFGGDEGDSGSDATLTDVFLYNRPLSRGELKMIKEVED
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                                          (00:02:28)
[INFO]       Auto_mut: Residue number 172 from chain A and a score of 1.341 (valine) selected for  
                       automated muatation                                                         (00:02:29)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.823 omitted from automated   
                       muatation (excluded by the user).                                           (00:02:29)
[INFO]       Auto_mut: Residue number 142 from chain A and a score of 0.804 (valine) selected for  
                       automated muatation                                                         (00:02:29)
[INFO]       Auto_mut: Residue number 173 from chain A and a score of 0.568 (leucine) selected for 
                       automated muatation                                                         (00:02:29)
[INFO]       Auto_mut: Residue number 6 from chain A and a score of 0.542 (leucine) selected for   
                       automated muatation                                                         (00:02:29)
[INFO]       Auto_mut: Residue number 179 from chain A and a score of 0.365 (methionine) selected  
                       for automated muatation                                                     (00:02:29)
[INFO]       Auto_mut: Residue number 101 from chain A and a score of 0.292 (valine) selected for  
                       automated muatation                                                         (00:02:29)
[INFO]       Auto_mut: Mutating residue number 172 from chain A (valine) into glutamic acid        (00:02:29)
[INFO]       Auto_mut: Mutating residue number 142 from chain A (valine) into glutamic acid        (00:02:29)
[INFO]       Auto_mut: Mutating residue number 172 from chain A (valine) into aspartic acid        (00:02:29)
[INFO]       Auto_mut: Mutating residue number 142 from chain A (valine) into lysine               (00:03:47)
[INFO]       Auto_mut: Mutating residue number 172 from chain A (valine) into arginine             (00:03:54)
[INFO]       Auto_mut: Mutating residue number 172 from chain A (valine) into lysine               (00:03:58)
[INFO]       Auto_mut: Mutating residue number 142 from chain A (valine) into aspartic acid        (00:05:24)
[INFO]       Auto_mut: Mutating residue number 173 from chain A (leucine) into glutamic acid       (00:05:32)
[INFO]       Auto_mut: Mutating residue number 173 from chain A (leucine) into aspartic acid       (00:05:40)
[INFO]       Auto_mut: Mutating residue number 173 from chain A (leucine) into lysine              (00:06:47)
[INFO]       Auto_mut: Mutating residue number 142 from chain A (valine) into arginine             (00:06:51)
[INFO]       Auto_mut: Mutating residue number 173 from chain A (leucine) into arginine            (00:06:58)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into glutamic acid         (00:08:09)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into aspartic acid         (00:08:13)
[INFO]       Auto_mut: Mutating residue number 179 from chain A (methionine) into glutamic acid    (00:08:23)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into lysine                (00:09:24)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (leucine) into arginine              (00:09:26)
[INFO]       Auto_mut: Mutating residue number 179 from chain A (methionine) into lysine           (00:09:45)
[INFO]       Auto_mut: Mutating residue number 179 from chain A (methionine) into aspartic acid    (00:10:45)
[INFO]       Auto_mut: Mutating residue number 101 from chain A (valine) into glutamic acid        (00:11:06)
[INFO]       Auto_mut: Mutating residue number 101 from chain A (valine) into aspartic acid        (00:11:19)
[INFO]       Auto_mut: Mutating residue number 179 from chain A (methionine) into arginine         (00:12:07)
[INFO]       Auto_mut: Mutating residue number 101 from chain A (valine) into lysine               (00:12:23)
[INFO]       Auto_mut: Mutating residue number 101 from chain A (valine) into arginine             (00:12:34)
[INFO]       Auto_mut: Effect of mutation residue number 172 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.2180 kcal/mol, Difference in average score from 
                       the base case: -0.0322                                                      (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 172 from chain A (valine) into lysine:    
                       Energy difference: -0.2570 kcal/mol, Difference in average score from the   
                       base case: -0.0295                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 172 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.0814 kcal/mol, Difference in average score from 
                       the base case: -0.0307                                                      (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 172 from chain A (valine) into arginine:  
                       Energy difference: -0.4774 kcal/mol, Difference in average score from the   
                       base case: -0.0147                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 142 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.1682 kcal/mol, Difference in average score from  
                       the base case: -0.0579                                                      (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 142 from chain A (valine) into lysine:    
                       Energy difference: -0.7366 kcal/mol, Difference in average score from the   
                       base case: -0.0389                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 142 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.2169 kcal/mol, Difference in average score from 
                       the base case: -0.0510                                                      (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 142 from chain A (valine) into arginine:  
                       Energy difference: -1.0218 kcal/mol, Difference in average score from the   
                       base case: -0.0424                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into glutamic  
                       acid: Energy difference: 2.3680 kcal/mol, Difference in average score from  
                       the base case: 0.0008                                                       (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into lysine:   
                       Energy difference: 1.9284 kcal/mol, Difference in average score from the    
                       base case: -0.0024                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.4167 kcal/mol, Difference in average score from  
                       the base case: 0.0026                                                       (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 173 from chain A (leucine) into arginine: 
                       Energy difference: 1.4215 kcal/mol, Difference in average score from the    
                       base case: -0.0034                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into glutamic    
                       acid: Energy difference: 0.9070 kcal/mol, Difference in average score from  
                       the base case: -0.0492                                                      (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into lysine:     
                       Energy difference: 0.5195 kcal/mol, Difference in average score from the    
                       base case: -0.0362                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into aspartic    
                       acid: Energy difference: 1.4568 kcal/mol, Difference in average score from  
                       the base case: -0.0395                                                      (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (leucine) into arginine:   
                       Energy difference: 0.8319 kcal/mol, Difference in average score from the    
                       base case: -0.0425                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 179 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.4878 kcal/mol, Difference in average    
                       score from the base case: -0.0276                                           (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 179 from chain A (methionine) into        
                       lysine: Energy difference: -0.3030 kcal/mol, Difference in average score    
                       from the base case: -0.0305                                                 (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 179 from chain A (methionine) into        
                       aspartic acid: Energy difference: 0.5700 kcal/mol, Difference in average    
                       score from the base case: -0.0316                                           (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 179 from chain A (methionine) into        
                       arginine: Energy difference: -1.8457 kcal/mol, Difference in average score  
                       from the base case: -0.0257                                                 (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1345 kcal/mol, Difference in average score from 
                       the base case: -0.0517                                                      (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain A (valine) into lysine:    
                       Energy difference: -0.7912 kcal/mol, Difference in average score from the   
                       base case: -0.0495                                                          (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.7341 kcal/mol, Difference in average score from  
                       the base case: -0.0514                                                      (00:13:54)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain A (valine) into arginine:  
                       Energy difference: -0.3919 kcal/mol, Difference in average score from the   
                       base case: -0.0540                                                          (00:13:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:59)
Show buried residues
Minimal score value
-3.9441
Maximal score value
1.3412
Average score
-0.8428
Total score value
-194.678
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 0.8234
2 A A 0.2822
3 N A -0.5537
4 S A -0.0834
5 V A 0.0481
6 L A 0.5419
7 S A -0.5565
8 T A -0.8010
9 W A -0.5627
10 R A -1.8943
11 Q A -1.7574
12 L A -0.9953
13 D A -1.2926
14 A A -1.4675
15 S A -1.3244
16 F A 0.0000
17 S A -1.3697
18 E A -1.9772
19 S A -1.4201
20 S A -1.1093
21 I A 0.0000
22 P A -0.3857
23 T A -0.2784
24 A A -0.1692
25 G A -0.3598
26 L A 0.0000
27 V A -0.0474
28 G A 0.0000
29 F A 0.0000
30 L A 0.0000
31 S A -1.4275
32 N A -2.1698
33 T A 0.0000
34 T A -0.9447
35 S A -0.9307
36 S A -0.9875
37 G A -1.7080
38 D A -1.9343
39 T A -1.2767
40 W A 0.0000
41 I A -1.0594
42 D A 0.0000
43 G A -0.8032
44 Y A 0.0000
45 R A -1.7818
46 S A -1.0839
47 M A -0.8708
48 N A -1.2183
49 A A 0.0000
50 T A -0.7022
51 V A 0.0000
52 T A -1.3893
53 K A -2.3805
54 A A -1.8557
55 A A -1.5503
56 K A -2.8776
57 V A -2.0810
58 E A -2.8940
59 N A -2.5536
60 G A 0.0000
61 F A 0.0000
62 K A -1.7492
63 F A 0.0000
64 T A -1.1616
65 G A -1.2049
66 P A -1.8716
67 G A -1.9492
68 S A 0.0000
69 R A -1.5513
70 A A 0.0000
71 T A -0.4114
72 W A 0.0000
73 P A -0.4001
74 V A 0.0000
75 N A 0.0000
76 S A -1.6359
77 R A -1.9161
78 W A -0.4198
79 D A -1.3257
80 I A 0.0426
81 K A -1.7171
82 Q A -1.3047
83 Y A 0.0000
84 G A -0.4922
85 F A 0.0897
86 V A 0.0000
87 D A 0.0000
88 Y A 0.0432
89 N A -0.7486
90 F A 0.0000
91 T A 0.0000
92 I A 0.0000
93 V A 0.0000
94 A A 0.0000
95 M A -0.5461
96 A A 0.0000
97 T A -1.7459
98 I A 0.0000
99 H A -1.6222
100 Q A -1.0769
101 V A 0.2922
102 P A -0.4658
103 S A -0.9263
104 E A -1.8329
105 S A -1.1023
106 T A 0.0000
107 P A -0.5159
108 L A 0.0000
109 L A 0.0000
110 G A 0.0000
111 A A 0.0000
112 S A 0.0000
113 L A 0.0000
114 R A -3.2340
115 G A -2.8472
116 N A -3.1144
117 K A -3.6286
118 R A -3.9441
119 T A -2.6191
120 K A -1.9096
121 L A 0.0000
122 I A 0.0000
123 G A 0.0000
124 L A 0.0000
125 S A 0.0000
126 Y A 0.0000
127 G A 0.0000
128 A A -0.5532
129 G A -0.5853
130 G A -0.8558
131 K A -1.2758
132 W A 0.0000
133 E A 0.0000
134 T A 0.0000
135 V A 0.0000
136 Y A -1.0445
137 D A -1.8316
138 G A -1.8669
139 T A -1.5095
140 K A -1.6704
141 T A -0.1338
142 V A 0.8042
143 Q A -0.3153
144 G A -0.7219
145 G A -0.5878
146 T A -1.2831
147 W A 0.0000
148 E A -2.5374
149 P A -1.9279
150 G A -2.1117
151 R A -2.5056
152 E A -2.7178
153 Y A 0.0000
154 Q A 0.0000
155 V A 0.0000
156 A A 0.0000
157 L A 0.0000
158 M A 0.0000
159 L A 0.0000
160 Q A -1.3582
161 D A -1.9807
162 G A 0.0000
163 N A -0.8955
164 K A -0.9150
165 G A 0.0000
166 F A 0.0000
167 V A 0.0000
168 Y A 0.0000
169 V A 0.0000
170 D A -0.3899
171 G A 0.0000
172 V A 1.3412
173 L A 0.5679
174 V A 0.0000
175 G A -0.5380
176 N A -1.2974
177 P A -0.5876
178 A A -0.2648
179 M A 0.3654
180 L A 0.0000
181 P A -1.0693
182 T A -1.4336
183 P A -1.5325
184 E A -2.5481
185 E A -2.4964
186 R A -1.6283
187 W A -0.5503
188 T A -1.3339
189 E A -1.5727
190 F A 0.0000
191 S A 0.0000
192 H A -0.7793
193 F A 0.0000
194 Y A 0.0000
195 F A 0.0000
196 G A 0.0000
197 G A 0.0000
198 D A -1.9831
199 E A -2.9603
200 G A -2.4891
201 D A -2.6497
202 S A -2.1252
203 G A -1.8766
204 S A 0.0000
205 D A -1.1120
206 A A 0.0000
207 T A -0.9340
208 L A 0.0000
209 T A -0.9884
210 D A -1.0018
211 V A 0.0000
212 F A 0.0000
213 L A 0.0000
214 Y A 0.0000
215 N A -0.6606
216 R A -0.9685
217 P A -1.0030
218 L A 0.0000
219 S A -1.5219
220 R A -2.0624
221 G A -1.7757
222 E A -1.4965
223 L A 0.0000
224 K A -1.8836
225 M A -1.3705
226 I A 0.0000
227 K A -2.7830
228 E A -3.0470
229 V A -2.0274
230 E A -3.0681
231 D A -3.0477
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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
VR142A -1.0218 -0.0424 View CSV PDB
VK101A -0.7912 -0.0495 View CSV PDB
MR179A -1.8457 -0.0257 View CSV PDB
VR101A -0.3919 -0.054 View CSV PDB
VK142A -0.7366 -0.0389 View CSV PDB
MK179A -0.303 -0.0305 View CSV PDB
VE172A -0.218 -0.0322 View CSV PDB
VK172A -0.257 -0.0295 View CSV PDB
LK6A 0.5195 -0.0362 View CSV PDB
LE6A 0.907 -0.0492 View CSV PDB
LR173A 1.4215 -0.0034 View CSV PDB
LK173A 1.9284 -0.0024 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018