Project name: 367eccb03852183

Status: done

Started: 2024-06-11 18:56:50
Settings
Chain sequence(s) H: EVQLVESGAEVKKPGSSVKVSCRASGTFYKYAINWVRQAPGQGLEWMGGIIPFFGTTNYAQKFQGRLTITADGSTNTAYMQLDSLRSEDTAVYYCAGPSITESHYCLDCAAKDYYYGLDVWGQGTTVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP
L: QSVLTQPPSASGTPGQSVTISCSGSRSNIGGNTVNWYQHLPGMAPKLLIYSSNQRSSGVPDRFSGSKSGTSASLAISGLQSEDDADYYCASWDDSLNGVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT
input PDB
Selected Chain(s) H,L
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                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:50)
[INFO]       Auto_mut: Residue number 170 from chain H and a score of 1.370 (leucine) selected for 
                       automated muatation                                                         (00:02:52)
[INFO]       Auto_mut: Mutating residue number 170 from chain H (leucine) into glutamic acid       (00:02:52)
[INFO]       Auto_mut: Mutating residue number 170 from chain H (leucine) into lysine              (00:02:52)
[INFO]       Auto_mut: Mutating residue number 170 from chain H (leucine) into aspartic acid       (00:02:52)
[INFO]       Auto_mut: Mutating residue number 170 from chain H (leucine) into arginine            (00:04:15)
[INFO]       Auto_mut: Effect of mutation residue number 170 from chain H (leucine) into glutamic  
                       acid: Energy difference: -0.1030 kcal/mol, Difference in average score from 
                       the base case: -0.0298                                                      (00:05:40)
[INFO]       Auto_mut: Effect of mutation residue number 170 from chain H (leucine) into lysine:   
                       Energy difference: -0.3033 kcal/mol, Difference in average score from the   
                       base case: -0.0257                                                          (00:05:40)
[INFO]       Auto_mut: Effect of mutation residue number 170 from chain H (leucine) into aspartic  
                       acid: Energy difference: 0.6892 kcal/mol, Difference in average score from  
                       the base case: -0.0300                                                      (00:05:40)
[INFO]       Auto_mut: Effect of mutation residue number 170 from chain H (leucine) into arginine: 
                       Energy difference: 0.4020 kcal/mol, Difference in average score from the    
                       base case: -0.0286                                                          (00:05:40)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:42)
Show buried residues
Minimal score value
-3.1078
Maximal score value
1.3698
Average score
-0.641
Total score value
-279.4613
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 Q L -1.0917
2 S L -0.4012
3 V L 0.6795
4 L L 0.0000
5 T L -0.3086
6 Q L 0.0000
7 P L -0.6667
8 P L -0.9681
9 S L -1.0610
11 A L -0.7379
12 S L -0.4830
13 G L 0.0000
14 T L -0.5990
15 P L -1.2864
16 G L -1.5299
17 Q L -1.8405
18 S L -1.2383
19 V L 0.0000
20 T L -0.2033
21 I L 0.0000
22 S L -0.3508
23 C L 0.0000
24 S L -0.2598
25 G L -0.5216
26 S L -1.1951
27 R L -2.4316
27A S L -1.7376
27B N L 0.0000
28 I L 0.0000
29 G L -1.5275
30 G L -1.4008
31 N L -1.0167
32 T L -0.4448
33 V L 0.0000
34 N L -0.2174
35 W L 0.0000
36 Y L 0.0000
37 Q L 0.0000
38 H L 0.0000
39 L L 0.0728
40 P L 0.1512
41 G L -0.1370
42 M L 0.3406
43 A L -0.1686
44 P L 0.0000
45 K L -1.3340
46 L L 0.0000
47 L L 0.0000
48 I L 0.0000
49 Y L -0.3972
50 S L -0.6903
51 S L 0.0000
52 N L -2.0050
53 Q L -1.9437
54 R L -1.9768
55 S L -1.3751
56 S L -0.8561
57 G L -0.8898
58 V L -1.1484
59 P L -1.3187
60 D L -2.3454
61 R L -1.5344
62 F L 0.0000
63 S L -1.3073
64 G L 0.0000
65 S L -1.1746
66 K L -1.3180
67 S L -0.8626
68 G L -1.1976
69 T L -1.2236
70 S L -0.8916
71 A L 0.0000
72 S L -0.6025
73 L L 0.0000
74 A L -0.2716
75 I L 0.0000
76 S L -1.2806
77 G L -1.4645
78 L L 0.0000
79 Q L -1.7351
80 S L -1.6358
81 E L -2.3843
82 D L 0.0000
83 D L -1.3107
84 A L 0.0000
85 D L 0.0000
86 Y L 0.0000
87 Y L 0.0000
88 C L 0.0000
89 A L 0.0000
90 S L 0.0000
91 W L 0.0000
92 D L 0.0000
93 D L -2.0359
94 S L -1.2045
95 L L -0.5963
95A N L -1.6846
95B G L 0.0000
96 V L -0.0686
97 V L 0.0000
98 F L 0.0000
99 G L 0.0000
100 G L -1.1055
101 G L 0.0000
102 T L 0.0000
103 K L -1.9091
104 L L 0.0000
105 T L -0.4551
106 V L 0.0000
106A L L 0.4831
107 G L -0.4196
108 Q L -0.7827
109 P L -1.1798
110 K L -2.2274
111 A L -1.2802
112 A L -0.8210
113 P L 0.0000
114 S L -0.6565
115 V L 0.0000
116 T L -0.5101
117 L L 0.0000
118 F L 0.0000
119 P L -0.0456
120 P L 0.0000
121 S L -0.5189
122 S L -0.7858
123 E L -1.4088
124 E L 0.0000
125 L L -1.4803
126 Q L -1.8531
127 A L -1.4377
128 N L -2.1527
129 K L -1.6554
130 A L 0.0000
131 T L 0.0000
132 L L 0.0000
133 V L 0.0000
134 C L 0.0000
135 L L 0.0000
136 I L 0.0000
137 S L -0.6354
138 D L -1.4587
139 F L 0.0000
140 Y L -1.0460
141 P L -0.8113
142 G L -0.6597
143 A L -0.1593
144 V L -0.0756
145 T L -0.0904
146 V L 0.0819
147 A L -0.3775
148 W L 0.0000
149 K L -0.9216
150 A L 0.0000
151 D L -1.5798
152 S L -0.8358
153 S L -0.6484
154 P L -0.8201
155 V L -0.5888
156 K L -1.5328
157 A L -0.7775
158 G L -0.6709
159 V L -0.3378
160 E L -0.2820
161 T L 0.1030
162 T L 0.0802
163 T L -0.1416
164 P L -0.3183
165 S L -0.6478
166 K L -1.3628
167 Q L -1.3196
168 S L -1.4879
169 N L -2.2364
170 N L -1.8194
171 K L -1.6544
172 Y L -0.8905
173 A L 0.0000
174 A L 0.0000
175 S L 0.0000
176 S L 0.0000
177 Y L 0.0000
178 L L 0.0000
179 S L -0.3357
180 L L -0.7430
181 T L -1.5036
182 P L -2.2246
183 E L -3.0767
184 Q L -2.3322
185 W L 0.0000
186 K L -3.1078
187 S L -2.4465
188 H L -2.4914
189 R L -2.6139
190 S L -1.6212
191 Y L 0.0000
192 S L 0.0000
193 C L 0.0000
194 Q L -1.0762
195 V L 0.0000
196 T L -0.7351
197 H L 0.0000
198 E L -2.2753
199 G L -1.4554
200 S L -0.9463
201 T L -0.8256
202 V L -0.8874
203 E L -2.2370
204 K L -1.8581
205 T L -1.0279
206 V L -0.3995
207 A L -0.8260
208 P L -1.0244
209 T L -0.5391
1 E H -2.0329
2 V H -1.2975
3 Q H -1.5949
4 L H 0.0000
5 V H -0.0591
6 E H 0.0000
7 S H -0.7746
8 G H -1.0025
9 A H -1.0838
10 E H -1.5865
11 V H -0.9932
12 K H -1.7653
13 K H -2.4666
14 P H -2.0580
15 G H -1.6510
16 S H -1.3630
17 S H -1.4546
18 V H 0.0000
19 K H -2.0139
20 V H 0.0000
21 S H -0.6373
22 C H 0.0000
23 R H -1.4873
24 A H 0.0000
25 S H -0.9946
26 G H -0.7933
27 T H -0.2776
28 F H -0.0375
29 Y H 0.4906
30 K H 0.4353
31 Y H 0.3684
32 A H 0.0000
33 I H 0.0000
34 N H 0.0000
36 W H 0.0000
37 V H 0.0000
38 R H 0.0000
39 Q H -0.7057
40 A H -1.0870
41 P H -1.0729
42 G H -1.2255
43 Q H -1.7443
44 G H -1.1829
45 L H 0.0000
46 E H -0.7200
47 W H 0.0000
48 M H 0.0000
49 G H 0.0000
50 G H 0.0000
51 I H 0.0000
52 I H 0.0000
52A P H 0.3429
53 F H 1.2872
54 F H 1.0495
55 G H 0.1182
56 T H 0.1751
57 T H 0.0062
58 N H 0.0000
59 Y H -0.7871
60 A H -1.3429
61 Q H -2.4113
62 K H -2.6304
63 F H 0.0000
64 Q H -2.3372
65 G H -1.6246
66 R H -1.3522
67 L H 0.0000
68 T H -0.7279
69 I H 0.0000
70 T H -0.4347
71 A H -0.5693
72 D H -1.1384
73 G H -0.8361
74 S H -0.8075
75 T H -0.9972
76 N H -1.1713
77 T H -0.9672
78 A H 0.0000
79 Y H -0.5950
80 M H 0.0000
81 Q H -1.2793
82 L H 0.0000
82A D H -1.3907
82B S H -1.3522
82C L H 0.0000
83 R H -3.0809
84 S H -2.3924
85 E H -2.5574
86 D H 0.0000
87 T H -1.0136
88 A H 0.0000
89 V H 0.1448
90 Y H 0.0000
91 Y H 0.0000
92 C H 0.0000
93 A H 0.0000
94 G H 0.0000
95 P H 0.0000
96 S H -0.1278
97 I H 0.5293
98 T H -0.2967
99 E H -1.1370
100 S H -1.0731
100A H H -1.0639
100B Y H -0.3135
100C C H 0.1822
100D L H 1.0390
100E D H -0.6775
100F C H -0.1642
100G A H -0.3350
100H A H -0.6676
100I K H -1.1164
100J D H -1.0132
100K Y H 0.0000
100L Y H -0.0117
100M Y H 0.3727
100N G H 0.0310
100O L H 0.0000
101 D H -1.1113
102 V H -1.1283
103 W H -0.5332
104 G H 0.0000
105 Q H -0.9106
106 G H -0.3270
107 T H 0.0000
108 T H -0.3645
109 V H 0.0000
110 T H -0.9672
111 V H 0.0000
112 S H -1.1474
113 S H -0.9413
114 A H -0.5850
115 S H -0.6435
116 T H -0.7237
117 K H -1.0173
118 G H -1.2120
119 P H -0.4472
120 S H -0.2776
121 V H 0.0000
122 F H 0.0000
123 P H -0.9564
124 L H 0.0000
125 A H -0.8513
126 P H -0.5109
135 T H -0.2738
136 A H -0.1819
137 A H -0.1654
138 L H 0.0000
139 G H 0.0000
140 C H 0.0000
141 L H 0.0000
142 V H 0.0000
143 K H 0.0000
144 D H -0.1500
145 Y H 0.0000
146 F H -0.0711
147 P H 0.0000
148 E H -0.6587
149 P H -0.6882
150 V H -0.3816
151 T H -0.5838
152 V H 0.0000
153 S H -0.4564
154 W H 0.0000
155 N H -0.7169
156 S H -0.6739
157 G H -0.5452
158 A H -0.2310
159 L H 0.0002
160 T H -0.1734
161 S H -0.2426
162 G H -0.2900
163 V H 0.1754
164 H H -0.1502
165 T H -0.1081
166 F H 0.0000
167 P H -0.2915
168 A H 0.2521
169 V H 0.0000
170 L H 1.3698
171 Q H 0.3248
172 S H -0.1284
173 S H -0.1817
174 G H 0.0410
175 L H 0.2538
176 Y H 0.5422
177 S H 0.0000
178 L H 0.0000
179 S H 0.0000
180 S H 0.0000
181 V H 0.0000
182 V H 0.0000
183 T H -0.2332
184 V H 0.0000
185 P H -0.3979
186 S H -0.4347
187 S H -0.5567
188 S H -0.6424
189 L H -0.8413
190 G H -1.0192
191 T H -1.0265
192 Q H -1.4754
193 T H -1.2205
194 Y H 0.0000
195 I H -1.1960
196 C H 0.0000
197 N H -1.6230
198 V H 0.0000
199 N H -1.7322
200 H H 0.0000
201 K H -2.7392
202 P H -1.7280
203 S H -1.7706
204 N H -2.5700
205 T H -1.9846
206 K H -2.6397
207 V H -1.6183
208 D H -2.6232
209 K H -2.1411
210 R H -2.7211
211 V H 0.0000
212 E H -2.5341
213 P H -1.1858
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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
LK170H -0.3033 -0.0257 View CSV PDB
LE170H -0.103 -0.0298 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018