Project name: VHL_R114Q

Chain sequence(s)	A: MEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVQSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	Yes
pH calculations	Yes
alphaCutter usage	No
Dynamic mode	No
Automated mutations	No

Simulation log

[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:24)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/73ce82b9bdd6cfa/tmp/folded.pdb                (00:03:24)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:22)

• Minimal score value: -4.2108
• Maximal score value: 1.8652
• Average score: -1.1054
• Total score value: -176.8674

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index	residue name	chain	Aggrescan4D score	mutation
1	M	A	0.1335
2	E	A	-1.7389
3	A	A	-1.2553
4	G	A	-2.1059
5	R	A	-2.9697
6	P	A	-2.0290
7	R	A	-2.5977
8	P	A	-1.5231
9	V	A	-0.0579
10	L	A	-0.4834
11	R	A	-0.6732
12	S	A	0.0000
13	V	A	0.6819
14	N	A	-1.2877
15	S	A	-1.8815
16	R	A	-2.9241
17	E	A	-2.9314
18	P	A	-2.1273
19	S	A	0.0000
20	Q	A	-1.8318
21	V	A	0.0000
22	I	A	-0.7839
23	F	A	0.0000
24	C	A	-1.1308
25	N	A	0.0000
26	R	A	-2.1798
27	S	A	0.0000
28	P	A	-0.9727
29	R	A	-0.9208
30	V	A	-0.0363
31	V	A	0.0000
32	L	A	0.1481
33	P	A	0.0000
34	V	A	0.0000
35	W	A	-0.3653
36	L	A	0.0000
37	N	A	-1.1203
38	F	A	-0.7984
39	D	A	-2.3664
40	G	A	-1.7694
41	E	A	-2.7155
42	P	A	-1.5948
43	Q	A	-1.1059
44	P	A	-0.4934
45	Y	A	0.1528
46	P	A	-0.1567
47	T	A	0.0505
48	L	A	0.0000
49	P	A	-0.6451
50	P	A	-1.0358
51	G	A	-1.3022
52	T	A	-1.0032
53	G	A	-1.5536
54	R	A	-1.9818
55	R	A	-2.4726
56	I	A	-1.6131
57	H	A	-1.6678
58	S	A	0.0000
59	Y	A	-1.5753
60	R	A	-1.9001
61	G	A	-0.2540
62	H	A	0.0000
63	L	A	0.0000
64	W	A	0.0000
65	L	A	0.0000
66	F	A	0.0000
67	R	A	0.0000
68	D	A	0.0000
69	A	A	-0.2128
70	G	A	-0.5029
71	T	A	-0.7586
72	H	A	-0.7506
73	D	A	-0.6677
74	G	A	-0.5772
75	L	A	0.0000
76	L	A	-0.6414
77	V	A	0.0000
78	N	A	-1.4370
79	Q	A	-1.7845
80	T	A	-1.4575
81	E	A	-1.6940
82	L	A	-0.3326
83	F	A	0.0000
84	V	A	1.5903
85	P	A	0.0000
86	S	A	-0.0896
87	L	A	-0.3439
88	N	A	-0.7484
89	V	A	0.4116
90	D	A	-1.5395
91	G	A	-1.5064
92	Q	A	-1.4944
93	P	A	-0.8452
94	I	A	0.2780
95	F	A	0.4392
96	A	A	0.0000
97	N	A	-0.8653
98	I	A	0.0000
99	T	A	-0.7127
100	L	A	0.3237
101	P	A	0.8041
102	V	A	1.8652
103	Y	A	0.5759
104	T	A	0.1295
105	L	A	0.4854
106	K	A	-1.2013
107	E	A	-1.4217
108	R	A	-1.2419
109	C	A	-0.2979
110	L	A	-0.6996
111	Q	A	-0.3519
112	V	A	0.7091
113	V	A	0.7915
114	Q	A	-0.3254
115	S	A	0.5456
116	L	A	1.4070
117	V	A	-0.1019
118	K	A	-2.0536
119	P	A	-2.3962
120	E	A	-3.3993
121	N	A	-2.9448
122	Y	A	0.0000
123	R	A	-3.9638
124	R	A	-3.3465
125	L	A	-1.8092
126	D	A	-1.9829
127	I	A	-0.2314
128	V	A	0.9030
129	R	A	-1.6730
130	S	A	-0.8606
131	L	A	-1.0725
132	Y	A	0.0000
133	E	A	-3.4861
134	D	A	-2.8336
135	L	A	0.0000
136	E	A	-3.4927
137	D	A	-3.5186
138	H	A	-2.7647
139	P	A	-1.9579
140	N	A	-2.2327
141	V	A	-1.8861
142	Q	A	-2.9158
143	K	A	-3.1926
144	D	A	-2.9003
145	L	A	0.0000
146	E	A	-3.9546
147	R	A	-4.2108
148	L	A	-2.9473
149	T	A	-2.4994
150	Q	A	-3.3543
151	E	A	-3.9755
152	R	A	-3.4703
153	I	A	-1.8655
154	A	A	-2.3475
155	H	A	-3.1018
156	Q	A	-3.2246
157	R	A	-2.9564
158	M	A	-1.2422
159	G	A	-2.0463
160	D	A	-2.6452

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is partially or entirely disordered. Average score is recommended for pH analysis.

pH	Average A4D Score	Max A4D Score
4.0	-1.0314	2.4698
4.5	-1.1133	2.4698
5.0	-1.217	2.4698
5.5	-1.323	2.4698
6.0	-1.4143	2.4698
6.5	-1.482	2.4698
7.0	-1.526	2.4697
7.5	-1.5533	2.4697
8.0	-1.5713	2.4696
8.5	-1.5823	2.4693
9.0	-1.5843	2.4682