Contacts of the helix formed by residues 1 - 33 (chain B) in PDB entry 1W5J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 1 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 5.2 22.2 - - - -
34A ARG* 3.9 18.4 - - - +
2B MET* 1.3 67.2 + - - +
3B ARG* 3.3 5.7 - - - +
4B GLN* 3.1 38.1 + - + +
5B ILE* 3.0 30.9 + - + +
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Residues in contact with MET 2 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.8 21.5 - - + -
34A ARG* 3.1 57.8 - - - +
1B ARG* 1.3 76.1 - - - +
3B ARG* 1.4 52.6 + - - +
5B ILE* 3.1 13.9 + - + +
6B GLU* 2.8 55.7 + - - +
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Residues in contact with ARG 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 3.3 3.3 - - - +
2B MET* 1.4 76.0 - - - +
4B GLN* 1.3 62.6 + - + +
6B GLU* 3.5 14.7 + - - +
7B ASP* 3.2 29.8 + - - +
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Residues in contact with GLN 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ARG* 3.1 39.6 + - + +
3B ARG* 1.3 75.1 - - + +
5B ILE* 1.3 67.6 + - + +
7B ASP* 3.3 9.7 + - - +
8B ARG* 2.9 23.6 + - - +
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Residues in contact with ILE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 3.8 27.8 - - + +
30A LEU* 4.3 34.1 - - + -
31A LEU* 3.8 31.0 - - + -
34A ARG* 4.6 11.0 - - + +
1B ARG* 3.0 22.8 + - + +
2B MET* 3.6 19.1 - - - +
4B GLN* 1.3 75.7 - - + +
6B GLU* 1.3 64.7 + - + +
8B ARG* 3.2 7.6 + - - +
9B LEU* 2.9 32.0 + - + +
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B MET* 2.8 47.3 + - + +
3B ARG* 3.7 10.9 + - - +
5B ILE* 1.3 78.1 - - + +
7B ASP* 1.3 58.0 + - - +
9B LEU* 3.4 12.1 + - + +
10B GLU* 3.0 25.3 + - - +
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Residues in contact with ASP 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 3.2 17.7 + - - +
4B GLN* 3.3 11.6 + - - +
6B GLU* 1.3 76.0 - - - +
8B ARG* 1.3 66.0 + - - +
10B GLU* 3.2 8.8 + - - +
11B GLU* 3.0 35.0 + - - +
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Residues in contact with ARG 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 3.8 16.8 + - - -
23A GLU* 2.9 42.3 + - - +
26A ARG* 4.8 5.7 - - - +
27A ILE* 4.0 22.4 - - + -
4B GLN 2.9 16.9 + - - +
5B ILE* 3.7 5.8 - - - +
7B ASP* 1.3 75.8 - - - +
9B LEU* 1.3 57.8 + - - +
11B GLU* 2.9 36.4 + - - +
12B ILE* 2.9 43.0 + - + +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.8 28.5 - - + -
27A ILE* 4.0 19.7 - - + -
31A LEU* 6.2 1.6 - - + -
5B ILE* 2.9 31.5 + - + +
6B GLU* 3.6 14.1 - - + +
8B ARG* 1.3 73.2 - - - +
10B GLU* 1.3 59.4 + - - +
12B ILE* 3.2 6.1 + - + +
13B LEU* 2.9 36.9 + - + +
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU 3.0 14.4 + - - +
7B ASP* 3.2 11.9 + - - +
9B LEU* 1.3 78.8 - - - +
11B GLU* 1.3 61.5 + - + +
13B LEU* 3.5 21.5 - - - +
14B SER* 3.0 24.0 + - - -
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP* 3.0 27.8 + - - +
8B ARG* 2.9 51.4 + - - +
10B GLU* 1.3 77.0 - - + +
12B ILE* 1.3 57.6 + - - +
14B SER* 3.4 8.0 + - - -
15B LYS* 3.0 27.4 + - - +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.8 30.0 - - + +
23A GLU* 4.2 17.9 - - + -
24A LEU* 3.7 31.4 - - + -
27A ILE* 3.7 22.0 - - + -
8B ARG* 2.9 28.0 + - + +
9B LEU* 3.4 9.2 - - + +
11B GLU* 1.3 72.5 - - - +
13B LEU* 1.3 67.4 + - + +
15B LYS* 3.1 7.4 + - - +
16B LEU* 2.9 32.6 + - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 2.9 21.7 + - + +
10B GLU* 3.5 29.6 - - - +
12B ILE* 1.3 74.4 - - + +
14B SER* 1.3 57.0 + - - +
16B LEU* 3.3 13.2 + - + +
17B TYR* 2.9 58.8 + - + +
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 3.0 17.7 + - - -
11B GLU* 3.4 9.2 - - - -
12B ILE 3.1 0.2 - - - -
13B LEU* 1.3 79.5 - - - +
15B LYS* 1.3 63.8 + - - +
17B TYR* 3.6 7.1 + - - +
18B HIS* 3.3 27.2 + - - -
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 3.7 50.4 - - + +
20A ILE* 3.8 10.5 - - + -
11B GLU 3.0 17.8 + - - +
12B ILE* 3.1 4.7 + - - +
14B SER* 1.3 75.2 + - - +
16B LEU* 1.3 64.3 + - - +
18B HIS* 3.4 17.6 + - + +
19B ILE* 3.0 23.8 + - + +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.7 23.3 - - + -
20A ILE* 3.6 25.1 - - + -
24A LEU* 5.5 4.0 - - + -
12B ILE* 2.9 37.7 + - + +
13B LEU* 3.6 14.1 - - + +
15B LYS* 1.3 73.6 - - - +
17B TYR* 1.3 52.5 + - + +
19B ILE* 3.1 10.0 + - + +
20B CYS* 2.7 41.6 + - - -
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 2.9 49.6 + - + +
14B SER* 3.9 6.3 - - - +
16B LEU* 1.3 75.6 - - + +
18B HIS* 1.4 56.3 + - - +
20B CYS* 2.9 32.2 + - + +
21B ASN* 3.0 24.9 + - - +
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 3.3 20.5 + - - -
15B LYS* 3.4 26.0 + - + +
17B TYR* 1.4 73.2 - - - +
19B ILE* 1.3 61.9 + - + +
21B ASN* 3.4 13.9 + - - +
22B GLU* 3.0 31.4 + - + +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.0 26.4 - - + +
16A LYS* 4.0 28.5 - - + -
17A LEU* 3.8 35.2 - - + -
20A ILE* 4.3 8.5 - - + -
15B LYS* 3.0 21.4 + - + +
16B LEU* 3.1 12.3 + - + +
18B HIS* 1.3 74.5 - - + +
20B CYS* 1.3 67.7 + - - +
22B GLU* 3.2 5.8 + - - +
23B LEU* 2.9 41.9 + - + +
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Residues in contact with CYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 2.7 25.0 + - - -
17B TYR* 2.9 22.2 + - + +
19B ILE* 1.3 75.1 - - - +
21B ASN* 1.3 56.1 + - - +
23B LEU* 3.3 10.2 + - - +
24B ALA* 2.7 37.9 + - - +
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Residues in contact with ASN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.0 22.3 + - - +
18B HIS* 3.7 16.5 - - - +
20B CYS* 1.3 77.1 - - - +
22B GLU* 1.3 62.9 + - + +
24B ALA* 3.9 6.4 - - - +
25B ARG* 3.1 25.3 + - - +
28B ARG* 4.4 2.9 + - - -
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ARG* 3.9 30.5 - - + +
13A ILE* 4.0 17.5 - - + -
18B HIS* 3.0 25.1 + - + +
19B ILE* 3.2 4.5 + - - +
21B ASN* 1.3 75.4 - - + +
23B LEU* 1.3 59.2 + - - +
25B ARG* 3.3 11.0 + - - +
26B ILE* 2.9 32.3 + - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.2 18.6 - - + -
13A ILE* 4.0 24.5 - - + -
17A LEU* 5.8 2.5 - - + -
19B ILE* 2.9 38.5 + - + +
20B CYS* 3.6 9.4 - - - +
22B GLU* 1.3 74.3 - - - +
24B ALA* 1.3 60.4 + - - +
26B ILE* 3.2 8.1 + - + +
27B ARG* 2.9 29.7 + - - +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B CYS 2.7 21.2 + - - +
21B ASN* 3.9 7.4 - - - +
23B LEU* 1.3 73.6 - - - +
25B ARG* 1.3 58.9 + - - +
27B ARG* 3.4 8.9 + - - +
28B ARG* 2.8 51.0 + - - +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A TYZ 2.9 46.2 + - - +
9A ARG* 5.6 8.1 - - - +
21B ASN 3.1 19.4 + - - +
22B GLU* 3.5 10.1 - - - +
24B ALA* 1.3 78.5 - - - +
26B ILE* 1.3 61.4 + - + +
28B ARG* 3.3 25.7 + - - +
29B LEU* 2.9 38.8 + - + +
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.8 33.0 - - + +
9A ARG* 3.8 29.6 - - + -
10A LEU* 4.1 25.4 - - + -
13A ILE* 4.0 14.4 - - + -
22B GLU 2.9 22.7 + - - +
23B LEU* 3.2 10.1 + - + +
25B ARG* 1.3 67.7 - - + +
27B ARG* 1.3 70.1 + - - +
29B LEU* 3.0 12.0 + - + +
30B LEU* 2.8 38.7 + - + +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU 2.9 16.7 + - - +
24B ALA* 3.5 9.4 - - - +
26B ILE* 1.3 80.9 - - - +
28B ARG* 1.3 74.1 + - + +
30B LEU* 3.4 12.5 + - - +
31B GLY* 3.1 40.9 + - - +
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN 4.4 3.2 + - - -
24B ALA* 2.8 37.1 + - - +
25B ARG* 3.3 37.0 - - - +
26B ILE 3.2 0.4 - - - -
27B ARG* 1.3 84.7 - - + +
29B LEU* 1.3 62.8 + - + +
31B GLY* 3.1 9.0 + - - -
32B GLU* 3.1 21.8 + - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A TYZ 3.5 54.7 - - + +
6A ILE* 4.1 28.0 - - + -
25B ARG* 2.9 46.8 + - + +
26B ILE* 3.0 8.7 + - + +
28B ARG* 1.3 69.2 - - + +
30B LEU* 1.3 67.2 + - - +
32B GLU* 3.1 21.0 + - + +
33B ARG* 3.4 13.6 + - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 3.9 25.6 - - + -
6A ILE* 3.7 26.2 - - + -
26B ILE* 2.8 39.4 + - + +
27B ARG* 3.8 10.8 - - - +
29B LEU* 1.3 71.4 - - - +
31B GLY* 1.3 56.7 + - - +
33B ARG* 3.0 33.3 + - - +
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG* 3.1 31.8 + - - +
28B ARG 3.1 6.9 + - - -
29B LEU 3.1 1.0 - - - -
30B LEU* 1.3 75.3 - - - +
32B GLU* 1.3 61.3 + - - +
33B ARG 3.2 6.6 + - - +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.1 22.9 - - + +
29B LEU* 3.1 14.5 + - + +
31B GLY* 1.3 75.6 - - - +
33B ARG* 1.3 62.4 + - - +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A TYZ 3.0 24.7 + - - -
2A ARG 3.8 0.4 - - - -
3A MET* 3.3 37.3 - - - +
6A ILE* 4.8 7.1 - - - +
29B LEU 3.4 11.4 + - - +
30B LEU* 3.0 26.3 + - - +
31B GLY 3.2 5.9 - - - +
32B GLU* 1.3 83.9 - - - +
33C ARG* 2.3 103.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il