Contacts of the helix formed by residues 3 - 44 (chain D) in PDB entry 5KHT
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 ALA 3 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 2.9 33.8 + - + +
2D ASP* 1.3 72.7 - - - +
4D ILE* 1.3 52.3 + - - +
5D LYS* 2.8 7.2 - - - +
6D LYS* 2.7 41.0 + - + +
7D LYS* 3.3 7.8 + - - +
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Residues in contact with ILE 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1B GLY* 5.0 11.4 - - - -
1B MET 5.6 2.9 - - - +
4B ILE* 3.5 34.1 - - + -
5B LYS* 4.1 30.5 - - + +
8B MET* 3.5 17.7 - - + +
1D MET* 3.3 18.9 + - - +
2D ASP* 4.0 8.1 - - - +
3D ALA* 1.3 73.9 - - - +
5D LYS* 1.3 55.8 + - - +
7D LYS* 3.1 13.8 + - + +
8D MET* 3.0 26.5 + - - +
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Residues in contact with LYS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.8 25.6 - - + -
2D ASP* 3.0 42.5 + - - +
3D ALA* 2.8 1.3 - - - -
4D ILE* 1.3 77.3 - - - +
6D LYS* 1.3 64.6 + - + +
8D MET* 3.4 11.8 + - - +
9D GLN* 3.3 18.2 + - - +
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Residues in contact with LYS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ALA* 2.7 29.4 + - + +
5D LYS* 1.3 75.4 - - + +
7D LYS* 1.3 61.9 + - - +
9D GLN* 3.4 22.9 + - - +
10D MET* 3.1 30.6 + - + +
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Residues in contact with LYS 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 5.6 3.8 - - - +
8B MET* 3.6 30.0 - - + -
12B LYS* 5.8 6.3 - - - +
3D ALA 3.3 5.3 + - - +
4D ILE* 3.1 18.7 + - + +
6D LYS* 1.3 74.6 - - - +
8D MET* 1.3 58.3 + - - +
10D MET* 3.1 22.3 + - + +
11D LEU* 2.9 44.9 + - + +
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Residues in contact with MET 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.1 17.9 - - + +
7B LYS* 4.1 16.2 - - + +
8B MET* 3.5 49.4 - - + +
11B LEU* 3.5 28.0 - - + +
4D ILE 3.0 19.1 + - - +
5D LYS* 3.4 11.7 - - + +
6D LYS 3.3 0.2 - - - -
7D LYS* 1.3 77.7 - - - +
9D GLN* 1.3 55.9 + - - +
11D LEU* 3.5 0.8 + - - -
12D LYS* 3.0 29.5 + - - +
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Residues in contact with GLN 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LYS 3.3 9.0 + - - +
6D LYS* 3.4 29.6 - - - +
7D LYS 3.2 0.4 - - - -
8D MET* 1.3 76.5 - - - +
10D MET* 1.3 74.2 + - - +
12D LYS* 3.3 9.7 + - - +
13D LEU* 3.2 46.3 + - + +
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Residues in contact with MET 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LYS* 3.1 14.4 - - + +
7D LYS* 3.1 27.2 + - + +
9D GLN* 1.3 86.9 - - - +
11D LEU* 1.3 63.2 + - + +
13D LEU* 3.4 7.8 + - - +
14D ASP* 3.1 32.3 + - - +
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET* 3.9 18.6 - - + +
11B LEU* 3.6 24.9 - - + +
12B LYS* 3.7 36.1 - - + +
15B LYS* 3.9 31.1 - - + +
7D LYS* 2.9 41.4 + - + +
10D MET* 1.3 75.8 - - + +
12D LYS* 1.3 64.1 + - - +
14D ASP* 3.2 7.9 + - - +
15D LYS* 2.9 24.1 + - - +
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Residues in contact with LYS 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.9 21.7 - - + +
8D MET 3.0 17.6 + - - +
9D GLN* 3.3 8.2 + - - +
11D LEU* 1.3 75.4 - - - +
13D LEU* 1.3 71.4 + - - +
15D LYS* 3.2 5.5 + - + +
16D GLU* 2.9 46.4 + - + +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.2 37.1 + - + +
10D MET* 3.7 6.7 - - - +
12D LYS* 1.3 90.4 - - - +
14D ASP* 1.3 64.4 + - - +
16D GLU* 3.4 9.1 + - + +
17D ASN* 3.0 25.2 + - - +
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Residues in contact with ASP 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 3.5 37.4 + - - +
19B LEU* 5.3 2.4 - - - +
10D MET* 3.1 25.8 + - - +
11D LEU* 3.2 10.9 + - - +
13D LEU* 1.3 78.0 - - - +
15D LYS* 1.3 61.7 + - - +
17D ASN* 3.5 6.6 + - - +
18D ALA* 3.2 22.0 + - - +
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Residues in contact with LYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.0 21.4 - - + +
14B ASP* 3.6 36.0 + - + +
15B LYS* 4.0 27.5 - - + +
18B ALA* 4.4 2.0 - - + -
11D LEU 2.9 13.2 + - - +
12D LYS* 3.2 11.2 + - + +
14D ASP* 1.3 78.0 - - - +
16D GLU* 1.3 64.6 + - - +
18D ALA* 3.1 7.5 + - - +
19D LEU* 2.9 49.1 + - + +
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Residues in contact with GLU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LYS* 2.9 34.6 + - + +
13D LEU* 3.8 9.9 - - + +
15D LYS* 1.3 86.7 + - - +
17D ASN* 1.3 58.0 + - - +
19D LEU* 3.3 22.1 + - - +
20D ASP* 2.9 40.9 + - - +
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU 3.0 18.4 + - - +
14D ASP* 3.7 7.6 - - - +
16D GLU* 1.3 76.2 - - - +
18D ALA* 1.3 57.6 + - - +
20D ASP* 3.3 13.6 + - - +
21D ARG* 3.0 41.9 + - - +
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 3.8 6.5 - - + +
19B LEU* 3.7 47.1 - - + +
22B ALA* 3.5 8.4 - - + +
14D ASP 3.2 12.0 + - - +
15D LYS* 3.1 9.7 + - - +
17D ASN* 1.3 73.4 + - - +
19D LEU* 1.3 62.4 + - - +
21D ARG* 3.2 13.2 + - - +
22D ALA* 2.9 25.3 + - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 3.8 20.9 - - + -
21B ARG* 3.6 30.5 - - - +
15D LYS* 2.9 35.6 + - - +
16D GLU* 3.6 30.3 - - - +
18D ALA* 1.3 76.4 - - - +
20D ASP* 1.3 59.2 + - - +
22D ALA* 3.3 5.1 + - - +
23D GLU* 3.0 38.2 + - - +
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Residues in contact with ASP 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLU* 2.9 26.6 + - - +
17D ASN* 3.5 16.0 + - - +
19D LEU* 1.3 77.6 - - - +
21D ARG* 1.3 62.3 + - - +
23D GLU* 3.4 12.1 + - - +
24D GLN* 3.0 24.8 + - - +
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Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 3.7 27.1 - - - +
22B ALA* 3.6 21.9 - - + +
23B GLU* 3.8 20.6 + - - +
26B GLU* 3.1 38.5 + - - +
17D ASN* 3.0 30.6 + - - +
18D ALA* 3.4 10.7 - - - +
20D ASP* 1.3 75.8 - - - +
22D ALA* 1.3 62.5 + - - +
24D GLN* 3.3 6.6 + - - +
25D ALA* 3.1 24.9 + - - +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA 4.8 0.4 - - - +
21B ARG* 3.5 41.3 - - + +
22B ALA* 3.7 17.2 - - - +
25B ALA* 4.4 4.3 - - - -
18D ALA 2.9 13.1 + - - +
19D LEU* 3.3 8.7 + - - +
21D ARG* 1.3 76.3 - - - +
23D GLU* 1.3 57.8 + - - +
24D GLN 3.3 0.2 + - - -
25D ALA* 3.3 2.4 + - - +
26D GLU* 2.9 37.3 + - - +
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 3.8 21.6 + - - +
19D LEU* 3.0 23.4 + - - +
20D ASP* 3.9 12.4 - - - +
22D ALA* 1.3 75.8 - - - +
24D GLN* 1.3 61.7 + - - +
26D GLU* 3.4 8.6 + - - +
27D ALA* 3.0 24.4 + - - +
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLN* 3.3 33.0 + - - +
28C ASP* 3.3 20.5 + - - +
20D ASP 3.0 17.0 + - - +
21D ARG* 3.6 7.2 - - - +
22D ALA 3.2 0.2 - - - -
23D GLU* 1.3 76.2 - - - +
25D ALA* 1.3 59.9 + - - +
27D ALA* 3.2 8.8 + - - +
28D ASP* 3.0 61.0 + - - +
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.7 32.5 - - + +
26B GLU* 4.0 16.8 - - + +
29B ASN* 4.9 5.2 - - + -
21D ARG 3.1 13.3 + - - +
24D GLN* 1.3 81.1 - - - +
26D GLU* 1.3 57.8 + - - +
28D ASP* 3.3 10.6 + - - +
29D ASN* 2.9 36.1 + - - +
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG* 2.8 51.5 + - - +
25B ALA* 3.9 14.9 - - + +
22D ALA* 2.9 21.4 + - - +
23D GLU* 3.9 7.9 - - - +
25D ALA* 1.3 76.7 - - - +
27D ALA* 1.3 62.4 + - - +
29D ASN* 3.3 12.5 + - - +
30D TYR* 3.2 20.4 + - - +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLU 3.0 17.7 + - - +
24D GLN* 3.4 10.8 - - - +
26D GLU* 1.3 75.2 - - - +
28D ASP* 1.3 67.2 + - - +
30D TYR* 3.3 15.9 + - - +
31D HIS* 3.2 24.8 + - + +
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Residues in contact with ASP 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASN* 3.5 20.2 - - - +
24C GLN* 5.0 2.9 + - - -
28C ASP* 4.4 3.3 - - - +
31C HIS* 3.8 30.8 - - + +
24D GLN* 3.0 43.9 + - - +
25D ALA* 3.5 7.7 - - - +
27D ALA* 1.3 76.2 - - - +
29D ASN* 1.3 57.9 + - - +
31D HIS* 3.1 7.9 + - - +
32D LEU* 2.9 30.2 + - - +
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Residues in contact with ASN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.1 25.9 + - - +
28B ASP* 3.5 15.2 + - - +
29B ASN* 3.0 33.1 - - - +
32B LEU* 3.7 18.1 - - + +
25D ALA 2.9 23.5 + - - +
26D GLU* 3.5 12.3 - - - +
27D ALA 3.2 0.4 - - - -
28D ASP* 1.3 74.5 - - - +
30D TYR* 1.3 58.6 + - - +
32D LEU* 3.3 4.3 + - - +
33D GLU* 2.8 39.2 + - - +
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Residues in contact with TYR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LYS* 3.3 18.0 + - - -
45A GLU* 4.3 0.2 + - - -
35C GLU* 2.5 29.7 + - - -
38C ARG* 3.3 10.2 + - - -
26D GLU 3.2 11.8 + - - +
27D ALA* 3.5 9.2 - - - +
28D ASP 3.3 0.4 - - - -
29D ASN* 1.3 74.6 - - - +
31D HIS* 1.3 93.1 + + - +
33D GLU* 3.3 13.2 + - + +
34D ASN* 3.2 42.4 + - - -
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Residues in contact with HIS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C HIS* 3.4 49.4 + + + +
32C LEU* 4.8 13.4 - - + +
34C ASN* 5.5 4.3 + - + +
35C GLU* 3.9 30.2 + - + +
27D ALA* 3.2 27.4 + - + +
28D ASP* 3.1 5.0 + - - +
30D TYR* 1.3 102.4 - + - +
32D LEU* 1.3 63.8 + - - +
34D ASN* 3.5 7.5 + - - +
35D GLU* 3.2 24.3 + - - +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 3.4 33.0 - - - +
32B LEU* 3.8 19.3 - - + -
33B GLU* 3.7 40.8 - - + +
36B VAL* 3.9 18.5 - - + +
101B PEG 5.4 2.0 - - - +
30C TYR* 6.5 0.2 - - + -
31C HIS* 3.8 19.1 - - + -
28D ASP* 2.9 18.4 + - + +
29D ASN* 3.7 6.5 - - - +
31D HIS* 1.3 77.3 - - - +
33D GLU* 1.3 57.4 + - - +
35D GLU* 3.1 10.1 + - + +
36D VAL* 2.8 32.1 + - - +
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.6 29.4 - - + +
29D ASN* 2.8 22.9 + - - +
30D TYR* 3.7 12.6 - - + +
31D HIS 3.3 0.2 - - - -
32D LEU* 1.3 77.4 - - - +
34D ASN* 1.3 57.2 + - - +
36D VAL* 3.3 8.6 + - + +
37D ALA* 3.0 27.5 + - - +
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Residues in contact with ASN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU* 3.5 15.3 + - - +
38C ARG* 3.6 26.9 + - - +
30D TYR* 3.2 47.9 + - - -
31D HIS* 3.8 9.0 + - - +
33D GLU* 1.3 75.5 - - - +
35D GLU* 1.3 59.2 + - + +
37D ALA* 3.3 8.3 + - - +
38D ARG* 3.0 28.1 + - - +
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.1 18.8 - - + -
40B LYS* 4.2 14.7 + - - -
101B PEG 6.0 0.4 - - - +
31C HIS* 6.2 0.7 - - + +
34C ASN* 3.7 38.0 + - + +
31D HIS 3.2 12.4 + - - +
32D LEU* 3.1 12.6 + - + +
34D ASN* 1.3 76.6 - - + +
36D VAL* 1.3 65.7 + - - +
38D ARG* 2.8 48.0 + - - +
39D LEU* 2.9 31.8 + - + +
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.3 15.3 - - + +
35B GLU* 4.1 22.0 - - + +
36B VAL* 3.7 18.8 - - + +
39B LEU* 3.9 14.6 - - + +
32D LEU 2.8 21.0 + - - +
33D GLU* 3.3 9.4 + - - +
35D GLU* 1.3 76.6 - - - +
37D ALA* 1.3 57.2 + - - +
39D LEU* 3.4 0.6 + - - -
40D LYS* 2.9 55.0 + - + +
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLU 3.0 13.0 + - - +
34D ASN* 3.7 11.9 - - - +
35D GLU 3.2 0.2 - - - -
36D VAL* 1.3 76.4 - - - +
38D ARG* 1.3 62.5 + - - +
40D LYS* 3.4 8.2 + - - +
41D LYS* 3.3 42.7 + - - +
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Residues in contact with ARG 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 4.6 0.6 - - - +
45B GLU* 2.9 42.0 + - - -
41C LYS* 5.7 8.5 - - - +
34D ASN 3.0 15.9 + - - +
35D GLU* 2.8 42.9 + - - +
37D ALA* 1.3 77.8 - - - +
39D LEU* 1.3 74.8 + - - +
41D LYS* 3.4 11.4 + - - +
42D LEU* 3.3 37.4 + - + +
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 3.9 25.6 - - + +
39B LEU* 3.6 22.4 - - + +
40B LYS* 3.7 24.7 - - + -
43B VAL* 4.0 18.6 - - + +
45B GLU* 3.6 20.9 - - - +
35D GLU* 2.9 24.0 + - - +
38D ARG* 1.3 102.3 - - - +
40D LYS* 1.3 64.5 - - - +
42D LEU* 3.0 8.4 + - + +
43D VAL* 2.9 26.9 + - - +
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Residues in contact with LYS 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 5.3 2.8 + - - -
38B ARG* 4.5 4.8 - - - +
39B LEU* 3.9 11.9 - - + +
36D VAL* 2.9 38.9 + - + +
37D ALA* 3.8 7.9 - - - +
39D LEU* 1.3 75.8 - - - +
41D LYS* 1.3 57.5 + - + +
43D VAL 3.3 1.2 + - - -
44D GLY 2.8 25.6 + - - -
45D GLU* 2.9 65.3 + - + +
46D ARG 4.5 12.9 - - - -
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Residues in contact with LYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ALA* 3.3 31.9 + - - +
38D ARG* 3.6 10.7 - - - +
39D LEU 3.2 0.6 - - - -
40D LYS* 1.3 76.5 - - + +
42D LEU* 1.3 65.7 + - + +
44D GLY* 3.6 9.4 + - - -
45D GLU 5.5 0.7 - - - -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.0 19.6 - - + +
45B GLU* 3.7 22.9 - - - +
41C LYS* 6.3 0.4 - - - +
38D ARG* 3.3 27.5 + - + +
39D LEU* 3.0 13.5 + - + +
41D LYS* 1.3 83.6 - - + +
43D VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.7 18.8 - - + +
42B LEU* 3.9 29.8 - - + -
43B VAL* 3.5 21.8 - - + -
39D LEU 2.9 19.5 + - - +
40D LYS 3.8 3.8 - - - +
42D LEU* 1.3 76.3 - - - +
44D GLY* 1.3 59.1 + - - +
45D GLU* 4.2 20.9 - - + +
101D PEG 6.1 1.3 - - - -
----------------------------------------------------------
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Residues in contact with GLY 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LYS 2.8 6.2 + - - -
41D LYS* 3.6 8.2 + - - -
42D LEU 3.3 3.0 - - - -
43D VAL* 1.3 79.9 - - - +
45D GLU* 1.3 60.3 - - - +
46D ARG* 3.9 4.6 + - - +
101D PEG 4.3 4.2 + - - -
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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