Contacts of the helix formed by residues 18 - 48 (chain A) in PDB entry 1G6U
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 SER 18 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY 3.5 1.2 + - - -
17A PHE* 1.4 92.9 - - - +
19A PRO* 1.4 64.8 - - - +
20A GLU 3.6 1.6 - - - -
21A GLU* 3.3 26.1 + - - +
22A LEU* 2.9 24.1 + - - +
46B LEU* 4.6 6.0 - - - +
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Residues in contact with PRO 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.6 22.0 - - - +
17A PHE 2.9 6.5 - - - +
18A SER* 1.4 86.2 - - - +
20A GLU* 1.3 62.8 + - + +
22A LEU* 3.8 2.7 - - + +
23A ALA* 2.9 29.2 + - - +
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER 3.6 0.4 - - - -
19A PRO* 1.3 74.5 - - + +
21A GLU* 1.3 67.9 + - + +
23A ALA* 3.3 10.8 + - - +
24A ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 3.3 23.2 + - - +
20A GLU* 1.3 79.6 - - + +
22A LEU* 1.3 62.3 + - - +
24A ALA* 3.4 9.8 + - - +
25A LEU* 3.3 22.9 + - - +
46B LEU* 3.7 31.9 - - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.6 34.5 - - + +
12A LEU* 3.6 15.9 - - + -
13A LYS* 3.5 39.9 - - + +
17A PHE* 3.6 34.8 - - + +
18A SER 2.9 17.3 + - - +
19A PRO* 3.8 3.4 - - + +
21A GLU* 1.3 76.4 - - - +
23A ALA* 1.3 59.7 + - - +
25A LEU* 3.0 7.1 + - + +
26A GLU* 2.8 28.4 + - + +
43B LEU* 4.2 6.7 - - + -
46B LEU* 4.2 3.5 - - + +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 6.1 2.5 - - - +
19A PRO 2.9 18.6 + - - +
20A GLU* 3.3 15.9 + - - +
22A LEU* 1.3 73.0 - - - +
24A ALA* 1.3 66.4 + - - +
26A GLU* 3.3 17.5 + - - +
27A SER* 3.0 27.8 + - - -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 3.1 12.0 + - - +
21A GLU* 3.5 15.7 - - - +
22A LEU 3.2 0.2 - - - -
23A ALA* 1.3 77.4 - - - +
25A LEU* 1.4 64.9 + - + +
27A SER* 3.3 5.6 + - - -
28A GLU* 3.0 30.1 + - + +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.8 18.7 - - + +
21A GLU 3.3 11.0 + - - +
22A LEU* 3.0 9.7 + - + +
24A ALA* 1.4 80.0 - - + +
26A GLU* 1.3 63.1 + - - +
28A GLU* 3.2 6.4 + - + +
29A LEU* 2.9 24.8 + - - +
39B LEU* 4.0 24.8 - - + +
42B LYS* 3.9 26.7 - - + -
43B LEU* 3.8 34.3 - - + +
46B LEU* 3.8 25.8 - - + -
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.9 18.7 - - + +
10A GLN* 5.9 5.0 - - + +
13A LYS* 2.9 43.1 + - - +
22A LEU* 2.8 16.8 + - + +
23A ALA* 3.4 18.3 - - - +
25A LEU* 1.3 72.3 - - - +
27A SER* 1.3 59.4 + - - +
29A LEU* 3.3 5.8 + - + +
30A GLN* 2.9 53.2 + - + +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 3.0 16.6 + - - -
24A ALA* 3.8 5.4 - - - -
25A LEU 3.3 0.2 - - - -
26A GLU* 1.3 75.2 + - - +
28A GLU* 1.3 55.7 + - - +
30A GLN* 3.1 16.2 + - - +
31A ALA* 2.7 34.2 + - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.0 24.1 + - + +
25A LEU* 3.7 5.6 - - + +
27A SER* 1.3 76.1 - - - +
29A LEU* 1.3 57.5 + - - +
31A ALA* 3.1 11.9 + - - +
32A LEU* 2.9 27.2 + - - +
35B LYS* 3.3 32.3 + - - -
39B LEU* 3.6 24.2 - - + +
42B LYS* 3.3 14.0 + - - +
201B SO4 4.1 11.3 + - - -
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 4.0 18.2 - - + -
5A LEU* 3.9 23.3 - - + -
6A LYS* 3.6 48.5 - - + +
9A LEU* 3.9 9.6 - - + -
25A LEU 2.9 13.8 + - - +
26A GLU* 3.5 9.2 - - + +
27A SER 3.2 0.2 - - - -
28A GLU* 1.3 76.7 - - - +
30A GLN* 1.3 64.6 + - + +
32A LEU* 3.1 6.7 + - - +
33A GLU* 2.9 47.5 + - + +
39B LEU* 3.9 12.2 - - + +
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 6.3 0.4 - - - -
26A GLU* 2.9 42.9 + - + +
27A SER* 3.1 17.0 + - - +
29A LEU* 1.3 78.6 - - + +
31A ALA* 1.3 63.9 + - - +
33A GLU* 3.1 23.1 + - - +
34A LYS* 3.0 33.6 + - + +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 2.7 16.7 + - - +
28A GLU* 3.1 16.8 + - - +
30A GLN* 1.3 72.7 - - - +
32A LEU* 1.3 56.3 + - - +
34A LYS* 3.3 9.7 + - - +
35A LYS* 2.9 30.8 + - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.9 29.4 - - + -
28A GLU 2.9 12.0 + - - +
29A LEU* 3.1 8.5 + - - +
31A ALA* 1.3 76.9 - - - +
33A GLU* 1.3 57.6 + - - +
35A LYS* 3.2 8.3 + - - +
36A LEU* 2.8 25.5 + - + +
2B LEU* 4.3 9.6 - - + -
32B LEU* 3.7 33.8 - - + +
35B LYS* 3.8 15.7 - - + -
36B LEU* 3.7 38.4 - - + +
39B LEU* 4.2 10.3 - - + -
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 4.5 17.8 - - + +
6A LYS* 2.7 40.9 + - - +
29A LEU* 2.9 30.4 + - + +
30A GLN* 3.1 29.9 + - - +
32A LEU* 1.3 76.8 - - - +
34A LYS* 1.3 60.9 + - + +
36A LEU* 3.3 9.0 + - - +
37A ALA* 3.0 26.7 + - - +
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN* 3.0 22.0 + - + +
31A ALA* 3.5 10.8 - - - +
33A GLU* 1.3 77.5 - - + +
35A LYS* 1.3 59.0 + - + +
37A ALA* 3.2 9.6 + - + +
38A ALA* 2.9 28.6 + - - +
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA 2.9 15.3 + - - +
32A LEU* 3.2 8.0 + - - +
34A LYS* 1.3 73.9 - - + +
36A LEU* 1.3 57.2 + - - +
38A ALA* 3.0 15.5 + - - +
39A LEU* 2.9 50.2 + - - +
28B GLU* 2.9 30.0 + - - +
32B LEU* 3.7 25.3 - - + +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 4.1 13.9 - - + -
32A LEU* 2.8 17.2 + - + +
33A GLU* 3.5 7.2 - - - +
34A LYS 3.2 0.2 - - - -
35A LYS* 1.3 77.5 - - - +
37A ALA* 1.3 62.4 + - - +
39A LEU* 3.2 2.8 + - - +
40A LYS* 3.1 28.6 + - + +
1B SER* 3.7 34.5 - - - +
2B LEU* 3.9 23.1 - - + +
5B LEU* 3.5 33.7 - - + -
29B LEU* 4.2 3.6 - - + -
32B LEU* 3.8 11.8 - - + +
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU 3.0 14.4 + - - +
34A LYS* 3.2 13.9 + - + +
36A LEU* 1.3 76.0 - - - +
38A ALA* 1.3 58.6 + - - +
40A LYS* 3.2 12.4 + - - +
41A SER* 2.9 32.1 + - - +
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS 2.9 14.4 + - - +
35A LYS* 3.0 21.5 + - - +
37A ALA* 1.3 78.1 - - - +
39A LEU* 1.3 57.8 + - - +
41A SER* 3.2 7.4 + - - -
42A LYS* 2.9 29.0 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 2.9 34.5 + - - +
36A LEU 3.2 6.2 + - - +
38A ALA* 1.3 78.2 - - - +
40A LYS* 1.3 62.4 + - - +
42A LYS* 3.2 5.7 + - + +
43A LEU* 2.9 23.7 + - - +
5B LEU* 3.9 17.0 - - + -
25B LEU* 4.0 22.4 - - + +
28B GLU* 3.5 28.0 - - + +
29B LEU* 3.7 30.7 - - + +
32B LEU* 3.7 26.0 - - + -
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.1 27.5 + - + +
37A ALA* 3.2 11.6 + - - +
39A LEU* 1.3 75.7 - - - +
41A SER* 1.3 62.3 + - - +
43A LEU* 3.3 8.6 + - - +
44A GLN* 3.0 22.5 + - - +
1B SER 5.5 6.7 - - - +
4B ALA* 6.2 2.4 - - - +
5B LEU* 4.1 27.5 - - + +
8B GLU* 4.4 15.2 + - - -
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA* 2.9 14.2 + - - +
38A ALA* 3.6 11.3 - - - -
39A LEU 3.2 0.2 - - - -
40A LYS* 1.3 76.4 - - - +
42A LYS* 1.3 60.8 + - - +
44A GLN* 3.1 8.9 + - - +
45A ALA* 2.9 28.2 + - - +
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA 2.9 17.6 + - - +
39A LEU* 3.2 8.5 + - + +
41A SER* 1.3 74.1 - - - +
43A LEU* 1.3 63.2 + - - +
45A ALA* 3.2 15.6 + - + +
46A LEU* 3.0 34.7 + - + +
21B GLU* 4.4 18.9 + - - -
25B LEU* 3.7 24.7 - - + -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 2.9 13.6 + - - +
40A LYS* 3.5 10.5 - - - +
42A LYS* 1.3 78.0 - - - +
44A GLN* 1.3 63.3 + - - +
46A LEU* 3.1 7.2 + - + +
47A LYS* 3.1 29.1 + - - +
5B LEU* 3.9 19.3 - - + -
8B GLU* 3.7 37.0 - - + +
9B LEU* 4.1 5.6 - - + -
12B LEU* 3.8 22.0 - - + -
17B PHE* 4.2 7.4 - - + -
22B LEU* 3.9 23.3 - - + -
25B LEU* 4.0 14.5 - - + +
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Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS 3.0 13.8 + - - +
41A SER* 3.1 10.5 + - - +
43A LEU* 1.3 78.7 - - - +
45A ALA* 1.3 60.9 + - - +
47A LYS* 3.2 30.7 + - - +
48A GLY* 3.2 18.7 + - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER 2.9 12.7 + - - +
42A LYS* 3.2 22.6 + - + +
44A GLN* 1.3 74.5 - - - +
46A LEU* 1.4 62.3 + - - +
48A GLY* 3.1 16.0 + - - -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 3.0 26.8 + - + +
43A LEU* 3.1 8.9 + - - +
45A ALA* 1.4 76.9 - - - +
47A LYS* 1.3 59.9 + - - +
48A GLY 3.5 3.5 + - - -
17B PHE* 3.6 20.7 - - + -
18B SER* 4.1 8.2 - - - +
21B GLU* 3.5 48.7 - - + +
22B LEU* 4.2 12.6 - - + -
25B LEU* 3.8 29.6 - - + -
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.1 29.5 + - - +
44A GLN* 3.2 30.4 + - - +
46A LEU* 1.3 74.2 - - - +
48A GLY* 1.3 65.7 + - - +
8B GLU* 3.3 25.2 + - - -
12B LEU* 4.2 17.5 - - + -
17B PHE* 3.9 21.7 - - + -
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLN* 3.2 9.5 + - - +
45A ALA 3.1 16.4 + - - -
46A LEU 4.3 3.8 - - - -
47A LYS* 1.3 82.4 - - - +
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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