Contacts of the helix formed by residues 2 - 29 (chain A) in PDB entry 1GQA
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 ASP 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 1.3 79.0 - - - +
3A ALA* 1.3 64.5 + - - +
4A GLU* 3.2 12.1 + - - +
5A HIS* 2.8 66.1 + - - +
6A VAL* 3.1 11.1 + - - +
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Residues in contact with ALA 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA 3.6 1.8 + - - -
2A ASP* 1.3 74.2 - - - +
4A GLU* 1.3 62.5 + - - +
6A VAL* 3.1 5.2 + - - +
7A VAL* 2.9 27.6 + - - +
61A GLY 4.7 3.4 - - - +
62A THR* 4.3 20.5 - - + +
67A VAL* 3.8 28.0 - - + -
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Residues in contact with GLU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP* 3.2 15.7 + - - +
3A ALA* 1.3 79.0 - - - +
5A HIS* 1.3 62.8 + - + +
7A VAL* 3.4 7.0 + - - +
8A GLU* 2.9 53.6 + - + +
67A VAL* 5.5 1.3 - - - +
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Residues in contact with HIS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 4.4 15.7 - - + -
2A ASP* 2.8 39.3 + - - +
4A GLU* 1.3 83.6 - - + +
6A VAL* 1.3 66.1 + - - +
8A GLU* 3.3 21.8 + - - +
9A ALA* 3.0 23.4 + - - +
15D SER* 5.4 0.7 - - - +
18D ALA* 6.3 3.6 - - + -
19D LEU* 4.8 4.4 - - + +
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Residues in contact with VAL 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 4.3 15.5 - - + +
2A ASP 3.1 12.8 + - - +
3A ALA* 3.1 8.4 + - - +
5A HIS* 1.3 74.2 - - - +
7A VAL* 1.3 59.2 + - - +
9A ALA* 3.2 4.4 + - - +
10A ARG* 2.9 30.5 + - - +
56A ASP 3.7 13.0 - - - +
57A LEU* 3.4 26.8 - - - +
59A ALA* 4.2 17.3 - - + -
62A THR* 4.1 19.1 - - + -
19D LEU* 4.2 21.5 - - + -
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA 2.9 18.5 + - - +
4A GLU* 3.8 7.2 - - - +
6A VAL* 1.3 76.9 - - - +
8A GLU* 1.3 64.2 + - + +
10A ARG* 3.1 27.9 + - - +
11A LYS* 3.0 36.7 + - + +
62A THR* 4.1 5.2 - - - +
67A VAL* 3.9 19.3 - - + -
68A LYS 4.9 3.1 - - - +
69A GLY 3.5 26.5 - - - +
70A THR* 3.8 15.3 - - - +
131A HEC 4.7 0.7 - - - +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU* 2.9 49.4 + - + +
5A HIS* 3.6 21.5 + - - +
7A VAL* 1.3 78.5 - - + +
9A ALA* 1.3 59.3 + - - +
11A LYS* 4.0 10.3 - - - +
12A GLY* 2.9 25.1 + - - -
12D GLY* 5.1 0.5 - - - -
15D SER* 4.2 20.5 + - - +
131D HEC 4.6 6.6 - - - +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A HIS 3.0 16.5 + - - +
6A VAL 3.7 3.8 - - - +
8A GLU* 1.3 77.7 - - - +
10A ARG* 1.3 58.7 + - - +
12A GLY* 3.3 0.9 + - - -
13A TYR* 2.9 23.4 + - - +
57A LEU* 3.8 16.2 - - + -
15D SER* 3.8 29.1 - - - +
16D LEU* 3.5 16.7 - - + +
19D LEU* 3.9 15.5 - - + -
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 2.9 19.5 + - - +
7A VAL* 3.1 19.1 + - - +
9A ALA* 1.3 77.0 - - - +
11A LYS* 1.3 63.3 + - - +
13A TYR* 3.3 5.2 + - - +
14A PHE* 3.2 37.5 + - + -
57A LEU* 3.0 40.3 + - + +
58A TYR* 3.7 22.4 - - + +
62A THR* 2.7 48.3 + - - -
70A THR* 3.0 18.4 + - - -
72A ALA* 3.7 13.2 - - - +
77A TRP* 4.0 8.3 - - - -
131A HEC 2.8 27.8 + - + +
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.0 25.6 + - + +
8A GLU* 4.0 8.3 - - - +
10A ARG* 1.3 72.7 - - - +
12A GLY* 1.3 55.1 + - - +
14A PHE* 3.2 4.4 + - - +
15A SER* 2.8 38.1 + - - -
69A GLY* 2.9 32.8 + - - +
131A HEC 3.5 59.2 - - - +
8D GLU* 5.2 6.9 + - - +
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Residues in contact with GLY 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU 2.9 16.2 + - - -
9A ALA 3.3 1.8 + - - -
10A ARG 3.2 0.2 - - - -
11A LYS* 1.3 77.4 - - - +
13A TYR* 1.3 61.2 + - - +
15A SER* 3.0 8.8 + - - -
16A LEU* 3.0 27.2 + - - +
8D GLU* 4.8 2.0 - - - -
12D GLY* 3.5 32.9 - - - -
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Residues in contact with TYR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA 2.9 13.3 + - - +
10A ARG 3.4 9.0 - - - +
12A GLY* 1.3 74.8 - - - +
14A PHE* 1.3 96.2 + + - +
16A LEU* 3.2 8.0 + - + +
17A VAL* 3.1 35.8 + - + +
49A LEU* 3.1 41.9 + - + +
50A THR* 4.2 5.0 - - - -
52A TYR* 3.8 31.4 + + + -
54A PRO* 4.8 13.3 - - + +
57A LEU* 3.7 19.7 - - + -
58A TYR* 5.7 0.7 - - - -
90A PHE* 4.6 12.8 - + - -
16D LEU* 4.1 17.6 - - + +
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Residues in contact with PHE 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 3.2 32.7 + - + -
11A LYS* 4.0 1.1 - - - +
13A TYR* 1.3 99.4 - + - +
15A SER* 1.3 60.1 + - - +
17A VAL* 3.3 8.7 + - + +
18A ALA* 2.8 30.9 + - - +
57A LEU* 5.8 0.2 - - + -
58A TYR* 3.5 23.1 - - - -
90A PHE* 6.1 2.7 - + - -
131A HEC 3.2 118.9 - + + +
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS 2.8 19.8 + - - -
12A GLY* 3.0 11.0 + - - -
14A PHE* 1.3 74.1 - - - +
16A LEU* 1.3 56.7 + - - +
18A ALA* 3.4 7.1 + - - +
19A LEU* 2.9 28.6 + - - +
131A HEC 3.7 9.5 + - - +
5D HIS 5.5 1.1 - - - +
8D GLU* 3.3 33.8 + - - +
9D ALA* 4.0 21.9 - - - +
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY 3.0 15.0 + - - +
13A TYR* 3.2 7.8 + - + +
15A SER* 1.3 75.0 - - - +
17A VAL* 1.3 66.5 + - - +
19A LEU* 3.1 6.0 + - + +
20A GLU* 3.0 27.4 + - - +
49A LEU* 3.9 25.6 - - + -
9D ALA* 3.7 23.3 - - + +
13D TYR* 4.2 19.5 - - + +
16D LEU* 3.6 31.0 - - + -
49D LEU* 5.9 1.1 - - + -
52D TYR* 3.7 25.6 - - + +
57D LEU* 3.9 15.7 - - + -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.3 38.6 - - + +
14A PHE* 3.5 12.6 - - + +
16A LEU* 1.3 76.2 - - - +
18A ALA* 1.3 65.3 + - - +
20A GLU* 3.3 1.2 + - - +
21A PHE* 3.0 21.8 + - - +
46A LEU* 4.2 9.2 - - + +
49A LEU* 3.8 19.7 - - + +
90A PHE* 4.2 15.5 - - + -
131A HEC 3.8 42.8 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE 2.8 17.1 + - - +
15A SER* 3.7 6.5 - - - +
17A VAL* 1.3 76.7 - - - +
19A LEU* 1.3 57.3 + - - +
21A PHE* 5.2 0.4 - - - -
22A GLY* 2.9 29.3 + - - -
131A HEC 3.8 39.5 - - + -
5D HIS* 6.1 5.2 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER 2.9 17.2 + - - +
16A LEU* 3.1 10.1 + - - +
18A ALA* 1.3 77.9 - - - +
20A GLU* 1.3 65.0 + - + +
22A GLY* 4.4 0.2 - - - -
23A PRO* 3.2 22.3 - - + +
42A HIS* 5.0 0.8 + - + -
1D ALA 4.0 22.9 - - - +
5D HIS* 4.2 25.8 - - + +
6D VAL* 4.4 9.9 - - + -
9D ALA* 4.2 11.7 - - + -
52D TYR* 5.4 2.5 - - - +
56D ASP* 3.8 33.2 - - + +
57D LEU* 5.1 4.5 - - + -
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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
----------------------------------------------------------
16A LEU 3.0 15.2 + - - +
17A VAL 4.1 2.0 - - - +
19A LEU* 1.3 79.1 - - + +
21A PHE* 1.3 64.2 + - - +
23A PRO* 3.4 9.3 - - - +
24A LEU* 4.0 5.4 - - - +
42A HIS* 2.8 64.7 + - - +
45A ASP* 3.0 25.6 - - + +
46A LEU* 4.3 13.5 - - + -
49A LEU* 4.6 3.8 - - + -
52D TYR* 2.8 31.0 + - + +
53D ASP 4.9 0.2 - - - +
56D ASP* 3.0 24.8 - - - +
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Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL 3.0 18.0 + - - +
18A ALA* 4.1 2.5 - - - +
20A GLU* 1.3 77.4 - - - +
22A GLY* 1.3 66.6 + - - +
23A PRO 3.4 0.2 - - - -
24A LEU* 3.2 10.1 + - + +
25A ALA* 2.9 34.2 + - + +
46A LEU* 4.2 17.0 - - + +
97A LEU* 5.3 0.7 - - + -
112A VAL* 4.1 26.7 - - + -
115A VAL* 3.5 29.2 - - + -
116A GLY* 4.0 22.9 - - - -
119A CYS* 4.7 2.5 - - - -
131A HEC 3.8 39.5 - - + -
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Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 2.9 17.3 + - - -
19A LEU 4.4 0.2 - - - -
21A PHE* 1.3 78.4 - - - +
23A PRO* 1.3 61.7 - - - +
25A ALA* 3.2 7.5 + - - +
26A ALA* 2.9 27.8 + - - +
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Residues in contact with PRO 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.2 18.2 - - + +
20A GLU 3.4 8.1 - - - +
22A GLY* 1.3 87.7 - - - +
24A LEU* 1.4 59.4 + - - +
26A ALA* 3.6 7.4 - - + +
27A MET* 3.0 35.7 + - + +
32A MET* 3.9 20.0 - - + +
42A HIS* 3.6 41.3 - - + +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 4.0 16.2 - - - +
21A PHE* 3.2 11.3 + - + +
23A PRO* 1.4 74.6 - - - +
25A ALA* 1.3 64.1 + - - +
27A MET* 3.4 7.1 + - - +
28A ALA* 3.0 22.7 + - - +
39A ALA* 3.4 41.1 - - + +
42A HIS* 4.2 7.2 - - + -
43A ALA* 4.0 13.5 - - + +
46A LEU* 4.0 11.7 - - + -
97A LEU* 3.6 31.4 - - + -
101A ALA* 5.5 0.2 - - + -
108A LEU* 3.9 13.4 - - + +
112A VAL* 3.8 19.0 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 2.9 34.2 + - + +
22A GLY* 3.2 9.2 + - - +
24A LEU* 1.3 76.3 - - - +
26A ALA* 1.3 63.7 + - - +
28A ALA* 3.3 2.1 + - - +
29A LYS* 3.0 43.3 + - - +
112A VAL* 4.1 13.8 - - + +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 2.9 16.0 + - - +
23A PRO* 3.6 9.0 - - + +
24A LEU 3.3 0.2 - - - -
25A ALA* 1.3 78.0 - - - +
27A MET* 1.3 57.0 + - - +
29A LYS* 3.3 4.2 + - - +
30A GLY 3.0 7.1 + - - -
31A GLU* 2.9 49.2 + - + +
32A MET* 3.8 21.3 - - + -
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 3.0 22.4 + - + +
24A LEU* 3.7 5.6 - - - +
25A ALA 3.2 0.2 - - - -
26A ALA* 1.3 74.9 - - - +
28A ALA* 1.3 64.4 + - - +
30A GLY* 3.2 10.2 + - - -
32A MET* 3.4 38.9 - - + +
33A PRO 3.4 19.7 - - - +
34A TYR* 4.0 10.7 + - + -
35A ASP* 3.5 41.3 - - + +
38A ALA* 4.0 14.8 - - + -
39A ALA* 4.2 17.7 - - - +
42A HIS* 5.4 0.7 - - + -
105A GLN* 3.0 17.9 - - - +
108A LEU* 4.1 10.8 - - + -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 3.0 17.7 + - - +
25A ALA 3.3 5.8 + - - +
27A MET* 1.3 75.7 - - - +
29A LYS* 1.3 60.4 + - + +
105A GLN* 3.2 16.4 - - - +
108A LEU* 4.0 4.0 - - + +
109A ALA* 3.7 35.5 - - + +
112A VAL* 3.8 19.5 - - + -
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.0 35.0 + - - +
26A ALA* 3.6 4.7 - - - +
27A MET 3.2 0.2 - - - -
28A ALA* 1.3 79.7 - - + +
30A GLY* 1.3 57.6 + - - +
31A GLU* 3.1 33.9 + - + +
----------------------------------------------------------
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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