Contacts of the helix formed by residues 2 - 29 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ALA* 1.3 88.0 - - - +
3D ALA* 1.3 68.2 + - - +
4D GLU* 3.0 15.7 + - - +
5D HIS* 3.0 51.4 + - - +
6D VAL* 3.2 10.0 + - - +
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Residues in contact with ALA 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ALA 4.0 0.2 + - - -
2D ASP* 1.3 73.2 - - - +
4D GLU* 1.3 59.7 - - + +
6D VAL* 3.1 4.7 + - - +
7D VAL* 2.8 33.7 + - - +
61D GLY 4.7 2.9 - - - +
62D THR* 4.1 21.5 - - + -
67D VAL* 3.5 31.4 - - + -
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Residues in contact with GLU 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ASP* 3.0 13.8 + - - +
3D ALA* 1.3 81.0 - - + +
5D HIS* 1.3 62.7 + - + +
7D VAL* 3.5 7.4 + - - +
8D GLU* 3.1 27.9 + - - +
67D VAL* 6.4 2.2 - - + -
68D LYS* 3.2 32.4 + - + +
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Residues in contact with HIS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 5.5 1.4 - - - +
18A ALA* 6.1 4.7 - - + -
19A LEU* 4.2 8.5 - - + +
1D ALA* 4.6 14.7 - - + +
2D ASP* 3.0 43.4 + - - +
4D GLU* 1.3 76.5 - - + +
6D VAL* 1.3 64.9 + - - +
7D VAL 3.1 1.1 - - - -
8D GLU* 3.5 15.5 + - + +
9D ALA* 3.0 24.3 + - - +
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Residues in contact with VAL 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.4 11.4 - - + -
1D ALA 4.2 20.4 - - - +
2D ASP 3.2 14.6 + - - +
3D ALA* 3.1 8.2 + - - +
5D HIS* 1.3 76.8 - - - +
7D VAL* 1.3 57.5 + - - +
9D ALA* 3.3 3.0 + - - +
10D ARG* 3.0 28.1 + - - +
56D ASP 3.6 15.5 - - - +
57D LEU* 3.3 26.2 - - - +
59D ALA* 4.2 17.9 - - + -
62D THR* 4.2 17.7 - - + +
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Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ALA 2.8 21.6 + - - +
4D GLU* 3.8 7.4 - - - +
6D VAL* 1.3 76.3 - - - +
8D GLU* 1.3 57.7 + - - +
10D ARG* 3.2 16.2 + - - +
11D LYS* 3.0 39.9 + - + +
62D THR* 4.4 6.7 - - - +
67D VAL* 3.9 26.9 - - + -
68D LYS 4.9 4.0 - - - +
69D GLY* 3.7 26.5 - - - +
70D THR* 3.9 15.3 - - - +
131D HEC 5.0 0.2 - - - +
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Residues in contact with GLU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.2 8.0 + - - +
12A GLY* 4.8 1.5 - - - -
15A SER* 3.3 24.1 + - - +
131A HEC 3.2 19.9 - - - +
4D GLU 3.1 17.9 + - - +
5D HIS* 4.0 16.5 + - - +
7D VAL* 1.3 78.5 - - - +
9D ALA* 1.3 57.1 + - - +
11D LYS* 4.1 10.0 - - - +
12D GLY* 2.9 24.4 + - - -
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Residues in contact with ALA 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 4.0 25.5 - - - +
16A LEU* 3.7 15.7 - - + +
19A LEU* 4.2 11.7 - - + -
5D HIS 3.0 18.5 + - - +
6D VAL 3.9 2.2 - - - +
8D GLU* 1.3 73.1 - - - +
10D ARG* 1.3 59.6 + - - +
12D GLY* 3.2 1.1 + - - -
13D TYR* 2.8 30.0 + - - +
57D LEU* 3.8 18.6 - - + -
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Residues in contact with ARG 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D VAL* 3.0 20.9 + - - +
7D VAL* 3.2 12.2 + - - +
9D ALA* 1.3 75.4 - - - +
11D LYS* 1.3 64.5 + - - +
13D TYR* 3.2 5.9 + - - +
14D PHE* 3.1 36.2 + - + -
57D LEU* 3.0 40.8 + - + +
58D TYR* 3.7 22.0 - - + +
62D THR* 2.8 44.7 + - - -
70D THR* 2.5 29.7 + - - -
72D ALA* 3.5 13.9 - - - +
77D TRP* 4.1 6.4 - - - -
131D HEC 2.7 26.3 + - + +
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Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 3.0 29.2 + - + +
8D GLU* 4.1 8.1 - - - +
10D ARG* 1.3 74.3 - - - +
12D GLY* 1.3 57.9 + - - +
14D PHE* 3.1 5.8 + - - +
15D SER* 2.8 31.8 + - - -
69D GLY* 3.2 32.0 + - - +
130D ARG* 6.0 0.9 - - - +
131D HEC 3.4 58.9 - - - +
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Residues in contact with GLY 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU 5.1 0.7 - - - -
12A GLY* 3.5 33.3 - - - -
8D GLU 2.9 13.3 + - - -
9D ALA 3.5 4.5 - - - -
11D LYS* 1.3 77.8 - - - +
13D TYR* 1.3 59.2 + - - +
15D SER* 3.2 8.9 + - - -
16D LEU* 3.1 27.8 + - - +
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Residues in contact with TYR 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.2 18.0 - - + +
9D ALA 2.8 16.1 + - - +
10D ARG 3.3 8.3 - - - +
12D GLY* 1.3 69.6 - - - +
14D PHE* 1.3 87.3 + + - +
16D LEU* 3.3 6.6 + - - +
17D VAL* 3.0 48.5 + - + +
49D LEU* 3.1 44.1 + - + -
50D THR* 4.2 5.2 - - - -
52D TYR* 3.9 29.9 + + + -
54D PRO* 5.0 12.6 - - + +
57D LEU* 3.6 20.9 - - + -
58D TYR* 5.7 0.4 - - - -
90D PHE* 4.6 10.5 - + - -
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Residues in contact with PHE 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ARG* 3.1 28.6 + - + -
11D LYS 3.1 7.2 + - - +
13D TYR* 1.3 99.1 - + - +
15D SER* 1.3 60.9 + - - +
17D VAL* 3.7 8.4 - - + +
18D ALA* 2.8 30.8 + - - +
57D LEU* 5.8 0.2 - - + -
58D TYR* 3.6 22.9 - - - -
90D PHE* 5.9 2.2 - + - -
131D HEC 3.1 119.0 - + + +
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Residues in contact with SER 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A HIS 5.4 0.8 - - - +
8A GLU* 4.2 15.7 + - - +
9A ALA* 3.8 26.5 - - - +
11D LYS 2.8 17.3 + - - -
12D GLY* 3.2 13.0 + - - -
14D PHE* 1.3 76.5 - - - +
16D LEU* 1.3 57.4 + - - +
18D ALA* 3.8 5.0 - - - +
19D LEU* 3.0 27.2 + - - +
131D HEC 3.4 18.6 + - - +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.5 23.8 - - + +
13A TYR* 4.1 20.4 - - + -
16A LEU* 3.6 31.0 - - + -
49A LEU* 6.1 0.4 - - + -
52A TYR* 3.7 26.7 - - + +
57A LEU* 3.7 16.6 - - + -
12D GLY 3.1 15.4 + - - +
13D TYR* 3.6 5.6 - - - +
15D SER* 1.3 73.3 - - - +
17D VAL* 1.4 66.7 + - - +
19D LEU* 3.1 14.6 + - + +
20D GLU* 3.1 18.0 + - - +
49D LEU* 3.8 27.1 - - + -
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Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR* 3.0 46.3 + - + +
14D PHE* 3.7 12.1 - - + +
16D LEU* 1.4 75.1 - - - +
18D ALA* 1.3 63.6 + - - +
20D GLU* 3.3 0.9 + - - -
21D PHE* 2.9 25.5 + - - +
46D LEU* 3.9 8.1 - - + +
49D LEU* 3.7 21.7 - - + +
90D PHE* 3.9 20.4 - - + -
131D HEC 3.8 39.5 - - + -
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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
----------------------------------------------------------
5A HIS* 6.3 3.4 - - + -
14D PHE 2.8 21.6 + - - +
15D SER* 3.8 5.2 - - - +
17D VAL* 1.3 74.9 - - - +
19D LEU* 1.3 56.4 + - - +
21D PHE* 4.1 1.0 - - - +
22D GLY* 2.9 29.8 + - - -
131D HEC 3.9 38.8 - - + +
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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
----------------------------------------------------------
1A ALA* 4.1 26.0 - - + -
5A HIS* 4.8 4.0 - - + +
6A VAL* 4.2 21.1 - - + +
9A ALA* 3.9 20.0 - - + -
52A TYR* 4.7 2.2 - - - +
56A ASP* 3.7 34.4 - - + +
57A LEU* 4.0 14.8 - - + -
15D SER 3.0 19.5 + - - +
16D LEU* 3.1 6.5 + - + +
18D ALA* 1.3 74.9 - - - +
20D GLU* 1.3 62.5 + - + +
22D GLY* 4.3 0.5 - - - -
23D PRO* 3.1 23.7 - - - +
42D HIS* 5.0 0.7 + - - -
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.1 26.9 + - + +
53A ASP 5.0 0.5 - - - +
56A ASP* 2.9 26.3 - - - +
16D LEU 3.1 14.5 + - - +
17D VAL 4.0 0.9 - - - +
19D LEU* 1.3 77.8 - - - +
21D PHE* 1.3 65.0 + - - +
22D GLY 3.2 0.2 - - - -
23D PRO* 3.3 10.0 - - - +
24D LEU* 3.7 4.9 - - - +
42D HIS* 2.7 56.7 + - - +
45D ASP* 3.7 25.8 - - + +
46D LEU* 3.9 21.5 - - + -
49D LEU* 4.6 4.0 - - + -
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Residues in contact with PHE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D VAL 2.9 18.2 + - - +
18D ALA 4.1 2.0 - - - +
20D GLU* 1.3 77.8 - - - +
22D GLY* 1.3 66.4 + - - +
24D LEU* 3.1 10.2 + - + +
25D ALA* 3.0 34.3 + - + -
46D LEU* 4.3 17.2 - - + +
97D LEU* 6.0 0.7 - - + -
112D VAL* 3.9 28.7 - - + -
115D VAL* 3.4 34.8 - - + -
116D GLY* 4.0 21.1 - - - -
119D CYS* 4.6 2.7 - - - -
131D HEC 3.8 34.1 - - + -
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Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ALA 2.9 17.6 + - - -
19D LEU 4.3 0.4 - - - -
21D PHE* 1.3 75.9 - - - +
23D PRO* 1.3 62.9 - - - +
25D ALA* 3.2 8.3 + - - +
26D ALA* 3.0 27.4 + - - +
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Residues in contact with PRO 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU 3.1 17.0 - - - +
20D GLU 3.3 7.2 - - - +
22D GLY* 1.3 91.3 - - - +
24D LEU* 1.3 56.2 + - - +
26D ALA* 3.8 2.5 - - + +
27D MET* 3.0 36.6 + - + +
32D MET* 4.2 23.5 - - + +
42D HIS* 3.4 43.5 - - + +
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU 3.7 11.7 - - - +
21D PHE* 3.1 13.5 + - + +
23D PRO* 1.3 78.6 - - - +
25D ALA* 1.3 60.9 + - - +
27D MET* 3.5 4.6 + - + -
28D ALA* 3.2 22.7 + - - +
39D ALA* 3.7 39.0 - - + +
42D HIS* 3.9 8.7 - - + -
43D ALA* 4.0 12.1 - - + +
46D LEU* 3.8 19.7 - - + -
97D LEU* 3.6 32.8 - - + -
108D LEU* 3.7 15.7 - - + +
112D VAL* 3.7 14.0 - - + +
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PHE* 3.0 33.4 + - + +
22D GLY* 3.7 8.7 - - - +
24D LEU* 1.3 73.4 - - - +
26D ALA* 1.3 61.3 + - - +
28D ALA* 3.3 2.5 + - - +
29D LYS* 3.0 48.3 + - - +
112D VAL* 4.0 12.5 - - + +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLY 3.0 15.9 + - - +
23D PRO* 3.8 5.4 - - + +
25D ALA* 1.3 77.6 - - - +
27D MET* 1.3 59.2 + - - +
29D LYS* 3.3 2.0 + - - +
30D GLY 3.1 3.5 + - - -
31D GLU* 2.8 52.5 + - + +
32D MET* 3.3 21.0 + - + -
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Residues in contact with MET 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PRO* 3.0 22.7 + - - +
24D LEU* 3.8 5.6 - - + +
26D ALA* 1.3 78.1 - - - +
28D ALA* 1.3 59.5 + - - +
30D GLY* 3.2 10.9 + - - -
32D MET* 3.5 33.3 - - + +
33D PRO 3.5 10.3 - - - +
34D TYR* 3.5 29.2 + - + -
35D ASP* 3.7 26.7 - - - +
38D ALA* 5.3 2.5 - - - -
39D ALA* 3.6 24.5 - - + -
42D HIS* 6.2 1.1 - - - -
105D GLN* 3.2 17.3 - - - +
108D LEU* 3.5 17.9 - - + -
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU 3.2 15.4 + - - +
25D ALA 3.6 5.2 - - - +
26D ALA 3.2 0.2 - - - -
27D MET* 1.3 78.1 - - - +
29D LYS* 1.3 61.5 + - + +
105D GLN* 3.4 16.1 - - - +
108D LEU* 4.0 5.1 - - + +
109D ALA* 3.8 32.1 - - + +
112D VAL* 4.0 16.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA* 3.0 32.6 + - - +
26D ALA* 3.7 1.5 - - - +
27D MET 3.2 0.2 - - - -
28D ALA* 1.3 80.9 - - + +
30D GLY* 1.3 59.1 + - - +
31D GLU* 3.2 44.7 + - + +
----------------------------------------------------------
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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