Contacts of the helix formed by residues 39 - 66 (chain D) in PDB entry 1QGH
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 PHE 39 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D HIS 4.5 0.9 - - - -
32D TRP 5.5 0.2 - - - -
34D MET* 3.5 41.7 - - + -
36D GLY 2.8 16.8 + - - +
37D HIS 3.2 1.2 - - - -
38D ASN* 1.3 77.0 - - - +
40D PHE* 1.3 72.4 + + - +
43D HIS* 2.7 65.6 + + + +
95D MET* 3.7 9.5 - - - +
144G TRP* 4.0 16.4 - + - -
145G MET* 3.6 51.1 - - + -
148G ALA* 3.6 14.8 - - + -
149G PHE* 3.9 13.7 - - + +
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS 4.8 1.3 + - - +
38D ASN 3.3 1.0 - - - -
39D PHE* 1.3 92.3 - + - +
41D THR* 1.3 66.6 + - - +
43D HIS* 3.6 2.7 - + + +
44D GLU* 3.2 34.6 + - - +
41G THR* 3.8 15.9 - - - +
42G LEU* 3.7 22.7 - - + -
45G LYS* 3.5 37.0 - - + -
145G MET* 3.8 33.0 - - + -
146G PHE* 3.5 38.1 - + - -
149G PHE* 3.7 30.1 - + + -
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Residues in contact with THR 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS 5.1 0.9 - - - +
38D ASN* 3.3 34.5 - - + +
40D PHE* 1.3 79.1 - - - +
42D LEU* 1.3 60.8 + - + +
44D GLU* 3.2 8.8 + - - +
45D LYS* 2.9 26.3 + - - +
38G ASN* 6.0 0.7 - - - +
41G THR* 4.5 23.3 + - + +
37I HIS 5.6 1.6 - - - +
40I PHE* 4.1 21.5 - - - +
41I THR* 4.7 18.0 + - + +
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D MET* 3.5 18.4 - - + -
38D ASN* 2.9 33.7 + - + +
41D THR* 1.3 76.6 - - + +
43D HIS* 1.3 67.3 + - - +
45D LYS* 3.6 9.7 - - + +
46D MET* 2.9 30.8 + - + +
95D MET* 3.7 15.0 - - + -
99D MET* 4.4 13.7 - - + -
146D PHE* 4.7 4.0 - - + -
149D PHE* 3.4 33.9 - - + -
40I PHE* 3.8 35.0 - - + -
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Residues in contact with HIS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 3.7 7.1 + - - -
31D HIS* 2.8 86.0 + + - -
34D MET* 3.3 11.8 - - - -
39D PHE* 2.7 45.2 + + + +
40D PHE* 3.6 4.0 - + - +
42D LEU* 1.3 74.9 - - - +
44D GLU* 1.3 69.8 + - + +
47D ASP* 3.4 9.2 + - - +
141G LYS* 5.5 1.8 + - - -
144G TRP* 3.6 27.8 - + - -
145G MET* 4.6 9.8 - - - -
157J FE 4.0 2.0 - - - -
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE* 3.2 27.4 + - - +
41D THR* 3.7 7.9 - - - +
42D LEU 3.2 0.4 - - - -
43D HIS* 1.3 82.2 - - + +
45D LYS* 1.3 67.5 + - - +
47D ASP* 2.9 21.0 + - - +
48D ASP* 3.2 19.0 + - - +
45G LYS* 5.2 8.5 - - - +
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D THR* 2.9 17.1 + - - +
42D LEU* 3.1 12.8 + - + +
44D GLU* 1.3 78.0 - - - +
46D MET* 1.3 67.2 + - + +
48D ASP* 3.0 23.5 + - - +
49D LEU* 3.0 25.1 + - + +
142D HIS* 4.5 8.4 + - - -
145D MET* 4.1 17.6 - - - +
146D PHE* 3.9 25.7 - - + -
40I PHE* 3.4 39.8 - - + -
44I GLU* 5.2 8.1 - - - +
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Residues in contact with MET 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.3 19.9 - - + +
30D ILE* 4.0 22.0 - - + -
31D HIS* 3.8 24.7 - - + +
34D MET* 3.7 17.0 - - + -
42D LEU* 2.9 24.5 + - + +
43D HIS 3.8 2.5 - - - +
44D GLU 3.1 0.2 - - - -
45D LYS* 1.3 81.7 - - + +
47D ASP* 1.3 58.5 + - - +
49D LEU* 3.8 15.0 - - + +
50D TYR* 2.8 28.5 + - - +
99D MET* 4.4 9.2 - - + -
102D LEU* 4.1 9.0 - - + -
146D PHE* 3.6 37.9 - - + -
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Residues in contact with ASP 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASP* 4.6 2.1 - - - +
28D HIS* 4.8 8.1 - - - -
31D HIS* 3.3 35.1 + - - -
43D HIS* 3.4 6.6 + - - +
44D GLU* 2.9 13.8 + - - +
46D MET* 1.3 78.7 - - - +
48D ASP* 1.3 66.7 + - - +
50D TYR* 3.4 6.5 + - - +
51D SER* 3.2 26.2 + - - -
157J FE 3.7 7.8 - - - -
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Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU* 3.2 15.4 + - - +
45D LYS* 3.0 28.7 + - - +
47D ASP* 1.3 79.9 - - - +
49D LEU* 1.3 67.1 + - + +
51D SER* 3.3 6.7 + - - -
52D GLU* 3.0 23.5 + - - +
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 5.2 0.7 - - + -
27D ILE* 3.9 13.5 - - + -
45D LYS* 3.0 19.1 + - - +
46D MET* 3.6 24.2 - - + +
48D ASP* 1.3 77.6 - - + +
50D TYR* 1.3 64.6 + - - +
52D GLU* 4.3 2.7 - - - +
53D PHE* 2.8 47.7 + - + +
102D LEU* 3.8 39.0 - - + -
106D LEU* 5.5 2.5 - - + -
142D HIS* 3.6 35.9 - - + +
146D PHE* 4.0 11.9 - - + -
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Residues in contact with TYR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN* 5.4 1.2 + - - -
24B THR* 5.9 3.1 - - - +
50B TYR* 4.6 18.3 + + - -
54B GLY* 5.8 4.5 - - - -
57B MET* 4.4 8.0 - - - +
24D THR* 3.6 46.0 + - + +
25D VAL* 5.3 0.4 - - - +
27D ILE* 3.9 14.1 - - + +
28D HIS* 3.0 54.2 + + + +
46D MET 2.8 17.7 + - - +
47D ASP* 3.5 9.9 - - - +
49D LEU* 1.3 78.1 - - - +
51D SER* 1.3 64.9 + - - +
54D GLY* 2.9 28.2 + - - -
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Residues in contact with SER 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ASP 3.2 12.1 + - - -
48D ASP* 3.7 9.1 - - - -
49D LEU 3.2 0.4 - - - -
50D TYR* 1.3 84.9 - - - +
52D GLU* 1.3 60.5 + - - +
54D GLY* 3.3 1.5 + - - -
55D GLU* 2.9 36.9 + - - +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASP 3.0 15.8 + - - +
49D LEU* 3.7 5.1 - - - +
51D SER* 1.3 76.6 - - - +
53D PHE* 1.3 70.6 + - + +
55D GLU* 2.9 13.7 + - - +
56D GLN* 2.9 36.0 + - + +
138D SER* 2.6 26.7 + - - -
142D HIS* 2.7 32.2 + - - -
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Residues in contact with PHE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 4.2 16.0 - - + +
23D PHE* 3.8 34.3 - + + -
24D THR* 4.7 8.7 - - - +
27D ILE* 4.4 5.6 - - + -
49D LEU* 2.8 52.6 + - + +
50D TYR 4.6 0.2 - - - +
52D GLU* 1.3 86.2 - - + +
54D GLY* 1.3 56.6 + - - +
56D GLN* 3.3 37.9 + - - +
57D MET* 2.9 29.5 + - - +
106D LEU* 3.9 20.0 - - + -
109D LEU* 4.7 3.4 - - + -
139D ILE* 4.0 15.7 - - + -
142D HIS* 4.0 16.2 - + - -
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Residues in contact with GLY 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 5.3 1.2 + - - -
50B TYR* 5.8 3.8 - - - -
24D THR* 4.3 8.4 + - - -
50D TYR* 2.9 21.1 + - - -
51D SER* 3.7 2.0 - - - -
52D GLU 3.1 0.2 - - - -
53D PHE* 1.3 77.7 - - - +
55D GLU* 1.3 61.8 + - - +
57D MET* 3.3 15.2 - - - +
58D ASP* 3.1 21.3 + - - +
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D SER* 2.9 20.3 + - - +
52D GLU* 3.4 10.8 - - - +
54D GLY* 1.3 73.6 - - - +
56D GLN* 1.3 67.0 + - - +
57D MET 3.0 1.9 + - - -
58D ASP* 3.0 7.4 + - - +
59D GLU* 2.9 37.5 + - + +
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Residues in contact with GLN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 4.2 6.2 - - + +
52D GLU* 2.9 28.9 + - + +
53D PHE* 3.5 42.5 - - - +
55D GLU* 1.3 74.6 - - - +
57D MET* 1.3 54.3 + - - +
59D GLU* 3.1 2.6 + - - +
60D VAL* 2.7 40.0 + - - +
113D TYR* 3.0 26.3 + - - -
135D PHE* 3.4 62.5 + - + +
138D SER* 4.7 1.8 - - - -
139D ILE* 4.5 1.0 - - - +
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Residues in contact with MET 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.6 32.5 - - + +
32B TRP* 3.7 20.4 - - + -
50B TYR* 4.4 6.7 - - - +
17D VAL* 4.2 8.5 - - - +
20D LEU* 3.5 29.6 - - + +
21D ASN* 3.4 42.0 - - - +
24D THR* 6.0 4.0 - - + -
53D PHE 2.9 13.4 + - - +
54D GLY* 3.3 16.6 - - - +
55D GLU 3.0 0.2 - - - -
56D GLN* 1.3 77.2 - - - +
58D ASP* 1.3 64.4 + - - +
60D VAL* 3.2 2.5 + - - +
61D ALA* 3.0 19.6 + - - +
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Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.7 19.4 - - + +
31B HIS* 3.7 1.2 - - - -
32B TRP* 2.6 34.3 + - - -
47B ASP* 4.8 1.1 - - - +
54D GLY 3.1 8.7 + - - +
55D GLU* 3.0 10.3 + - - +
57D MET* 1.3 84.3 - - - +
59D GLU* 1.3 58.5 + - + +
61D ALA* 3.2 0.9 + - - +
62D GLU* 2.8 41.7 + - - +
157L FE 2.0 30.5 - - - -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D GLU* 2.9 28.6 + - + +
56D GLN* 3.6 6.9 - - - +
58D ASP* 1.3 76.0 - - + +
60D VAL* 1.3 65.4 + - - +
62D GLU* 3.8 6.8 - - - +
63D ARG* 2.9 25.8 + - - +
131D MET* 4.0 11.7 - - - +
135D PHE* 3.7 28.6 - - + -
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 3.6 38.4 - - + +
16D GLN* 4.2 11.2 - - + -
17D VAL* 3.8 11.4 - - + +
20D LEU* 4.2 10.8 - - + -
56D GLN 2.7 25.2 + - - +
57D MET* 3.7 4.9 - - - +
59D GLU* 1.3 71.0 - - - +
61D ALA* 1.3 65.8 + - - +
63D ARG* 3.1 3.3 + - - +
64D LEU* 2.9 22.0 + - - +
113D TYR* 4.9 1.8 - - - +
131D MET* 4.1 13.5 - - + -
132D LEU* 5.1 4.0 - - + -
135D PHE* 3.3 26.5 - - + -
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TRP* 3.4 43.7 - - + +
17D VAL* 4.0 16.8 - - + +
57D MET 3.0 10.5 + - - +
58D ASP 3.5 4.7 - - - +
60D VAL* 1.3 76.6 - - - +
62D GLU* 1.3 60.0 + - - +
64D LEU* 3.1 8.2 + - - +
65D LEU* 2.9 29.2 + - - +
71D PRO* 4.2 9.2 - - + +
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 3.1 12.5 + - - -
32B TRP* 3.8 13.0 - - + +
43B HIS* 3.7 7.0 + - - -
58D ASP* 2.8 27.1 + - - +
59D GLU* 4.3 5.0 - - - +
61D ALA* 1.3 75.6 - - - +
63D ARG* 1.3 58.7 + - - +
65D LEU* 3.3 7.9 + - - +
66D ALA* 2.8 29.3 + - - +
141F LYS* 2.8 33.1 + - + +
144F TRP* 3.8 29.2 - - + -
157L FE 2.0 31.7 - - - -
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 4.3 6.3 - - + -
59D GLU 2.9 18.5 + - - +
60D VAL 3.6 4.3 - - - +
62D GLU* 1.3 74.5 - - - +
64D LEU* 1.3 63.9 + - - +
66D ALA* 3.1 8.3 + - - +
67D ILE* 2.9 40.3 + - - +
125D ASP* 2.9 29.7 + - - -
127D VAL* 3.1 31.3 - - - +
128D THR* 2.9 22.4 + - - +
131D MET* 3.8 27.8 - - + -
136F LYS* 4.4 5.3 - - - +
137F ALA 4.9 1.0 + - - -
140F ASP* 2.9 40.6 + - - +
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LYS* 3.7 36.1 - - + +
13D LEU* 4.2 12.7 - - + +
14D ASN* 3.6 29.4 - - + +
17D VAL* 4.9 2.0 - - + -
60D VAL 2.9 12.1 + - - +
61D ALA* 3.2 8.7 - - - +
63D ARG* 1.3 75.1 - - - +
65D LEU* 1.3 60.6 + - - +
67D ILE* 3.1 14.4 + - + +
69D GLY* 2.6 49.5 + - - -
70D SER 3.8 4.5 - - - +
71D PRO* 3.5 34.8 - - + -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TRP* 3.5 44.2 - - + +
33B TYR* 4.6 10.1 - - + -
61D ALA 2.9 11.6 + - - +
62D GLU* 3.4 13.7 - - - +
64D LEU* 1.3 81.0 - - - +
66D ALA* 1.3 62.3 + - - +
68D GLY* 3.1 12.0 + - - -
69D GLY 3.7 12.9 + - - +
71D PRO* 3.5 24.7 - - + -
144F TRP* 3.8 32.5 - - + +
154F PRO* 3.3 18.8 - - + +
----------------------------------------------------------
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D GLU 2.8 18.1 + - - +
63D ARG* 3.5 20.4 + - - +
64D LEU 3.1 0.4 - - - -
65D LEU* 1.3 78.3 - - - +
67D ILE* 1.3 57.8 + - - +
68D GLY 3.1 2.8 + - - -
140F ASP* 4.1 32.5 - - + +
141F LYS* 4.7 4.7 - - + +
144F TRP* 4.1 15.3 - - + -
154F PRO* 4.2 10.1 - - - +
155F LEU* 4.3 9.4 - - - +
----------------------------------------------------------
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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