Contacts of the helix formed by residues 39 - 67 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F HIS 4.6 0.9 - - - -
32F TRP 5.6 0.4 - - - -
34F MET* 3.5 42.0 - - + -
36F GLY 2.7 17.5 + - - +
37F HIS 3.2 1.4 - - - -
38F ASN* 1.3 78.3 - - - +
40F PHE* 1.3 76.3 + + - +
43F HIS* 2.7 65.8 + + + +
95F MET* 3.7 8.8 - - + +
144J TRP* 4.1 16.2 - + - -
145J MET* 3.6 46.7 - - + -
148J ALA* 3.8 14.1 - - + -
149J PHE* 4.0 13.2 - - + +
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Residues in contact with PHE 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F HIS 4.9 1.5 + - - -
38F ASN 3.4 1.0 - - - -
39F PHE* 1.3 87.5 - + - +
41F THR* 1.3 65.0 + - + +
43F HIS* 3.6 3.2 - + - +
44F GLU* 3.1 37.4 + - - +
41J THR* 3.9 15.9 - - + +
42J LEU* 3.8 27.8 - - + -
45J LYS* 3.6 36.1 - - + -
145J MET* 3.9 30.7 - - + -
146J PHE* 3.5 30.1 - + - -
149J PHE* 3.7 31.4 - + + -
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Residues in contact with THR 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS 5.6 1.8 - - - +
40B PHE* 3.9 22.9 - - - +
41B THR* 4.6 21.3 + - + +
37F HIS 5.1 1.8 - - - +
38F ASN* 3.4 33.0 - - + +
40F PHE* 1.3 76.4 - - + +
42F LEU* 1.3 60.4 + - + +
44F GLU* 3.2 10.4 + - - +
45F LYS* 2.9 25.8 + - - +
38J ASN* 6.2 0.4 - - - +
41J THR* 4.9 17.3 - - + +
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Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.7 36.3 - - + -
34F MET* 3.7 17.5 - - + -
38F ASN* 2.9 32.1 + - + +
41F THR* 1.3 77.0 - - + +
43F HIS* 1.3 66.6 + - - +
45F LYS* 3.7 9.9 - - + +
46F MET* 3.0 30.7 + - + +
95F MET* 3.7 14.1 - - + -
99F MET* 4.2 16.2 - - + -
146F PHE* 4.6 3.1 - - + -
149F PHE* 3.4 34.1 - - + -
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Residues in contact with HIS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F HIS* 2.9 83.3 + + - -
34F MET* 3.4 12.4 - - - -
39F PHE* 2.7 47.2 + + + +
40F PHE* 3.6 4.7 - + - +
42F LEU* 1.3 73.7 - - - +
44F GLU* 1.3 71.6 + - + +
46F MET 3.5 3.3 + - - -
47F ASP* 3.5 3.0 + - - -
157F FE 4.0 1.4 - - - -
62H GLU* 3.8 7.7 + - - -
141J LYS* 5.7 1.0 + - - -
144J TRP* 3.8 27.0 - + - -
145J MET* 4.8 9.0 - - - -
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Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F PHE* 3.1 32.1 + - - +
41F THR* 3.8 5.7 - - - +
43F HIS* 1.3 85.1 - - + +
45F LYS* 1.3 65.6 + - - +
47F ASP* 3.0 20.1 + - - +
48F ASP* 3.2 17.7 + - - +
45J LYS* 5.5 6.1 - - - +
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Residues in contact with LYS 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.4 39.6 - - + -
44B GLU* 5.3 7.4 - - - +
41F THR* 2.9 16.3 + - - +
42F LEU* 3.1 13.2 + - + +
44F GLU* 1.3 76.8 - - - +
46F MET* 1.3 59.9 + - + +
48F ASP* 3.0 24.5 + - - +
49F LEU* 2.9 30.8 + - + +
142F HIS* 4.4 8.6 + - - -
145F MET* 3.9 19.4 - - - +
146F PHE* 3.8 27.3 - - + -
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Residues in contact with MET 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ILE* 3.2 20.8 - - + +
30F ILE* 4.1 19.7 - - + -
31F HIS* 3.7 24.7 - - + +
34F MET* 3.7 18.4 - - + -
42F LEU* 3.0 21.8 + - + +
43F HIS 3.7 2.5 - - - +
44F GLU 3.2 0.2 - - - -
45F LYS* 1.3 80.0 - - + +
47F ASP* 1.3 60.8 + - - +
49F LEU* 3.6 19.3 - - + -
50F TYR* 2.8 27.5 + - - +
99F MET* 4.6 6.3 - - + -
102F LEU* 4.0 12.1 - - + -
146F PHE* 3.5 37.9 - - + -
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Residues in contact with ASP 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F HIS* 4.9 8.3 - - - -
31F HIS* 3.1 37.4 + - - -
43F HIS* 3.5 6.0 + - - +
44F GLU* 3.0 14.2 + - - +
46F MET* 1.3 78.6 - - - +
48F ASP* 1.3 66.2 + - - +
50F TYR* 3.4 6.9 + - - +
51F SER* 3.1 27.7 + - - -
157F FE 3.8 8.0 - - - -
58H ASP* 4.7 0.5 - - - +
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Residues in contact with ASP 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLU* 3.7 13.8 - - - +
45F LYS* 3.0 28.5 + - - +
47F ASP* 1.3 79.2 - - - +
49F LEU* 1.3 62.2 + - + +
51F SER* 3.3 5.9 + - - -
52F GLU* 2.9 29.6 + - - +
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F PHE* 5.2 0.4 - - + -
27F ILE* 4.0 13.9 - - + -
45F LYS* 2.9 18.6 + - - +
46F MET* 3.6 35.7 - - + +
48F ASP* 1.3 74.5 - - + +
50F TYR* 1.3 67.1 + - - +
52F GLU* 4.4 2.9 - - - +
53F PHE* 2.9 48.1 + - + +
102F LEU* 3.8 27.1 - - + -
106F LEU* 5.6 2.5 - - + -
142F HIS* 3.5 35.2 - - + +
146F PHE* 4.1 10.5 - - + -
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Residues in contact with TYR 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F THR* 3.5 46.4 + - + +
25F VAL* 5.2 0.2 - - - -
27F ILE* 3.8 13.0 - - + +
28F HIS* 3.0 52.6 + + + +
46F MET 2.8 17.4 + - - +
47F ASP* 3.5 10.8 - - - +
48F ASP 3.2 0.2 - - - -
49F LEU* 1.3 78.8 - - - +
51F SER* 1.3 69.0 + - - +
54F GLY* 3.1 22.3 + - - -
21H ASN* 5.4 1.2 + - - -
24H THR* 5.8 3.3 - - - +
50H TYR* 4.6 17.6 + + - -
54H GLY* 5.9 3.5 - - - -
57H MET* 4.3 7.3 - - - +
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Residues in contact with SER 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ASP 3.1 15.1 + - - -
48F ASP* 3.8 5.4 - - - -
49F LEU 3.2 0.2 - - - -
50F TYR* 1.3 86.0 - - - +
52F GLU* 1.3 65.6 + - - +
54F GLY* 3.4 0.7 + - - -
55F GLU* 3.0 32.1 + - - +
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ASP 2.9 16.9 + - - +
49F LEU* 3.2 6.1 + - - +
51F SER* 1.3 78.6 - - - +
53F PHE* 1.3 77.3 + - + +
55F GLU* 2.9 19.3 + - - +
56F GLN* 3.0 20.8 + - + +
138F SER* 2.5 31.0 + - - -
142F HIS* 2.7 28.5 + - - -
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Residues in contact with PHE 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU* 4.2 13.9 - - + +
23F PHE* 3.8 37.2 - + + -
24F THR* 4.8 7.6 - - - +
27F ILE* 4.4 5.2 - - + -
49F LEU* 2.9 44.1 + - + +
50F TYR 4.7 0.7 - - - +
52F GLU* 1.3 81.6 - - + +
54F GLY* 1.3 56.5 + - - +
56F GLN* 3.0 39.1 + - - +
57F MET* 2.7 32.5 + - - +
106F LEU* 3.8 21.1 - - + -
109F LEU* 4.8 3.8 - - + -
139F ILE* 3.9 20.0 - - + -
142F HIS* 4.0 17.5 - + - -
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Residues in contact with GLY 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F THR* 4.3 9.1 + - - -
50F TYR* 3.1 20.2 + - - -
51F SER 3.8 1.3 - - - -
52F GLU 3.1 1.0 - - - -
53F PHE* 1.3 76.6 - - - +
55F GLU* 1.3 63.4 + - - +
57F MET* 3.3 14.9 - - - +
58F ASP* 3.1 21.3 + - - +
28H HIS* 5.3 1.0 + - - -
50H TYR* 5.7 4.9 - - - -
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Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F SER* 3.0 19.0 + - - +
52F GLU* 2.9 11.2 + - - +
54F GLY* 1.3 77.6 - - - +
56F GLN* 1.3 65.9 + - - +
58F ASP* 3.1 6.6 + - - +
59F GLU* 2.9 38.7 + - + +
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Residues in contact with GLN 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU* 4.1 5.9 - - + +
52F GLU* 3.0 27.3 + - + +
53F PHE* 3.4 42.8 - - + +
55F GLU* 1.3 74.6 - - - +
57F MET* 1.3 53.3 - - - +
59F GLU* 3.2 3.5 + - - +
60F VAL* 2.8 40.7 + - - +
113F TYR* 2.8 26.9 + - - -
135F PHE* 3.4 60.3 + - + +
138F SER* 4.8 1.2 - - - -
139F ILE* 4.5 0.6 - - - +
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Residues in contact with MET 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F VAL* 4.2 8.5 - - - +
20F LEU* 3.5 34.1 - - + -
21F ASN* 3.4 38.1 - - - +
24F THR* 6.1 3.6 - - + -
53F PHE 2.7 17.2 + - - +
54F GLY* 3.3 10.5 - - - +
56F GLN* 1.3 78.4 - - - +
58F ASP* 1.3 64.2 + - - +
60F VAL* 3.3 2.5 + - - +
61F ALA* 3.0 19.9 + - - +
28H HIS* 3.5 35.7 - - + +
32H TRP* 3.8 18.6 - - + -
50H TYR* 4.4 6.5 - - - +
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Residues in contact with ASP 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLY 3.1 13.5 + - - +
55F GLU* 3.1 7.4 + - - +
57F MET* 1.3 80.8 - - - +
59F GLU* 1.3 53.7 + - + +
61F ALA* 3.2 1.4 + - - +
62F GLU* 2.7 49.0 + - - +
28H HIS* 3.6 14.9 - - + -
31H HIS* 3.6 5.7 - - - -
32H TRP* 2.6 34.0 + - - -
47H ASP* 4.8 1.2 - - - +
157K FE 1.8 33.1 - - - -
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Residues in contact with GLU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F GLU* 2.9 29.7 + - + +
56F GLN 3.6 7.1 + - - +
58F ASP* 1.3 74.3 - - + +
60F VAL* 1.3 64.8 + - - +
62F GLU* 3.7 5.6 - - - +
63F ARG* 2.8 25.6 + - - +
131F MET* 4.0 11.1 - - - +
135F PHE* 3.7 28.6 - - + -
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Residues in contact with VAL 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LEU* 3.6 39.1 - - + +
16F GLN* 4.3 7.0 - - + -
17F VAL* 3.7 15.9 - - + +
20F LEU* 4.1 11.4 - - + -
56F GLN 2.8 26.4 + - - +
57F MET* 3.6 5.6 - - - +
59F GLU* 1.3 71.8 - - - +
61F ALA* 1.3 66.3 + - - +
63F ARG* 3.0 3.5 + - - +
64F LEU* 2.9 21.5 + - - +
113F TYR* 4.8 1.8 - - + +
131F MET* 4.2 13.2 - - + -
132F LEU* 5.2 3.1 - - + -
135F PHE* 3.4 25.6 - - + -
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F VAL* 3.9 19.3 - - + -
57F MET 3.0 13.1 + - - +
58F ASP 3.6 0.9 - - - +
60F VAL* 1.3 79.4 - - - +
62F GLU* 1.3 65.0 + - - +
64F LEU* 3.1 7.7 + - - +
65F LEU* 3.0 24.4 + - - +
71F PRO* 4.1 10.9 - - + +
32H TRP* 3.5 39.9 - - + -
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ASP* 2.7 26.1 + - - +
59F GLU* 4.2 4.7 - - - +
61F ALA* 1.3 80.3 - - - +
63F ARG* 1.3 60.7 + - - +
65F LEU* 3.3 8.0 - - + +
66F ALA* 2.9 22.9 + - - +
31H HIS* 3.1 12.5 + - - -
32H TRP* 3.9 13.7 - - + -
43H HIS* 3.7 6.4 + - - -
141K LYS* 2.8 33.5 + - + +
144K TRP* 3.8 30.3 - - + -
157K FE 2.1 31.7 - - - -
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Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LEU* 4.2 7.0 - - + -
59F GLU 2.8 18.3 + - - +
60F VAL 3.0 4.0 + - - +
62F GLU* 1.3 75.0 - - - +
64F LEU* 1.3 64.9 + - - +
66F ALA* 2.9 12.1 + - - +
67F ILE* 2.9 45.2 + - + +
125F ASP* 2.9 26.7 + - - -
127F VAL* 3.3 31.2 - - - +
128F THR* 2.8 21.0 + - - +
131F MET* 4.0 26.7 - - + -
136K LYS* 4.4 5.9 - - - +
137K ALA 5.0 0.8 + - - -
140K ASP* 2.7 40.0 + - - +
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Residues in contact with LEU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LYS* 3.8 35.4 - - + +
13F LEU* 4.2 12.7 - - + +
14F ASN* 3.5 42.2 - - + +
17F VAL* 5.1 1.6 - - + -
60F VAL 2.9 11.9 + - - +
61F ALA* 3.3 8.7 - - - +
63F ARG* 1.3 77.5 - - - +
65F LEU* 1.3 61.7 + - - +
67F ILE* 3.0 16.4 + - + +
69F GLY* 2.8 45.2 + - - -
70F SER 3.8 3.8 - - - +
71F PRO* 3.6 21.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ALA 3.0 12.0 + - - +
62F GLU* 3.3 14.6 - - - +
64F LEU* 1.3 81.3 - - - +
66F ALA* 1.3 60.8 + - - +
68F GLY* 3.0 13.7 + - - -
69F GLY 3.7 13.0 + - - +
71F PRO* 3.5 25.4 - - + -
32H TRP* 3.5 41.3 - - + +
33H TYR* 4.6 11.2 - - + -
144K TRP* 3.8 34.5 - - + +
154K PRO* 3.4 18.1 - - + +
----------------------------------------------------------
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Residues in contact with ALA 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F GLU 2.9 13.9 + - - +
63F ARG* 2.9 26.2 + - - +
65F LEU* 1.3 78.2 - - - +
67F ILE* 1.3 60.1 + - - +
68F GLY 3.1 2.8 + - - -
140K ASP* 4.0 27.1 - - + +
141K LYS* 4.8 3.8 - - + +
144K TRP* 4.1 15.7 - - + +
154K PRO* 4.1 10.5 - - - +
155K LEU* 4.1 10.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F THR* 4.0 16.2 - - + -
10F LYS* 3.4 38.0 + - + -
13F LEU* 3.8 28.0 - - + -
63F ARG* 2.9 49.9 + - - +
64F LEU* 3.0 15.3 + - + +
66F ALA* 1.3 76.8 - - - +
68F GLY* 1.3 57.7 + - - +
125F ASP* 4.0 7.9 - - - +
155K LEU* 3.5 16.7 - - - +
----------------------------------------------------------
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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