Contacts of the helix formed by residues 9 - 33 (chain H) 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 THR 9 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ASP* 1.3 70.8 - - - +
10H LYS* 1.3 59.8 + - - +
12H PHE* 3.0 3.5 + - + +
13H LEU* 2.7 42.7 + - + +
67H ILE* 3.8 16.2 - - + -
119H LEU* 3.2 21.7 - - + +
120H THR* 4.1 8.7 + - - +
123H GLU* 2.9 28.3 + - - +
125H ASP* 3.8 23.7 - - - +
128H THR* 3.9 13.2 - - + -
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Residues in contact with LYS 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ASP* 3.2 14.6 + - - +
9H THR* 1.3 76.8 - - - +
11H GLU* 1.3 68.9 + - - +
14H ASN* 2.9 30.7 + - - +
64H LEU* 3.7 18.5 - - + +
67H ILE* 3.5 38.4 + - + -
68H GLY* 3.8 14.7 + - - -
69H GLY* 4.1 16.6 - - - -
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Residues in contact with GLU 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 3.9 18.2 - - + +
8H ASP* 2.6 38.9 + - + +
10H LYS* 1.3 82.6 - - - +
12H PHE* 1.3 63.5 + - - +
14H ASN* 4.0 5.0 + - - +
15H HIS* 3.0 23.6 + - - +
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Residues in contact with PHE 12 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 4.0 19.0 - - + +
8H ASP 2.7 16.2 + - - +
9H THR* 3.4 9.4 - - + +
11H GLU* 1.3 74.5 - - - +
13H LEU* 1.3 80.7 + - + +
15H HIS* 3.1 16.5 + - + +
16H GLN* 3.1 48.0 + - + +
112H GLU* 3.1 30.3 - - + -
113H TYR* 3.9 11.0 - + - -
115H GLN* 4.7 4.0 - - + -
116H GLY* 3.5 26.0 - - - -
119H LEU* 4.3 13.5 - - + -
128H THR* 5.9 0.2 - - + -
132H LEU* 4.0 20.6 - - + -
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Residues in contact with LEU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H THR* 2.7 28.2 + - + +
10H LYS 3.7 3.4 - - - +
12H PHE* 1.3 95.8 - - + +
14H ASN* 1.3 58.3 + - - +
16H GLN* 2.9 21.5 + - + +
17H VAL* 2.9 11.0 + - - +
60H VAL* 3.5 25.2 - - + +
63H ARG* 4.2 6.1 - - + -
64H LEU* 4.1 23.8 - - + +
67H ILE* 3.9 17.7 - - + -
128H THR* 3.7 32.8 - - + -
131H MET* 4.4 10.8 - - + -
132H LEU* 4.4 3.8 - - + -
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Residues in contact with ASN 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LYS 2.9 16.7 + - - +
11H GLU* 4.1 5.6 + - - +
13H LEU* 1.3 76.2 - - - +
15H HIS* 1.3 62.1 + - - +
17H VAL* 3.2 6.1 + - - +
18H ALA 3.2 16.8 + - - -
64H LEU* 3.6 14.0 - - + +
70H SER 3.1 20.6 + - - -
71H PRO* 3.1 6.9 - - - +
72H PHE* 2.7 73.8 + - + +
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Residues in contact with HIS 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 6.1 2.0 - - + -
11H GLU 3.0 14.6 + - - +
12H PHE* 3.1 13.9 + - + +
14H ASN* 1.3 77.3 - - - +
16H GLN* 1.3 61.9 + - - +
18H ALA* 3.3 5.4 + - - +
19H ASN* 3.0 27.8 + - - -
72H PHE* 4.3 6.0 - - - -
81H ASN* 2.9 32.2 + - + -
83H SER* 2.8 40.0 + - - -
112H GLU* 3.1 20.5 + - - -
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Residues in contact with GLN 16 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H PHE* 3.4 49.4 - - + +
13H LEU* 2.9 7.6 + - + +
15H HIS* 1.3 83.1 + - - +
17H VAL* 1.3 66.3 + - - +
19H ASN* 3.0 20.4 + - - +
20H LEU* 2.7 40.0 + - + +
60H VAL* 4.3 11.9 - - + -
109H LEU* 3.7 4.7 - - - +
112H GLU* 2.9 29.1 + - - +
113H TYR* 3.6 24.5 - - + +
132H LEU* 5.9 0.7 - - + -
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Residues in contact with VAL 17 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TRP* 4.4 11.9 - - + -
13H LEU 2.9 18.6 + - - +
14H ASN* 3.2 19.9 + - - +
16H GLN* 1.3 77.0 - - - +
18H ALA* 1.3 65.1 + - - +
20H LEU* 3.4 4.1 + - - +
21H ASN* 2.9 33.9 + - - +
57H MET* 4.5 6.1 - - - +
60H VAL* 3.8 16.8 - - + +
61H ALA* 3.9 21.5 - - + +
64H LEU* 4.9 2.5 - - + -
71H PRO* 4.6 3.8 - - + -
72H PHE* 3.9 12.6 - - + +
78H PHE* 3.7 22.7 - - + -
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Residues in contact with ALA 18 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ASN 3.2 7.2 + - - +
15H HIS 3.4 8.7 - - - +
17H VAL* 1.3 78.5 - - - +
19H ASN* 1.3 63.6 + - - +
21H ASN* 3.1 13.3 + - - +
22H VAL* 3.2 15.4 + - - +
72H PHE* 4.2 3.6 - - + -
78H PHE* 3.6 38.8 - - - +
81H ASN* 3.9 14.4 - - + -
82H ALA* 3.7 14.4 - - - +
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Residues in contact with ASN 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H HIS* 3.0 16.8 + - - +
16H GLN* 3.0 29.2 + - - +
18H ALA* 1.3 75.7 - - - +
20H LEU* 1.3 58.0 + - - +
22H VAL* 3.2 3.8 + - - +
23H PHE* 2.8 30.8 + - - +
82H ALA* 3.4 4.6 - - - -
83H SER* 2.7 46.9 + - - -
84H VAL* 3.0 24.5 + - + +
108H LEU* 4.1 3.6 - - - +
109H LEU* 4.1 6.2 - - + +
112H GLU* 3.1 13.5 + - - -
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLN* 2.7 30.4 + - + +
19H ASN* 1.3 73.1 - - - +
21H ASN* 1.3 57.5 + - - +
23H PHE* 3.6 4.8 - - + +
24H THR* 2.8 33.0 + - - -
53H PHE* 4.2 25.7 - - + +
56H GLN* 4.1 7.6 - - + +
57H MET* 3.5 44.2 - - + +
60H VAL* 4.1 10.8 - - + -
109H LEU* 4.2 26.5 - - + -
113H TYR* 3.5 26.5 - - - +
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Residues in contact with ASN 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F VAL* 4.5 7.8 - - - +
28F HIS* 5.4 1.6 - - - -
50F TYR* 5.4 1.4 + - - -
75F LEU* 4.3 4.1 - - + +
17H VAL* 2.9 25.5 + - - +
18H ALA 3.5 6.1 - - - +
20H LEU* 1.3 77.4 - - - +
22H VAL* 1.3 62.2 + - - +
24H THR* 3.2 25.1 - - - +
25H VAL* 3.4 12.5 + - - +
57H MET* 3.3 35.6 - - - +
78H PHE* 3.2 52.7 - - + -
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Residues in contact with VAL 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F LEU* 4.2 24.0 - - + -
18H ALA 3.2 4.9 + - - +
19H ASN 3.2 6.8 + - - +
21H ASN* 1.3 73.0 - - - +
23H PHE* 1.3 66.0 + - - +
25H VAL* 3.2 4.9 + - - +
26H LYS* 2.9 21.6 + - - +
78H PHE* 4.6 3.8 - - + +
79H LEU* 5.0 6.7 - - + -
82H ALA* 3.5 28.0 - - + -
84H VAL* 3.5 32.1 - - + +
85H GLU 4.6 0.2 - - - +
86H GLU* 4.0 30.3 - - + +
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Residues in contact with PHE 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ASN 2.8 17.9 + - - +
20H LEU* 3.6 8.1 - - + +
22H VAL* 1.3 76.3 - - - +
24H THR* 1.3 65.0 + - - +
26H LYS* 2.9 14.5 + - + +
27H ILE* 2.9 37.8 + - + +
49H LEU* 5.3 0.9 - - + -
53H PHE* 3.8 43.7 - + + -
84H VAL* 4.3 4.5 - - + +
102H LEU* 3.5 34.1 - - + -
105H THR* 3.4 31.0 - - + -
106H LEU* 3.7 18.2 - - + -
109H LEU* 3.6 18.4 - - + -
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Residues in contact with THR 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F TYR* 5.8 3.4 - - - +
20H LEU 2.8 15.0 + - - +
21H ASN* 3.2 23.6 - - - +
23H PHE* 1.3 78.9 - - - +
25H VAL* 1.3 72.8 + - + +
27H ILE* 3.2 19.4 + - - +
28H HIS 3.2 9.0 + - - -
50H TYR* 3.5 49.1 + - + +
53H PHE* 4.7 4.6 - - - +
54H GLY* 4.3 12.4 + - - -
57H MET* 6.1 3.8 - - + -
----------------------------------------------------------
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Residues in contact with VAL 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ASN* 4.5 8.3 - - - +
73F SER* 3.7 22.6 - - - +
74F THR* 3.9 7.4 - - - -
75F LEU* 3.8 17.0 - - + -
78F PHE* 3.6 33.4 - - + -
21H ASN 3.4 12.6 - - - +
22H VAL 3.2 7.5 + - - +
24H THR* 1.3 79.5 - - + +
26H LYS* 1.3 67.6 + - - +
28H HIS* 3.1 14.2 + - + +
29H GLN* 2.9 20.3 + - - +
50H TYR* 6.1 0.2 - - - +
86H GLU* 4.8 1.3 - - - +
----------------------------------------------------------
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Residues in contact with LYS 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F SER 5.4 0.9 - - - -
22H VAL* 2.9 12.7 + - + +
23H PHE* 3.3 19.5 - - + +
25H VAL* 1.3 79.7 - - - +
27H ILE* 1.3 61.8 + - - +
29H GLN* 3.1 17.7 + - - +
30H ILE* 3.0 33.4 + - + +
84H VAL* 4.3 11.0 - - - -
85H GLU 2.9 29.4 + - - -
86H GLU* 4.1 11.6 - - + +
87H ALA 4.9 2.4 - - - +
101H ASP* 3.1 38.8 + - - +
102H LEU* 5.2 0.2 - - - -
105H THR* 3.6 24.7 - - - +
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Residues in contact with ILE 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H PHE* 2.9 54.1 + - + +
24H THR* 3.4 14.6 - - - +
25H VAL 3.1 0.2 - - - -
26H LYS* 1.3 76.5 - - - +
28H HIS* 1.3 62.3 + - - +
30H ILE* 3.3 11.3 + - + +
31H HIS* 3.0 22.8 + - + +
46H MET* 3.2 40.0 - - + +
49H LEU* 3.9 31.6 - - + +
50H TYR* 3.9 11.0 - - + +
53H PHE* 4.5 3.1 - - + -
102H LEU* 4.9 6.7 - - + -
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Residues in contact with HIS 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ASN* 5.4 1.3 - - - -
54F GLY 5.3 1.2 + - - -
57F MET* 3.5 30.8 - - + +
58F ASP* 3.6 27.6 + - + +
24H THR 3.2 3.7 + - - +
25H VAL* 3.1 14.9 + - + +
27H ILE* 1.3 75.9 - - - +
29H GLN* 1.3 66.8 + - - +
31H HIS* 3.1 14.6 + + - +
32H TRP* 2.8 48.2 + + + -
47H ASP* 4.9 5.4 + - - -
50H TYR* 3.0 54.3 + + + +
----------------------------------------------------------
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Residues in contact with GLN 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F SER* 3.0 47.6 + - - +
74F THR* 4.1 1.0 - - - +
25H VAL 2.9 12.8 + - - +
26H LYS* 3.3 19.6 - - - +
28H HIS* 1.3 77.6 - - - +
30H ILE* 1.3 67.9 + - - +
32H TRP* 4.3 3.1 - - - -
33H TYR* 3.0 35.0 + - + +
87H ALA 3.2 27.0 + - - +
89H TYR* 4.0 21.7 + - + +
93H LYS* 4.6 13.1 - - - +
98H LEU* 5.4 3.1 - - + +
101H ASP* 4.7 8.9 + - - -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H LYS* 3.0 25.9 + - + +
27H ILE* 3.6 9.0 - - - +
29H GLN* 1.3 81.4 - - + +
31H HIS* 1.3 58.5 - - - +
33H TYR* 5.2 0.2 - - - -
34H MET* 3.0 49.9 + - + +
46H MET* 4.1 7.2 - - + -
98H LEU* 3.9 46.9 - - + +
99H MET* 3.5 24.5 - - + -
101H ASP* 5.3 4.0 - - - +
102H LEU* 4.0 28.0 - - + +
----------------------------------------------------------
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Residues in contact with HIS 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ASP* 3.6 6.3 - - - -
62F GLU* 3.1 2.4 + - - -
27H ILE* 3.0 18.7 + - + +
28H HIS* 3.2 16.2 - - - +
30H ILE* 1.3 79.2 - - - +
32H TRP* 1.3 82.0 - + - +
34H MET* 3.8 11.1 - - - +
43H HIS* 2.9 80.9 + + - -
46H MET* 3.8 16.9 - - + +
47H ASP* 3.4 20.6 + - - -
144K TRP* 4.6 1.0 - - - -
157K FE 2.4 28.4 - - - -
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Residues in contact with TRP 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F VAL* 4.5 4.3 - - + -
21F ASN* 5.0 2.2 - - - -
57F MET* 3.8 27.8 - - + -
58F ASP* 2.6 28.5 + - - -
61F ALA* 3.5 26.9 - - + +
62F GLU* 3.9 17.6 + - + +
65F LEU* 3.5 31.7 - - + +
71F PRO* 3.9 16.8 - - + -
72F PHE 3.6 20.2 - - - -
73F SER* 4.1 16.4 - - - -
78F PHE* 5.0 3.1 - + - -
25H VAL* 6.1 0.2 - - + -
28H HIS* 2.8 43.2 + + + +
29H GLN* 3.8 2.5 - - - +
31H HIS* 1.3 93.2 - + - +
33H TYR* 1.3 67.4 + - + +
34H MET* 3.5 2.5 + - - +
144K TRP* 3.9 12.6 + + - -
----------------------------------------------------------
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Residues in contact with TYR 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 4.6 6.1 - - + -
70F SER* 3.2 24.3 + - - -
71F PRO* 2.4 52.6 + - + -
73F SER* 3.6 24.2 + - - -
29H GLN* 3.0 28.0 + - + +
30H ILE* 5.1 0.9 - - - -
32H TRP* 1.3 80.7 - - + +
34H MET* 1.3 68.9 + - - +
35H ARG* 3.5 12.2 + - - +
89H TYR* 3.4 70.0 + + + +
93H LYS 5.4 0.9 - - - +
98H LEU* 4.7 2.6 - - + +
----------------------------------------------------------
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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