Contacts of the helix formed by residues 39 - 67 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 3.9 16.8 - + - -
145B MET* 3.4 53.6 - - + -
148B ALA* 3.8 12.8 - - + -
149B PHE* 4.1 12.1 - - + +
31J HIS 4.5 0.7 - - - -
32J TRP 5.4 0.2 - - - -
34J MET* 3.4 44.0 - - + -
36J GLY 2.8 18.6 + - - +
37J HIS 3.2 1.4 - - - -
38J ASN* 1.3 78.7 - - - +
40J PHE* 1.3 80.7 + + - +
43J HIS* 2.8 53.4 + + + +
95J MET* 3.5 10.6 - - + +
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Residues in contact with PHE 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 4.0 13.7 - - - +
42B LEU* 3.7 23.6 - - + -
45B LYS* 3.4 37.9 - - + -
145B MET* 3.8 32.8 - - + -
146B PHE* 3.5 42.0 - + - -
149B PHE* 3.9 23.6 - + + -
37J HIS 4.8 1.0 + - - -
38J ASN 3.3 0.8 - - - -
39J PHE* 1.3 90.1 - + - +
41J THR* 1.3 66.1 - - + +
43J HIS* 3.5 3.4 - + - +
44J GLU* 3.2 37.1 + - - +
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Residues in contact with THR 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASN* 6.4 0.4 - - - +
41B THR* 4.7 17.4 + - + +
37F HIS 5.7 1.3 - - - +
40F PHE* 3.9 23.0 - - - +
41F THR* 4.7 20.4 + - + -
37J HIS 5.1 1.1 - - - +
38J ASN* 3.3 34.3 - - + +
40J PHE* 1.3 78.5 - - + +
42J LEU* 1.3 60.8 + - + +
44J GLU* 3.4 7.8 + - - +
45J LYS* 2.9 27.2 + - - +
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Residues in contact with LEU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F PHE* 3.8 35.2 - - + -
34J MET* 3.5 17.7 - - + -
38J ASN* 2.9 26.4 + - + +
41J THR* 1.3 79.2 - - + +
43J HIS* 1.3 66.0 + - - +
45J LYS* 3.6 10.4 - - + +
46J MET* 2.8 31.8 + - + +
95J MET* 3.5 23.6 - - + -
99J MET* 4.0 15.5 - - - -
146J PHE* 4.6 4.5 - - + -
149J PHE* 3.5 30.7 - - + -
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Residues in contact with HIS 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS* 5.3 2.0 + - - -
144B TRP* 3.6 28.7 - + - -
145B MET* 4.6 9.8 - - - -
157H FE 4.2 1.6 - - - -
31J HIS* 2.9 81.3 + + - -
34J MET* 3.3 11.4 - - - -
39J PHE* 2.8 41.7 + + + +
40J PHE* 3.5 4.3 - + - +
42J LEU* 1.3 79.4 - - - +
44J GLU* 1.3 67.5 + - + +
47J ASP* 3.4 8.9 + - - +
62L GLU* 3.7 7.5 + - - -
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Residues in contact with GLU 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LYS* 5.4 7.1 - - - +
40J PHE* 3.2 31.9 + - - +
41J THR* 4.0 5.7 - - - +
43J HIS* 1.3 83.9 - - + +
45J LYS* 1.3 66.0 + - - +
47J ASP* 2.9 19.9 + - + +
48J ASP* 3.1 18.9 + - - +
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Residues in contact with LYS 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F PHE* 3.6 36.0 - - + -
44F GLU* 5.5 7.2 - - - +
41J THR* 2.9 19.2 + - - +
42J LEU* 3.2 12.1 + - + +
44J GLU* 1.3 77.1 - - - +
46J MET* 1.3 68.0 + - + +
48J ASP* 3.0 22.3 + - - +
49J LEU* 2.9 24.9 + - + +
142J HIS* 4.3 9.1 + - - -
145J MET* 4.0 19.8 - - - +
146J PHE* 3.8 28.9 - - + -
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Residues in contact with MET 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J ILE* 3.3 15.5 - - + +
30J ILE* 4.1 21.1 - - + -
31J HIS* 3.7 24.5 - - + +
34J MET* 3.8 17.0 - - + -
42J LEU* 2.8 22.9 + - + +
43J HIS 3.9 1.8 - - - +
44J GLU 3.2 0.2 - - - -
45J LYS* 1.3 84.1 - - + +
47J ASP* 1.3 58.6 + - - +
49J LEU* 3.7 17.7 - - + -
50J TYR* 2.8 31.5 + - - +
99J MET* 4.4 6.5 - - + -
102J LEU* 3.9 12.3 - - + -
146J PHE* 3.5 38.4 - - + -
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Residues in contact with ASP 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H FE 3.8 7.2 - - - -
28J HIS* 4.8 9.0 - - - -
31J HIS* 3.3 38.3 + - - -
43J HIS* 3.4 7.1 + - - +
44J GLU* 2.9 14.0 + - - +
46J MET* 1.3 75.7 - - - +
48J ASP* 1.3 68.6 + - - +
50J TYR* 3.3 6.1 + - - +
51J SER* 3.2 26.4 + - - -
58L ASP* 4.6 1.4 - - - +
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Residues in contact with ASP 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J GLU* 3.5 14.7 - - - +
45J LYS* 3.0 26.7 + - - +
47J ASP* 1.3 84.2 - - - +
49J LEU* 1.3 57.4 + - + +
51J SER* 3.4 5.5 + - - -
52J GLU* 3.0 29.0 + - - +
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Residues in contact with LEU 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J PHE* 5.2 0.4 - - + -
27J ILE* 3.9 14.1 - - + -
45J LYS* 2.9 19.4 + - - +
46J MET* 3.7 34.3 - - + +
48J ASP* 1.3 74.5 - - + +
50J TYR* 1.3 68.9 + - - +
52J GLU* 4.4 2.7 - - - +
53J PHE* 2.8 48.0 + - + +
102J LEU* 3.8 27.8 - - + -
106J LEU* 5.4 2.7 - - + -
142J HIS* 3.6 35.4 - - + +
146J PHE* 4.0 12.6 - - + -
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Residues in contact with TYR 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J THR* 3.5 47.7 + - + +
25J VAL* 5.2 0.2 - - - -
27J ILE* 3.8 13.0 - - + +
28J HIS* 3.1 53.0 + + + +
46J MET 2.8 17.3 + - - +
47J ASP* 3.5 10.3 - - - +
48J ASP 3.3 0.2 - - - -
49J LEU* 1.3 79.1 - - - +
51J SER* 1.3 69.7 + - - +
54J GLY* 3.0 22.3 + - - -
21L ASN* 5.5 1.0 + - - -
24L THR* 5.8 3.3 - - - +
50L TYR* 4.6 16.6 + + - -
54L GLY* 5.8 5.4 - - - -
57L MET* 4.4 6.9 - - - +
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Residues in contact with SER 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J ASP 3.2 14.6 + - - -
48J ASP* 3.8 5.2 - - - -
50J TYR* 1.3 83.3 - - - +
52J GLU* 1.3 66.1 + - - +
54J GLY* 3.3 1.6 + - - -
55J GLU* 2.9 30.7 + - - +
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Residues in contact with GLU 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J ASP 3.0 17.1 + - - +
49J LEU* 3.7 6.2 - - - +
51J SER* 1.3 77.6 - - - +
53J PHE* 1.3 72.9 + - + +
55J GLU* 3.0 12.0 + - - +
56J GLN* 2.9 34.6 + - + +
138J SER* 2.6 30.7 + - - -
142J HIS* 2.8 27.4 + - - -
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Residues in contact with PHE 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 4.1 14.8 - - + +
23J PHE* 3.7 37.5 - + + -
24J THR* 4.8 8.3 - - - +
27J ILE* 4.3 4.3 - - + -
49J LEU* 2.8 45.9 + - + +
50J TYR 4.6 0.7 - - - +
52J GLU* 1.3 87.9 - - + +
54J GLY* 1.3 60.8 + - - +
56J GLN* 3.0 37.8 + - - +
57J MET* 2.8 30.4 + - - +
106J LEU* 3.9 20.4 - - + -
109J LEU* 4.7 3.1 - - + -
139J ILE* 4.0 20.4 - - + -
142J HIS* 4.1 12.8 - + - -
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Residues in contact with GLY 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J THR* 4.3 9.7 + - - -
50J TYR* 3.0 20.7 + - - -
51J SER* 3.7 1.8 - - - -
53J PHE* 1.3 77.2 - - - +
55J GLU* 1.3 61.1 + - - +
57J MET* 3.4 14.7 - - - +
58J ASP* 3.2 21.3 + - - +
28L HIS* 5.3 1.4 + - - -
50L TYR* 5.8 4.3 - - - -
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Residues in contact with GLU 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J SER* 2.9 21.0 + - - +
52J GLU* 3.6 9.7 - - - +
54J GLY* 1.3 76.4 - - - +
56J GLN* 1.3 67.0 + - - +
58J ASP* 3.2 6.0 + - - +
59J GLU* 2.9 39.8 + - + +
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Residues in contact with GLN 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 4.1 6.6 - - + +
52J GLU* 2.9 28.2 + - + +
53J PHE* 3.0 42.8 + - - +
55J GLU* 1.3 74.8 - - - +
57J MET* 1.3 59.0 + - - +
59J GLU* 3.1 2.9 + - - +
60J VAL* 2.8 35.4 + - - +
113J TYR* 3.0 26.0 + - - -
135J PHE* 3.5 60.1 + - + +
138J SER* 4.9 1.0 - - - -
139J ILE* 4.5 1.0 - - - +
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Residues in contact with MET 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J VAL* 4.2 8.9 - - - +
20J LEU* 3.6 31.2 - - + +
21J ASN* 3.4 41.3 - - - +
24J THR* 5.9 4.7 - - + -
53J PHE 2.8 17.1 + - - +
54J GLY* 3.4 12.3 - - - +
56J GLN* 1.3 79.0 - - - +
58J ASP* 1.3 64.0 + - - +
60J VAL* 3.1 2.1 + - - +
61J ALA* 3.0 20.3 + - - +
28L HIS* 3.5 33.7 - - + +
32L TRP* 3.8 19.3 - - + -
50L TYR* 4.3 6.7 - - - +
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Residues in contact with ASP 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157G FE 1.7 32.7 - - - -
54J GLY 3.2 13.6 + - - +
55J GLU* 3.2 5.8 + - - +
57J MET* 1.3 84.5 - - - +
59J GLU* 1.3 59.5 + - + +
61J ALA* 3.4 3.6 + - - +
62J GLU* 2.8 42.2 + - - +
28L HIS* 3.6 17.5 - - + -
31L HIS* 3.6 6.0 - - - -
32L TRP* 2.7 29.2 + - - -
47L ASP* 4.5 2.1 - - - +
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Residues in contact with GLU 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J GLU* 2.9 33.3 + - + +
56J GLN 3.6 3.4 - - - +
58J ASP* 1.3 76.6 - - + +
60J VAL* 1.3 65.9 + - - +
62J GLU* 3.9 5.4 - - - +
63J ARG* 3.0 24.3 + - - +
131J MET* 4.0 12.6 - - - +
135J PHE* 3.8 27.7 - - + -
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Residues in contact with VAL 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LEU* 3.4 42.2 - - + +
16J GLN* 4.3 9.6 - - + -
17J VAL* 3.8 9.9 - - + +
20J LEU* 4.1 15.5 - - + -
56J GLN 2.8 22.2 + - - +
57J MET 3.6 4.5 - - - +
59J GLU* 1.3 73.7 - - - +
61J ALA* 1.3 64.5 + - - +
63J ARG* 3.1 3.3 + - - +
64J LEU* 2.9 22.3 + - - +
113J TYR* 4.9 2.0 - - + +
131J MET* 4.2 12.1 - - + -
132J LEU* 5.2 3.8 - - + -
135J PHE* 3.5 24.7 - - + -
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Residues in contact with ALA 61 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J VAL* 3.9 20.2 - - + -
57J MET 3.0 12.2 + - - +
58J ASP 3.7 1.3 - - - +
60J VAL* 1.3 79.0 - - - +
62J GLU* 1.3 57.5 + - - +
64J LEU* 3.3 7.2 + - - +
65J LEU* 3.0 29.2 + - - +
71J PRO* 4.2 8.8 - - + +
32L TRP* 3.5 41.7 - - + -
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Residues in contact with GLU 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LYS* 3.0 29.9 + - + +
144C TRP* 3.8 31.1 - - + -
157G FE 2.0 32.6 - - - -
58J ASP* 2.8 26.1 + - - +
59J GLU* 4.3 4.9 - - - +
61J ALA* 1.3 74.7 - - - +
63J ARG* 1.3 60.9 + - - +
65J LEU* 3.3 8.4 - - + +
66J ALA* 2.9 28.1 + - - +
31L HIS* 2.9 13.2 + - - -
32L TRP* 4.0 13.0 - - + -
43L HIS* 3.7 6.3 + - - -
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Residues in contact with ARG 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LYS* 4.6 4.8 - - - +
137C ALA 4.9 1.2 + - - -
140C ASP* 2.8 40.6 + - - +
13J LEU* 4.2 7.4 - - + -
59J GLU 3.0 18.8 + - - +
60J VAL 3.5 4.3 - - - +
62J GLU* 1.3 74.6 - - - +
64J LEU* 1.3 65.3 + - - +
66J ALA* 3.2 9.1 + - - +
67J ILE* 3.0 39.3 + - + +
125J ASP* 2.8 30.7 + - - -
127J VAL* 3.2 31.7 - - - +
128J THR* 2.9 20.1 + - - +
131J MET* 3.9 27.4 - - + -
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Residues in contact with LEU 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J LYS* 3.7 37.9 - - + +
13J LEU* 4.2 11.4 - - + +
14J ASN* 3.7 28.0 - - + +
17J VAL* 4.9 2.2 - - + -
60J VAL 2.9 12.3 + - - +
61J ALA 3.3 8.7 - - - +
63J ARG* 1.3 75.7 - - - +
65J LEU* 1.3 60.9 + - - +
67J ILE* 3.0 15.7 + - + +
69J GLY* 2.7 47.1 + - - -
70J SER 3.9 4.3 - - - +
71J PRO* 3.6 33.7 - - + -
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Residues in contact with LEU 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TRP* 3.7 34.1 - - + +
154C PRO* 3.3 16.8 - - + +
61J ALA 3.0 12.4 + - - +
62J GLU* 3.3 14.1 - - - +
64J LEU* 1.3 78.2 - - - +
66J ALA* 1.3 58.3 + - - +
68J GLY* 2.9 18.9 + - - -
69J GLY 3.7 12.5 - - - +
70J SER* 4.6 0.7 - - - -
71J PRO* 3.3 26.7 - - + -
32L TRP* 3.7 41.3 - - + +
33L TYR* 4.7 9.2 - - + -
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Residues in contact with ALA 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ASP* 4.0 30.2 - - + +
141C LYS* 4.7 4.5 - - - -
143C ILE* 6.2 0.2 - - - +
144C TRP* 4.0 16.6 - - + -
154C PRO* 4.0 11.5 - - - +
155C LEU* 4.1 10.0 - - - +
62J GLU 2.9 18.8 + - - +
63J ARG* 3.5 20.0 - - - +
64J LEU 3.1 0.6 - - - -
65J LEU* 1.3 78.6 - - - +
67J ILE* 1.3 58.6 + - - +
68J GLY 3.1 1.1 + - - -
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Residues in contact with ILE 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ASP* 6.2 0.2 - - - -
155C LEU* 3.3 19.9 - - - +
9J THR* 3.8 29.6 - - + -
10J LYS* 3.5 36.4 + - + -
13J LEU* 3.9 16.4 - - + -
63J ARG* 3.0 45.8 + - - +
64J LEU* 3.0 17.9 + - + +
66J ALA* 1.3 76.2 - - - +
68J GLY* 1.3 58.1 + - - +
69J GLY 4.3 0.2 - - - +
125J ASP* 4.0 7.2 - - - +
128J THR* 4.9 0.4 - - - +
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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