Contacts of the helix formed by residues 36 - 64 (chain F) in PDB entry 3BVI
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 LEU 36 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005A HIS* 5.5 2.5 - - + -
30F TRP* 4.2 22.9 - - + -
31F CYS* 2.8 24.3 + - + +
32F TYR* 4.8 0.4 - - - +
34F HIS* 3.6 13.5 - - + +
35F SER* 1.3 82.1 - - - +
37F ASP* 1.3 58.9 + - - +
38F GLY 3.2 3.5 + - - -
39F ALA* 4.5 2.0 - - + -
40F GLY 2.9 21.8 + - - -
83F LEU* 4.1 31.0 - - + +
151F LEU* 4.1 34.3 - - + +
152F TYR* 5.7 0.9 - - - -
155F ASP* 3.3 30.8 - - + +
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Residues in contact with ASP 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F CYS 4.3 0.2 + - - -
32F TYR* 3.6 32.4 - - + +
35F SER 3.5 5.6 - - - +
36F LEU* 1.3 72.2 - - - +
38F GLY* 1.3 61.2 + - - +
40F GLY 3.6 0.7 - - - +
41F LEU* 2.8 30.0 + - - +
155F ASP* 3.5 5.2 + - - +
156F GLN* 4.8 0.2 + - - -
159F LYS* 2.8 31.5 + - - -
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Residues in contact with GLY 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ASP* 1.3 78.2 + - - +
39F ALA* 1.3 62.7 + - - +
41F LEU* 3.4 4.1 + - - +
42F PHE* 3.0 23.4 + - - +
155F ASP* 3.1 25.5 + - - -
158F VAL* 3.7 7.7 - - - +
159F LYS* 3.6 26.2 + - - -
162F ALA* 4.6 0.3 - - - +
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Residues in contact with ALA 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F CYS* 3.7 15.3 - - + -
36F LEU* 3.9 1.6 - - + +
38F GLY* 1.3 71.5 - - - +
40F GLY* 1.3 66.3 + - - +
42F PHE* 3.4 0.7 + - - +
43F LEU* 3.0 30.1 + - - +
83F LEU* 3.6 31.2 - - + -
87F PHE* 4.1 10.3 - - + -
155F ASP* 2.9 14.2 + - - +
158F VAL* 3.6 18.1 - - + +
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Residues in contact with GLY 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F SER* 2.6 31.7 + - - -
31F CYS* 3.5 3.0 - - - +
32F TYR* 3.3 26.0 - - - -
36F LEU 2.9 17.6 + - - -
37F ASP 3.7 1.8 - - - -
38F GLY 3.2 0.2 - - - -
39F ALA* 1.3 77.2 - - - +
41F LEU* 1.3 54.5 + - - +
44F PHE* 3.0 16.6 + - - +
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Residues in contact with LEU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TYR* 3.3 16.5 + - - +
37F ASP 2.8 20.4 + - - +
38F GLY* 3.8 4.0 - - - +
40F GLY* 1.3 68.9 - - - +
42F PHE* 1.3 67.0 + - - +
44F PHE* 3.2 7.6 + - + +
45F ASP* 2.9 45.5 + - - +
159F LYS* 5.1 9.4 - - + +
162F ALA* 4.0 16.6 - - + -
163F LYS* 4.6 17.3 - - + -
166F LYS* 3.8 24.5 - - - +
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Residues in contact with PHE 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F GLY 3.0 8.2 + - - +
39F ALA 3.4 2.2 + - - +
41F LEU* 1.3 78.5 - - - +
43F LEU* 1.3 61.2 + - + +
45F ASP* 3.4 4.3 + - - +
46F HIS* 2.9 32.6 + + + +
87F PHE* 3.9 18.2 - + - -
133F LEU* 3.8 27.8 - - + -
134F PHE* 3.7 34.5 - + - -
137F ILE* 3.3 29.2 - - + -
158F VAL* 3.4 26.2 - - + -
161F ILE* 3.9 18.2 - - + -
162F ALA* 3.7 21.5 - - + +
165F ARG* 4.7 4.9 - - - -
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 3.7 42.2 - - + +
27F MET* 3.9 24.2 - - + -
28F SER* 3.9 7.2 - - - +
31F CYS* 3.9 24.2 - - - -
39F ALA 3.0 21.0 + - - +
42F PHE* 1.3 80.7 - - + +
44F PHE* 1.3 60.4 + - - +
46F HIS* 4.2 2.7 - - - -
47F ALA* 2.9 28.4 + - - +
86F ILE* 4.0 10.3 - - + -
87F PHE* 4.2 15.9 - - + -
90F ALA* 5.1 0.9 - - + -
134F PHE* 4.1 20.4 - - + -
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Residues in contact with PHE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 3.9 38.1 - - + -
58A ILE* 3.9 12.8 - - + -
59A ILE* 3.7 34.1 - - + -
62A ASN* 4.3 7.6 - - - -
25F MET* 3.5 30.6 - - + +
28F SER* 3.5 12.0 + - - +
32F TYR* 4.7 4.7 - + + +
40F GLY 3.0 19.5 + - - +
41F LEU* 3.2 11.4 + - + +
43F LEU* 1.3 72.6 - - - +
45F ASP* 1.3 82.6 + - - +
47F ALA* 3.2 7.6 + - - +
48F ALA* 3.1 22.2 + - + +
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Residues in contact with ASP 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU* 2.9 24.9 + - - +
42F PHE* 3.7 5.2 - - + +
44F PHE* 1.3 92.8 - - - +
46F HIS* 1.3 58.2 + - - +
48F ALA* 3.3 7.4 + - - +
49F GLU* 3.1 26.3 + - - +
162F ALA* 4.3 7.0 - - + +
166F LYS* 2.9 45.7 + - - +
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Residues in contact with HIS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 3.4 33.7 - + - -
42F PHE* 2.9 23.3 + - + +
43F LEU* 3.8 7.4 - - - +
44F PHE 3.2 0.4 - - - -
45F ASP* 1.3 74.9 - - - +
47F ALA* 1.3 64.5 + - - +
49F GLU* 3.1 9.2 + - - +
50F GLU* 3.0 31.9 + - - +
94F GLU* 2.9 21.6 + - - -
130F GLU* 3.4 37.5 + - + +
133F LEU* 6.2 1.4 - - - +
134F PHE* 3.4 34.9 - + + -
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Residues in contact with ALA 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 4.1 0.2 - - - -
21F SER* 3.0 44.0 + - - +
24F TYR* 3.7 14.0 - - + +
25F MET* 3.6 22.4 - - + +
43F LEU 2.9 14.7 + - - +
44F PHE 3.4 9.2 - - - +
46F HIS* 1.3 74.3 - - - +
48F ALA* 1.3 63.8 + - - +
50F GLU* 3.2 13.2 + - - +
51F TYR 3.2 4.3 + - - -
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 3.9 11.9 + - - -
55A LYS* 3.9 30.1 - - + +
25F MET* 4.5 0.2 - - - +
44F PHE* 3.1 16.4 + - + +
45F ASP* 3.5 12.8 - - - +
46F HIS 3.2 0.2 - - - -
47F ALA* 1.3 77.9 - - - +
49F GLU* 1.3 55.2 + - - +
51F TYR* 3.3 5.9 + - - +
52F GLU* 3.1 31.8 + - + +
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F ASP 3.1 13.5 + - - +
46F HIS* 3.1 14.1 + - - +
48F ALA* 1.3 73.9 - - - +
50F GLU* 1.3 64.4 + - - +
52F GLU* 3.1 21.1 + - - +
53F HIS* 3.1 39.8 + - - +
56F LYS* 5.1 4.3 + - - -
126F GLU* 4.0 8.0 - - - +
130F GLU* 3.7 21.7 - - - +
165F ARG* 6.3 0.4 - - - +
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLU* 3.3 39.9 - - - +
20F SER* 4.1 17.4 + - - -
21F SER 4.2 3.8 - - - +
24F TYR* 4.2 7.6 - - + -
46F HIS* 3.0 35.2 + - - +
47F ALA* 3.2 7.6 + - - +
49F GLU* 1.3 75.3 - - - +
51F TYR* 1.3 62.8 + - - +
53F HIS* 3.2 15.1 + - - +
54F ALA 3.1 17.7 + - - -
94F GLU* 3.7 6.4 - - - +
97F ILE* 5.2 1.6 - - - +
130F GLU* 2.9 19.2 - - - +
1006F FE 3.1 4.7 - - - -
1007F FE 2.5 23.3 - - - -
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Residues in contact with TYR 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 3.0 23.7 + - - -
22A ASN* 5.8 0.7 - - - -
25A MET* 3.5 17.6 - - + +
47A ALA 3.7 4.7 + - - -
48A ALA* 3.8 3.0 - - - -
51A TYR* 3.3 68.0 - + + +
17F GLU 5.2 0.4 - - - -
18F MET* 3.8 35.7 - - + -
21F SER* 4.1 8.2 + - - +
47F ALA 3.2 4.9 + - - -
48F ALA 3.6 7.4 - - - +
49F GLU 3.2 0.6 - - - -
50F GLU* 1.3 74.4 - - - +
52F GLU* 1.3 69.2 + - - +
54F ALA* 3.2 5.5 + - - +
55F LYS* 3.0 56.5 + - + +
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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
----------------------------------------------------------
52A GLU* 4.8 6.2 - - - +
55A LYS* 4.8 5.7 + - - -
48F ALA* 3.1 20.8 + - + +
49F GLU* 3.1 26.4 + - - +
51F TYR* 1.3 79.7 - - - +
53F HIS* 1.3 61.6 + - + +
55F LYS* 2.9 37.6 + - - +
56F LYS* 3.1 38.4 + - - +
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Residues in contact with HIS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLU* 4.0 12.2 + - - -
49F GLU* 3.1 23.4 + - + -
50F GLU* 3.2 18.7 + - - +
52F GLU* 1.3 75.9 - - + +
54F ALA* 1.3 64.1 + - - +
56F LYS* 3.2 6.3 + - - +
57F LEU* 3.0 28.6 + - - +
122F TRP* 3.8 24.8 - + + -
123F TYR* 4.0 16.2 - + + -
126F GLU* 3.5 24.8 + - + +
127F GLN* 5.3 0.2 - - - -
130F GLU* 2.9 30.3 + - - -
1006F FE 3.1 24.4 - - - -
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Residues in contact with ALA 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F VAL* 4.1 8.4 - - + +
17F GLU* 3.9 16.5 - - + +
18F MET* 3.8 33.0 - - + +
50F GLU 3.1 8.9 + - - +
51F TYR* 3.2 9.4 + - - +
53F HIS* 1.3 79.7 - - - +
55F LYS* 1.3 55.9 + - - +
57F LEU* 3.3 11.3 + - - +
58F ILE* 2.9 34.1 + - - +
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Residues in contact with LYS 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MET* 4.0 13.9 - - + -
44A PHE* 3.8 20.7 - - + -
48A ALA* 3.8 26.9 - - + +
52A GLU* 4.8 8.5 + - - -
18F MET* 5.9 0.2 - - + -
51F TYR* 3.0 44.8 + - + +
52F GLU* 2.9 47.4 + - - +
53F HIS 3.3 0.2 - - - -
54F ALA* 1.3 76.4 - - - +
56F LYS* 1.3 56.9 + - + +
58F ILE* 3.3 8.0 + - + +
59F ILE* 2.9 36.2 + - + +
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Residues in contact with LYS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLU* 5.1 6.1 + - - -
52F GLU* 3.1 28.0 + - - +
53F HIS* 3.2 3.7 + - - +
55F LYS* 1.3 76.9 - - + +
57F LEU* 1.3 62.0 + - - +
59F ILE* 3.5 16.9 + - + +
60F PHE 3.3 15.9 + - - -
119F PHE* 3.6 13.8 - - + -
122F TRP* 3.5 41.1 - - + -
126F GLU* 4.6 16.6 + - - -
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Residues in contact with LEU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU* 4.5 13.9 - - + +
13F GLN* 3.8 31.4 - - + +
14F VAL* 3.7 26.9 - - + +
17F GLU* 4.5 4.0 - - + -
53F HIS 3.0 18.7 + - - +
54F ALA* 3.6 6.7 - - - +
56F LYS* 1.3 77.5 - - - +
58F ILE* 1.3 62.7 + - - +
60F PHE* 3.2 5.6 + - - +
61F LEU* 3.1 28.2 + - + +
119F PHE* 3.9 24.9 - - + -
120F LEU* 4.4 6.3 - - + -
122F TRP* 4.8 4.0 - - + -
123F TYR* 4.2 30.3 - - + +
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Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET* 4.2 29.8 - - + +
28A SER* 6.4 0.2 - - - -
44A PHE* 3.7 14.8 - - + -
14F VAL* 3.9 26.5 - - + -
18F MET* 3.9 18.4 - - + -
54F ALA 2.9 22.5 + - - +
55F LYS* 3.3 4.5 + - - +
57F LEU* 1.3 73.5 - - - +
59F ILE* 1.3 56.2 + - - +
61F LEU* 3.1 9.0 + - - +
62F ASN* 2.8 53.7 + - - +
68F VAL* 4.0 24.9 - - + -
70F LEU* 4.9 0.9 - - + -
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Residues in contact with ILE 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.6 28.5 - - + -
55F LYS* 2.9 27.6 + - + +
56F LYS* 3.6 17.0 - - + +
57F LEU 3.3 0.2 - - - -
58F ILE* 1.3 75.7 - - - +
60F PHE* 1.3 56.1 + - - +
62F ASN* 3.3 9.0 + - - +
63F GLU* 2.9 52.1 + - + +
119F PHE* 6.6 0.2 - - + -
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Residues in contact with PHE 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU* 3.8 20.9 - - + -
10F LEU* 4.0 18.4 - - + -
56F LYS 3.3 1.6 + - - -
57F LEU* 3.2 7.7 + - - +
58F ILE 3.2 0.8 - - - -
59F ILE* 1.3 78.6 - - - +
61F LEU* 1.3 62.1 + - - +
63F GLU* 3.4 17.1 + - - +
64F ASN* 2.7 56.0 + - - -
115F ALA* 4.5 6.7 - - + -
116F THR* 3.8 24.9 - - + -
119F PHE* 3.4 70.2 - + + -
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU* 4.6 4.3 - - + -
7F ILE* 5.0 2.2 - - - +
10F LEU* 3.9 33.4 - - + +
11F ASN* 3.7 31.6 - - - +
14F VAL* 3.9 20.0 - - + -
57F LEU* 3.1 18.6 + - + +
58F ILE* 3.1 6.5 + - - +
60F PHE* 1.3 73.8 - - + +
62F ASN* 1.3 65.2 + - - +
64F ASN* 3.1 9.8 + - - -
66F VAL* 3.0 61.0 + - + +
68F VAL* 4.1 14.1 - - + -
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Residues in contact with ASN 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET 5.5 0.2 - - - +
28A SER* 4.2 3.2 + - - -
29A SER* 3.8 12.8 + - - -
32A TYR* 3.3 62.0 - - + +
33A THR* 5.9 0.6 - - - +
44A PHE* 4.0 11.9 - - - -
58F ILE* 2.8 34.8 + - - +
59F ILE* 3.5 10.3 - - - +
61F LEU* 1.3 71.3 - - - +
63F GLU* 1.3 63.2 + - + +
65F ASN* 3.1 19.5 + - - +
66F VAL 4.6 3.5 - - - +
68F VAL* 3.8 18.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 5.7 2.7 - - + -
1F MET* 4.5 8.0 - - - +
59F ILE* 2.9 38.6 + - + +
60F PHE* 3.6 22.2 - - - +
61F LEU 3.3 0.2 - - - -
62F ASN* 1.3 76.9 - - + +
64F ASN* 1.3 62.1 + - - +
65F ASN* 3.3 5.2 + - - +
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Residues in contact with ASN 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0F PRO* 3.6 0.3 - - - +
1F MET* 2.9 56.7 + - + +
2F LEU* 3.9 20.6 - - + +
60F PHE* 2.7 57.6 + - - +
61F LEU 3.1 5.6 + - - +
63F GLU* 1.3 80.0 + - - +
65F ASN* 1.3 64.5 + - - +
66F VAL* 3.2 13.3 + - + +
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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).
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