Contacts of the helix formed by residues 36 - 64 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TRP* 4.0 26.2 - - + -
31A CYS* 2.8 26.2 + - + +
32A TYR 4.5 0.2 + - - -
34A HIS* 3.5 13.0 - - + +
35A SER* 1.3 83.2 - - - +
37A ASP* 1.3 58.9 + - - +
38A GLY 3.1 3.3 + - - -
39A ALA* 3.4 2.3 + - + -
40A GLY* 2.8 23.7 + - - -
83A LEU* 3.8 30.1 - - + +
151A LEU* 4.3 32.1 - - + +
152A TYR* 5.9 0.7 - - - -
155A ASP* 3.4 28.3 - - + +
1005F HIS* 5.3 1.6 - - + +
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.8 32.0 - - + +
35A SER 3.5 6.5 - - - +
36A LEU* 1.3 74.6 - - - +
38A GLY* 1.3 59.6 + - - +
40A GLY 3.7 0.7 - - - -
41A LEU* 2.8 29.6 + - - +
155A ASP* 3.4 5.5 - - - +
159A LYS* 3.0 31.3 + - - -
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 1.3 76.8 + - - +
39A ALA* 1.3 63.8 + - - +
41A LEU* 3.3 5.1 + - - +
42A PHE* 3.1 22.0 + - - +
155A ASP* 2.9 31.3 + - - -
158A VAL* 3.9 1.8 - - - +
159A LYS* 3.7 28.3 + - - -
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A CYS* 3.7 24.0 - - + -
36A LEU* 4.0 2.2 - - + +
38A GLY* 1.3 68.3 - - - -
40A GLY* 1.3 60.3 + - - +
42A PHE* 3.2 1.6 + - - +
43A LEU* 2.9 34.8 + - + +
83A LEU* 4.0 20.6 - - + -
87A PHE* 4.1 11.0 - - + -
155A ASP* 2.7 17.4 + - - +
158A VAL* 3.8 17.3 - - + +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 2.7 37.1 + - - -
31A CYS* 3.5 3.1 - - - +
32A TYR* 3.3 22.6 - - - -
36A LEU 2.8 17.4 + - - -
37A ASP 3.7 1.1 - - - -
39A ALA* 1.3 76.4 - - - +
41A LEU* 1.3 61.9 + - - +
43A LEU 3.5 0.2 + - - -
44A PHE* 3.0 9.5 + - - +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.3 17.1 + - - +
37A ASP 2.8 21.4 + - - +
38A GLY* 3.7 5.2 - - - +
40A GLY* 1.3 71.9 - - - +
42A PHE* 1.3 64.6 + - - +
44A PHE* 3.3 7.0 + - + +
45A ASP* 3.0 43.4 + - - +
159A LYS* 4.8 7.0 - - + +
162A ALA* 3.8 20.4 - - + -
163A LYS* 4.3 26.0 - - + +
166A LYS* 4.3 15.0 - - + +
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 3.1 5.0 + - - +
39A ALA 3.2 3.6 + - - +
41A LEU* 1.3 78.6 - - - +
43A LEU* 1.3 61.8 + - + +
45A ASP* 3.4 4.7 + - + +
46A HIS* 3.0 31.6 + + + +
87A PHE* 3.9 17.0 - + - -
133A LEU* 3.7 29.2 - - + -
134A PHE* 3.6 35.4 - + - -
137A ILE* 3.4 26.9 - - + -
158A VAL* 3.4 26.0 - - + -
161A ILE* 4.0 18.2 - - + -
162A ALA* 3.8 21.1 - - + +
165A ARG* 4.7 7.2 - - - -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.7 34.3 - - + +
27A MET* 4.0 22.0 - - + +
28A SER* 3.7 15.5 - - - -
31A CYS* 3.9 24.9 - - - -
39A ALA 2.9 20.4 + - - +
42A PHE* 1.3 83.6 - - + +
44A PHE* 1.3 59.8 + - - +
46A HIS* 3.3 2.9 + - - +
47A ALA* 2.9 29.3 + - - +
86A ILE* 4.0 10.5 - - + -
87A PHE* 4.2 13.2 - - + -
90A ALA* 5.2 0.7 - - + -
134A PHE* 4.0 22.7 - - + -
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET* 3.5 25.8 - - + +
28A SER* 3.4 17.8 + - - +
32A TYR* 4.7 4.9 - + + +
40A GLY 3.0 12.3 + - - +
41A LEU* 3.6 9.4 - - + +
43A LEU* 1.3 75.7 - - - +
45A ASP* 1.3 79.7 + - - +
47A ALA* 3.2 4.9 + - - +
48A ALA* 3.1 22.2 + - + +
55F LYS* 3.8 33.4 - - + -
58F ILE* 3.7 20.4 - - + -
59F ILE* 3.6 33.7 - - + -
62F ASN* 4.0 15.7 - - - -
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Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.0 27.4 + - - +
42A PHE* 3.7 6.1 - - + +
44A PHE* 1.3 92.5 - - - +
46A HIS* 1.3 61.5 + - - +
48A ALA* 3.5 7.0 + - - +
49A GLU* 3.2 24.3 + - - +
162A ALA* 4.4 6.8 - - + +
166A LYS* 2.9 44.8 + - - +
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Residues in contact with HIS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.3 30.5 - + - -
42A PHE* 3.0 23.0 + + + +
43A LEU* 3.6 7.6 - - - +
44A PHE 3.2 0.4 - - - -
45A ASP* 1.3 75.2 - - - +
47A ALA* 1.3 63.1 + - - +
49A GLU* 3.2 9.9 + - - +
50A GLU* 3.0 31.2 + - - +
94A GLU* 2.8 22.6 + - - -
130A GLU* 3.3 38.8 - - + +
133A LEU* 6.0 0.6 - - - +
134A PHE* 3.4 34.0 - + + -
165A ARG* 5.4 6.8 + - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 3.2 42.3 + - - +
24A TYR* 3.5 19.1 - - + +
25A MET* 3.7 20.9 - - + +
43A LEU 2.9 9.2 + - - +
44A PHE 3.2 8.3 + - - +
46A HIS* 1.3 74.8 - - - +
48A ALA* 1.3 62.4 + - - +
50A GLU* 3.2 4.7 + - - +
51A TYR 3.2 16.8 + - - -
51F TYR* 4.0 0.4 - - - -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET* 4.5 0.8 - - + +
44A PHE* 3.1 15.9 + - + +
45A ASP* 3.7 11.2 - - - +
46A HIS 3.2 0.2 - - - -
47A ALA* 1.3 76.7 - - - +
49A GLU* 1.3 57.3 + - - +
51A TYR* 3.4 5.9 + - - +
52A GLU* 3.1 30.5 + - - +
51F TYR* 3.8 11.8 + - - -
55F LYS* 3.8 32.0 + - + +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASP 3.2 14.0 + - - +
46A HIS* 3.2 16.0 + - - +
48A ALA* 1.3 74.7 - - - +
50A GLU* 1.3 69.8 + - - +
52A GLU* 3.2 21.9 + - - +
53A HIS* 3.1 47.0 + - - -
126A GLU* 4.4 5.7 - - - +
130A GLU* 4.4 9.0 - - - +
165A ARG* 6.1 3.4 - - - +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 3.5 39.4 - - - +
20A SER* 3.9 8.8 + - - -
21A SER 4.0 4.0 - - - +
24A TYR* 3.9 23.2 - - + -
46A HIS* 3.0 30.4 + - - +
47A ALA* 3.2 6.9 + - - +
49A GLU* 1.3 75.5 - - - +
51A TYR* 1.3 58.1 + - - +
53A HIS* 3.2 15.6 + - - +
54A ALA 3.0 21.7 + - - -
93A HIS* 5.3 0.3 + - - -
94A GLU* 3.4 10.2 - - - +
97A ILE* 5.4 1.2 - - - +
130A GLU* 3.0 18.7 - - - +
1006A FE 3.9 0.5 - - - -
1007A FE 2.8 20.1 - - - -
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU 5.1 0.4 - - - -
18A MET* 3.8 34.8 - - + -
21A SER* 4.1 9.0 - - - +
47A ALA 3.2 5.8 + - - +
48A ALA 3.6 7.9 - - - +
49A GLU 3.2 0.2 - - - -
50A GLU* 1.3 78.1 - - - +
52A GLU* 1.3 59.0 + - - +
54A ALA* 3.3 5.8 + - - +
55A LYS* 3.0 62.4 + - + +
21F SER* 2.8 25.8 + - - -
22F ASN* 5.7 1.1 - - - -
25F MET* 3.8 14.7 - - + +
47F ALA 3.8 5.0 + - - -
48F ALA* 3.9 4.0 - - - -
51F TYR* 3.3 67.3 - + + +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA 3.1 21.4 + - - +
49A GLU* 3.2 29.8 + - - +
51A TYR* 1.3 75.7 - - - +
53A HIS* 1.3 65.2 + - + +
55A LYS* 2.9 36.7 + - - +
56A LYS* 3.1 43.2 + - - +
52F GLU* 4.8 6.1 - - - +
55F LYS* 4.8 5.4 + - - -
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.9 12.2 + - - -
49A GLU* 3.1 23.2 + - - -
50A GLU* 3.2 22.3 + - - +
52A GLU* 1.3 74.6 - - + +
54A ALA* 1.3 68.4 + - - +
56A LYS* 3.3 4.7 + - + +
57A LEU* 3.0 28.8 + - - +
122A TRP* 4.0 16.3 - + - -
123A TYR* 3.8 19.5 - + + -
126A GLU* 3.5 29.5 + - + +
127A GLN 5.4 0.2 - - - -
130A GLU* 2.9 33.0 + - - -
1006A FE 3.2 19.4 - - - -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.3 6.4 - - + +
17A GLU* 3.8 21.0 - - + +
18A MET* 3.7 35.7 - - + -
50A GLU 3.0 8.6 + - - +
51A TYR* 3.4 10.8 - - - +
53A HIS* 1.3 76.5 - - - +
55A LYS* 1.3 57.2 + - - +
57A LEU* 3.3 10.3 + - - +
58A ILE* 3.0 33.1 + - - +
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 5.9 0.4 - - + -
51A TYR* 3.0 50.4 + - + +
52A GLU* 2.9 44.3 + - - +
53A HIS 3.3 0.4 - - - -
54A ALA* 1.3 76.4 - - + +
56A LYS* 1.3 58.0 + - + +
58A ILE* 3.3 9.5 + - + +
59A ILE* 2.9 34.4 + - + +
25F MET* 4.1 10.8 - - + -
44F PHE* 3.9 18.4 - - + -
48F ALA* 3.9 27.5 - - + +
52F GLU* 4.8 7.5 + - - -
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 3.1 33.7 + - - +
53A HIS* 3.3 1.2 + - - +
55A LYS* 1.3 72.8 - - + +
57A LEU* 1.3 63.7 + - - +
59A ILE* 3.6 15.8 + - + +
60A PHE 3.3 15.2 + - - -
119A PHE* 3.6 14.8 - - + -
122A TRP* 3.7 40.6 - - + -
126A GLU* 4.7 17.4 + - - -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.5 20.6 - - + +
13A GLN* 3.8 39.7 - - + +
14A VAL* 3.7 16.6 - - + +
17A GLU* 4.2 5.4 - - + -
53A HIS 3.0 20.3 + - - +
54A ALA* 3.5 6.5 - - - +
56A LYS* 1.3 74.3 - - - +
58A ILE* 1.3 64.5 + - - +
60A PHE* 3.2 5.2 + - + +
61A LEU* 3.0 28.1 + - + +
119A PHE* 4.1 22.7 - - + -
120A LEU* 4.5 1.3 - - + -
122A TRP* 5.2 2.9 - - + -
123A TYR* 4.2 30.7 - - + +
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.8 25.6 - - + -
18A MET* 4.0 18.4 - - + -
54A ALA 3.0 19.4 + - - +
55A LYS* 3.6 8.1 - - - +
57A LEU* 1.3 75.8 - - - +
59A ILE* 1.3 57.7 + - - +
61A LEU* 3.0 9.6 + - - +
62A ASN* 2.8 45.1 + - - +
68A VAL* 4.1 26.5 - - + -
70A LEU* 4.8 1.6 - - + -
25F MET* 4.1 31.4 - - + +
28F SER* 6.4 0.2 - - - -
44F PHE* 3.9 14.8 - - + -
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 2.9 27.6 + - + +
56A LYS* 3.7 15.9 - - + +
57A LEU 3.3 0.2 - - - -
58A ILE* 1.3 74.1 - - - +
60A PHE* 1.3 57.1 + - - +
62A ASN* 3.3 10.2 + - + +
63A GLU* 2.9 55.6 + - + +
44F PHE* 3.7 31.2 - - + -
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.9 14.6 - - + -
10A LEU* 4.1 17.5 - - + -
56A LYS 3.3 2.2 + - - -
57A LEU* 3.2 8.3 + - - +
59A ILE* 1.3 79.0 - - - +
61A LEU* 1.3 62.8 + - + +
63A GLU* 3.4 16.4 + - - +
64A ASN* 2.7 56.4 + - - -
115A ALA* 4.5 7.0 - - + -
116A THR* 3.8 30.5 - - + -
119A PHE* 3.5 70.4 - + + -
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.4 5.4 - - + -
7A ILE* 5.1 1.8 - - - +
10A LEU* 3.9 33.2 - - + -
11A ASN* 3.6 31.0 - - - +
14A VAL* 4.1 19.3 - - + -
57A LEU 3.0 18.9 + - - +
58A ILE* 3.5 7.6 - - - +
60A PHE* 1.3 74.6 - - + +
62A ASN* 1.3 65.0 + - - +
64A ASN* 3.1 8.4 + - - -
66A VAL* 2.9 59.4 + - + +
68A VAL* 4.0 15.3 - - + -
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Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 2.8 37.2 + - - +
59A ILE* 3.5 12.3 - - + +
61A LEU* 1.3 72.1 - - - +
63A GLU* 1.3 57.3 + - + +
65A ASN* 3.0 24.1 + - - +
66A VAL 4.6 3.4 - - - +
68A VAL* 3.7 17.0 - - - +
25F MET 5.9 0.2 + - - -
28F SER* 4.2 6.7 + - - -
29F SER* 3.8 13.3 + - - -
32F TYR* 3.3 60.7 - - + +
33F THR* 5.9 0.2 - - - +
44F PHE* 4.3 6.1 - - - -
----------------------------------------------------------
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.2 9.5 - - - +
59A ILE* 2.9 40.5 + - + +
60A PHE* 3.7 19.3 - - - +
61A LEU 3.2 0.2 - - - -
62A ASN* 1.3 77.3 - - + +
64A ASN* 1.3 60.7 + - - +
65A ASN* 3.4 6.4 + - - +
32F TYR* 6.0 2.0 - - + -
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.0 52.3 + - + +
2A LEU* 3.7 33.9 - - + +
60A PHE* 2.7 56.4 + - - +
61A LEU 3.1 4.9 + - - +
63A GLU* 1.3 78.1 - - - +
65A ASN* 1.3 66.7 + - - +
66A VAL* 3.1 6.3 + - + +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il