Contacts of the helix formed by residues 36 - 64 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TRP* 4.0 26.0 - - + -
31B CYS* 2.8 32.3 + - + +
32B TYR* 4.7 0.2 - - - +
34B HIS* 3.7 9.9 - - + +
35B SER* 1.3 75.8 - - - +
37B ASP* 1.3 58.6 + - - +
38B GLY 3.3 0.3 + - - -
39B ALA* 4.5 1.8 - - + -
40B GLY* 2.8 23.4 + - - -
83B LEU* 3.6 31.2 - - + +
151B LEU* 4.3 18.6 - - + +
155B ASP* 3.2 33.2 - - + +
143D LEU* 4.1 21.8 - - + -
1005E HIS* 5.4 1.1 - - - +
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.8 32.1 - - + +
35B SER 3.5 2.4 - - - +
36B LEU* 1.3 72.6 - - - +
38B GLY* 1.3 61.7 + - - +
40B GLY 3.6 0.4 - - - -
41B LEU* 2.8 30.7 + - - +
155B ASP* 3.5 0.2 + - - -
159B LYS* 2.9 22.8 + - - -
136D ASP* 5.8 6.0 - - - +
140D LYS* 2.5 40.1 + - - +
157D TYR* 4.3 4.7 + - - -
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 1.3 81.0 - - - +
39B ALA* 1.3 55.8 + - - +
41B LEU* 3.4 3.5 + - - +
42B PHE* 3.1 26.7 + - - +
155B ASP* 3.0 29.4 + - - -
158B VAL* 3.9 1.7 - - - +
159B LYS* 3.6 31.1 + - - +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B CYS* 3.9 14.4 - - - -
36B LEU* 3.9 2.0 - - + +
38B GLY* 1.3 71.6 - - - +
40B GLY* 1.3 65.5 + - - +
42B PHE* 3.4 0.7 + - - +
43B LEU* 3.0 30.4 + - - +
83B LEU* 3.8 28.3 - - + -
87B PHE* 4.2 9.6 - - + -
155B ASP* 3.0 17.4 + - - +
158B VAL* 3.7 18.0 - - + +
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 2.6 32.4 + - - -
31B CYS* 3.6 2.8 - - - +
32B TYR* 3.3 27.7 - - - -
36B LEU 2.8 17.6 + - - -
37B ASP 3.4 1.5 + - - -
38B GLY 3.3 0.2 - - - -
39B ALA* 1.3 77.0 - - - +
41B LEU* 1.3 56.4 + - - +
44B PHE* 3.0 15.6 + - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.3 15.8 + - - +
37B ASP 2.8 17.9 + - - +
38B GLY 3.7 3.6 - - - +
40B GLY* 1.3 73.8 - - - +
42B PHE* 1.3 65.7 + - - +
44B PHE* 3.4 6.9 + - + +
45B ASP* 3.1 40.8 + - - +
159B LYS* 4.8 10.3 - - + +
162B ALA* 3.9 20.0 - - + -
163B LYS* 4.4 17.7 - - + -
166B LYS* 3.9 23.3 - - - +
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Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.1 7.8 + - - +
39B ALA 3.7 2.2 - - - +
41B LEU* 1.3 79.2 - - - +
43B LEU* 1.3 68.5 + - + +
45B ASP* 3.7 4.1 - - - +
46B HIS* 3.0 29.6 + - + +
87B PHE* 4.0 9.6 - + - -
133B LEU* 3.7 27.8 - - + -
134B PHE* 3.5 35.7 - + - -
137B ILE* 3.3 29.2 - - + -
158B VAL* 3.4 28.0 - - + -
161B ILE* 3.8 18.2 - - + -
162B ALA* 3.8 20.1 - - + +
165B ARG* 4.6 4.3 - - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.8 33.3 - - + +
27B MET* 3.9 25.4 - - + -
28B SER* 3.8 14.6 - - - -
31B CYS* 3.9 21.8 - - - -
39B ALA 3.0 20.7 + - - +
42B PHE* 1.3 89.0 - - + +
44B PHE* 1.3 62.1 + - - +
46B HIS* 3.7 3.7 - - - +
47B ALA* 2.9 28.8 + - - +
86B ILE* 4.0 10.8 - - + -
87B PHE* 4.0 17.0 - - + -
90B ALA* 5.3 0.4 - - + -
134B PHE* 4.0 12.6 - - + -
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 3.6 27.9 - - + +
28B SER* 3.5 11.4 + - - +
32B TYR* 4.7 4.9 - + + +
40B GLY 3.0 19.1 + - - +
41B LEU* 3.8 9.2 - - + +
43B LEU* 1.3 75.9 - - - +
45B ASP* 1.3 72.7 + - - +
47B ALA* 3.1 9.1 + - - +
48B ALA* 2.9 28.5 + - + +
55E LYS* 3.9 34.3 - - + -
58E ILE* 3.8 23.3 - - + -
59E ILE* 3.6 32.5 - - + -
62E ASN* 4.2 8.1 - - - -
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.1 24.0 + - - +
42B PHE* 3.7 4.9 - - - +
44B PHE* 1.3 90.8 - - - +
46B HIS* 1.3 61.3 + - - +
48B ALA* 3.4 6.8 + - - +
49B GLU* 3.0 27.4 + - - +
162B ALA* 4.5 7.3 - - + +
166B LYS* 3.2 42.6 + - - +
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.3 37.3 - + - -
42B PHE* 3.0 23.2 + - + +
43B LEU* 3.7 8.3 - - - +
44B PHE 3.3 0.2 - - - -
45B ASP* 1.3 72.3 - - - +
47B ALA* 1.3 65.9 + - - +
49B GLU* 3.1 8.5 + - - +
50B GLU* 2.9 36.7 + - + +
94B GLU* 2.9 22.7 + - - -
130B GLU* 3.3 38.9 + - + +
133B LEU* 6.1 1.4 - - - +
134B PHE* 3.6 28.8 - + + -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 2.8 42.7 + - - +
24B TYR* 3.6 14.0 - - + +
25B MET* 3.7 23.3 - - + +
43B LEU 2.9 14.8 + - - +
44B PHE 3.1 9.2 + - - +
46B HIS* 1.3 75.5 - - - +
48B ALA* 1.3 62.6 + - - +
50B GLU* 3.2 15.1 + - - +
51B TYR 3.2 2.9 + - - -
51E TYR* 4.4 0.2 - - - -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 4.5 0.6 - - + +
44B PHE* 2.9 16.9 + - + +
45B ASP* 3.7 12.1 - - - +
46B HIS 3.2 0.2 - - - -
47B ALA* 1.3 76.5 - - - +
49B GLU* 1.3 60.5 + - - +
51B TYR* 3.4 6.4 + - - +
52B GLU* 3.2 27.4 + - + +
51E TYR* 4.2 11.2 - - - -
55E LYS* 4.0 31.5 + - + +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP 3.0 15.1 + - - +
46B HIS* 3.1 13.0 + - - +
48B ALA* 1.3 75.8 - - - +
50B GLU* 1.3 66.6 + - - +
52B GLU* 3.2 29.6 + - - +
53B HIS* 3.1 39.8 + - - +
56B LYS* 4.9 6.1 + - - -
126B GLU* 4.7 5.8 - - - +
130B GLU* 4.2 11.0 - - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.5 27.0 - - - +
20B SER* 3.1 23.1 + - - +
21B SER* 4.0 11.7 - - - +
24B TYR* 4.0 5.6 - - + -
46B HIS* 2.9 37.3 + - + +
47B ALA* 3.2 8.0 + - - +
49B GLU* 1.3 75.4 - - - +
51B TYR* 1.3 62.1 + - - +
53B HIS* 3.2 12.9 + - - +
54B ALA 3.1 16.6 + - - -
93B HIS* 5.0 0.5 + - - -
94B GLU* 3.5 6.9 - - - +
97B ILE* 5.1 2.8 - - - +
130B GLU* 3.2 8.0 - - - +
1006B FE 3.1 9.2 - - - -
1007B FE 2.9 28.7 - - - -
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Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU 5.2 0.7 - - - -
18B MET* 4.3 20.4 - - + -
21B SER* 3.9 7.8 + - - +
47B ALA 3.2 2.6 + - - -
48B ALA 3.6 7.9 - - - +
49B GLU 3.2 0.8 - - - -
50B GLU* 1.3 77.8 - - - +
52B GLU* 1.3 60.9 + - - +
54B ALA* 3.1 7.7 + - + +
55B LYS* 2.9 62.2 + - + +
21E SER* 2.7 23.4 + - - -
25E MET* 3.7 15.6 - - + +
47E ALA 4.0 2.8 + - - -
48E ALA* 4.3 1.8 - - - -
51E TYR* 3.3 50.8 - + + +
1009E GOL 3.6 41.3 - - - -
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA 3.2 16.7 + - - +
49B GLU* 3.2 30.6 + - - +
51B TYR* 1.3 80.5 - - - +
53B HIS* 1.3 57.6 + - + +
55B LYS* 2.9 40.9 + - - +
56B LYS* 3.0 44.8 + - - +
52E GLU* 4.7 7.3 - - - +
55E LYS* 4.7 5.9 + - - -
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 4.0 11.2 + - - -
49B GLU* 3.1 21.9 + - + +
50B GLU* 3.3 16.3 + - - +
52B GLU* 1.3 75.2 - - + +
54B ALA* 1.3 65.4 + - - +
56B LYS* 3.2 6.1 + - - +
57B LEU* 3.1 28.0 + - - +
122B TRP* 3.9 19.7 - + + -
123B TYR* 4.1 17.1 - + + -
126B GLU* 3.2 31.0 + - + +
127B GLN* 5.3 2.0 - - - -
130B GLU* 2.9 36.2 + - - -
1006B FE 3.1 18.5 - - - -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.2 8.3 - - + +
17B GLU* 3.9 23.2 - - + +
18B MET* 4.2 28.9 - - + +
50B GLU 3.1 8.2 + - - +
51B TYR* 3.1 13.9 + - + +
53B HIS* 1.3 75.4 - - - +
55B LYS* 1.3 62.5 + - - +
57B LEU* 3.3 10.1 + - - +
58B ILE* 3.0 28.8 + - - +
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET* 6.5 0.2 - - + -
51B TYR* 2.9 42.4 + - + +
52B GLU* 2.9 45.9 + - - +
53B HIS 3.3 0.2 - - - -
54B ALA* 1.3 75.5 - - - +
56B LYS* 1.3 59.8 + - + +
58B ILE* 3.2 8.8 + - - +
59B ILE* 3.0 36.6 + - + +
25E MET* 3.9 13.9 - - + -
44E PHE* 3.9 22.8 - - + -
48E ALA* 3.8 27.4 + - + +
52E GLU* 4.9 7.1 + - - -
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Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 4.9 7.9 + - - -
52B GLU* 3.0 33.2 + - - +
53B HIS* 3.2 2.1 + - - +
55B LYS* 1.3 77.4 - - + +
57B LEU* 1.3 61.2 + - - +
59B ILE* 3.6 14.2 + - + +
60B PHE 3.3 15.4 + - - -
119B PHE* 3.5 15.4 - - + -
122B TRP* 3.6 41.6 - - + -
126B GLU* 4.5 16.8 + - - -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.3 21.1 - - + +
13B GLN* 3.9 36.8 - - + +
14B VAL* 3.8 20.2 - - + +
17B GLU* 4.5 4.7 - - + -
53B HIS 3.1 18.6 + - - +
54B ALA* 3.7 5.4 - - - +
56B LYS* 1.3 74.4 - - - +
58B ILE* 1.3 61.7 + - - +
60B PHE* 3.2 7.8 + - - +
61B LEU* 2.9 33.9 + - + +
119B PHE* 3.9 21.1 - - + -
120B LEU* 4.4 0.9 - - + -
122B TRP* 4.8 4.3 - - + -
123B TYR* 4.2 29.2 - - + +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.0 25.6 - - + -
18B MET* 4.1 15.3 - - + -
54B ALA 3.0 20.4 + - - +
55B LYS* 3.2 7.4 + - - +
57B LEU* 1.3 76.3 - - - +
59B ILE* 1.3 57.4 + - - +
61B LEU* 3.2 8.5 + - - +
62B ASN* 2.8 49.3 + - - +
68B VAL* 4.1 21.5 - - + -
70B LEU* 4.8 1.6 - - + -
25E MET* 3.9 35.7 - - + +
44E PHE* 3.9 14.1 - - + -
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 3.0 21.8 + - + +
56B LYS* 3.8 16.2 - - + +
57B LEU 3.3 0.2 - - - -
58B ILE* 1.3 74.9 - - - +
60B PHE* 1.3 63.1 + - - +
62B ASN* 3.2 9.9 + - + +
63B GLU* 3.0 36.1 + - + +
44E PHE* 3.5 33.0 - - + -
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.8 20.0 - - + -
10B LEU* 4.0 18.8 - - + -
56B LYS 3.3 3.2 + - - -
57B LEU* 3.2 8.8 + - + +
59B ILE* 1.3 79.1 - - - +
61B LEU* 1.3 63.5 + - + +
63B GLU* 3.1 30.0 - - - +
64B ASN* 2.8 45.3 + - - -
115B ALA* 4.4 8.5 - - + -
116B THR* 3.8 23.8 - - + -
119B PHE* 3.4 71.3 - + + -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 4.5 3.8 - - + -
7B ILE* 5.1 2.0 - - - +
10B LEU* 4.0 34.8 - - + +
11B ASN* 3.9 26.9 - - - +
14B VAL* 4.0 20.9 - - + -
57B LEU 2.9 18.3 + - - +
58B ILE* 3.2 6.9 + - - +
60B PHE* 1.3 76.1 - - - +
62B ASN* 1.3 63.7 + - - +
64B ASN* 3.1 8.1 + - - -
66B VAL* 3.0 62.5 + - + +
68B VAL* 4.0 15.0 - - + -
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 2.8 38.9 + - - +
59B ILE* 3.6 8.6 - - - +
61B LEU* 1.3 72.1 - - - +
63B GLU* 1.3 61.2 + - - +
65B ASN* 3.1 20.7 + - - +
66B VAL 4.6 3.2 - - - +
68B VAL* 3.7 17.5 - - - +
25E MET 5.9 0.4 + - - -
28E SER* 4.2 3.2 + - - -
29E SER* 3.9 13.6 + - - +
32E TYR* 3.3 60.9 - - + +
33E THR* 6.1 1.3 - - - +
44E PHE* 4.2 10.7 - - - -
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.1 10.4 - - - +
59B ILE* 3.0 25.8 + - + +
60B PHE* 3.1 45.5 - - - +
62B ASN* 1.3 75.8 - - - +
64B ASN* 1.3 63.7 + - - +
65B ASN* 3.3 5.1 + - - +
119B PHE* 5.6 0.6 - - - -
32E TYR* 5.7 1.3 - - - -
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Residues in contact with ASN 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B PRO* 3.5 0.2 - - - +
1B MET* 2.9 58.9 + - + +
2B LEU* 3.9 20.7 - - + +
60B PHE* 2.8 57.5 + - - +
61B LEU 3.1 5.7 + - - +
63B GLU* 1.3 81.9 + - - +
65B ASN* 1.3 65.7 + - - +
66B VAL* 3.1 13.8 + - + +
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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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