Contacts of the helix formed by residues 36 - 64 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.3 16.4 - - + -
1005C HIS* 5.8 0.9 - - - +
30D TRP* 3.8 28.9 - - + -
31D CYS* 2.9 27.5 + - + +
32D TYR 4.7 0.2 + - - -
34D HIS* 3.5 11.9 - - + +
35D SER* 1.3 80.1 - - - +
37D ASP* 1.3 58.3 + - - +
39D ALA* 4.4 2.7 - - + -
40D GLY 2.9 21.5 + - - -
83D LEU* 4.2 27.4 - - + +
151D LEU* 4.3 24.9 - - + +
155D ASP* 3.2 33.0 - - + +
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Residues in contact with ASP 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASP* 5.5 10.6 - - - +
140A LYS* 2.6 32.6 + - - -
157A TYR* 4.3 5.0 + - - -
32D TYR* 3.7 32.5 - - + +
35D SER 3.5 2.2 - - - +
36D LEU* 1.3 73.5 - - - +
38D GLY* 1.3 63.2 + - - +
40D GLY 3.5 0.2 - - - -
41D LEU* 2.9 30.5 + - - +
155D ASP* 3.2 0.2 - - - +
159D LYS* 3.1 25.6 + - - -
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Residues in contact with GLY 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASP* 1.3 77.7 + - - +
39D ALA* 1.3 62.1 + - - +
41D LEU* 3.5 3.4 + - - +
42D PHE* 3.2 21.5 + - - +
155D ASP* 2.9 29.7 + - - -
158D VAL* 3.8 5.4 - - - +
159D LYS* 3.7 27.1 + - - -
162D ALA* 4.5 0.2 - - - +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D CYS* 3.8 22.9 - - + -
36D LEU* 3.9 2.0 - - + +
38D GLY* 1.3 69.6 - - - -
40D GLY* 1.3 64.9 + - - +
42D PHE* 3.4 0.9 + - - +
43D LEU* 3.0 30.4 + - - +
83D LEU* 3.8 22.2 - - + -
87D PHE* 4.2 10.1 - - + -
155D ASP* 2.8 18.1 + - - +
158D VAL* 3.7 16.9 - - + +
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Residues in contact with GLY 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D SER* 2.8 30.7 + - - -
31D CYS* 3.7 2.2 - - - +
32D TYR* 3.3 26.9 - - - -
36D LEU 2.9 15.7 + - - -
37D ASP 3.3 3.6 + - - -
38D GLY 3.2 0.4 - - - -
39D ALA* 1.3 77.1 - - - +
41D LEU* 1.3 56.4 + - - +
44D PHE* 2.9 16.6 + - - +
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D TYR* 3.3 16.6 + - - +
37D ASP 2.9 16.8 + - - +
38D GLY 3.9 3.1 - - - +
40D GLY* 1.3 72.0 - - - +
42D PHE* 1.3 60.5 + - - +
44D PHE* 3.4 7.3 + - + +
45D ASP* 2.9 54.3 + - - +
159D LYS* 4.9 11.2 - - + -
162D ALA* 4.0 20.2 - - + -
163D LYS* 4.3 22.7 - - + +
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Residues in contact with PHE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLY 3.2 6.1 + - - +
39D ALA 3.7 2.2 - - - +
40D GLY 3.3 0.2 - - - -
41D LEU* 1.3 81.6 - - - +
43D LEU* 1.3 62.6 - - + +
45D ASP* 3.8 4.4 - - + +
46D HIS* 2.9 33.0 + - + +
87D PHE* 4.1 15.9 - + - -
133D LEU* 3.7 30.3 - - + -
134D PHE* 3.7 33.4 - + - -
137D ILE* 3.4 28.5 - - + -
158D VAL* 3.5 24.5 - - + -
161D ILE* 3.9 18.6 - - + -
162D ALA* 3.7 21.0 - - + +
165D ARG* 4.4 5.2 - - - -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 3.7 35.2 - - + +
27D MET* 3.9 24.2 - - + -
28D SER* 3.7 14.4 - - - +
31D CYS* 3.8 24.7 - - - -
39D ALA 3.0 21.3 + - - +
42D PHE* 1.3 83.5 - - + +
44D PHE* 1.3 59.8 + - - +
46D HIS* 3.8 2.9 - - - -
47D ALA* 2.9 29.5 + - - +
86D ILE* 4.0 10.5 - - + -
87D PHE* 4.2 12.6 - - + -
90D ALA* 5.1 0.7 - - + -
134D PHE* 4.1 20.9 - - + -
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Residues in contact with PHE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 3.8 35.4 - - + -
58C ILE* 3.8 23.3 - - + -
59C ILE* 3.7 29.6 - - + -
62C ASN* 4.2 8.3 - - - -
25D MET* 3.5 26.1 - - + +
28D SER* 3.4 12.7 + - - +
32D TYR* 4.6 4.0 - + + +
40D GLY 2.9 18.9 + - - +
41D LEU* 3.7 11.2 - - + +
43D LEU* 1.3 75.9 - - - +
45D ASP* 1.3 79.1 + - - +
47D ALA* 3.2 7.1 + - - +
48D ALA* 3.1 22.1 + - + +
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Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 2.9 40.5 + - - +
42D PHE* 3.8 5.2 - - + +
44D PHE* 1.3 93.2 - - - +
46D HIS* 1.3 62.2 + - - +
48D ALA* 3.4 7.0 + - - +
49D GLU* 3.1 21.7 + - - +
162D ALA* 4.3 14.3 - - + +
166D LYS 4.6 10.8 - - - +
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Residues in contact with HIS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 3.3 29.8 - + - -
42D PHE* 2.9 23.6 + - + +
43D LEU* 3.8 7.4 - - - +
44D PHE 3.2 0.2 - - - -
45D ASP* 1.3 74.6 - - - +
47D ALA* 1.3 62.4 + - - +
49D GLU* 3.3 6.9 + - - +
50D GLU* 3.1 34.8 + - - +
94D GLU* 3.0 21.4 + - - -
130D GLU* 3.2 43.3 + - + +
133D LEU* 6.2 1.6 - - - +
134D PHE* 3.5 30.5 - + + -
1007D FE 3.8 0.7 - - - -
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TYR* 4.0 2.5 - - - -
21D SER* 3.5 35.2 + - - +
24D TYR* 3.5 14.7 - - + +
25D MET* 3.7 21.5 - - + +
43D LEU 2.9 18.7 + - - +
44D PHE 3.4 5.4 - - - +
46D HIS* 1.3 76.3 - - - +
48D ALA* 1.3 60.6 + - - +
50D GLU* 3.2 14.5 + - - +
51D TYR 3.3 8.3 + - - -
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 3.8 12.4 + - - -
55C LYS* 3.8 34.4 + - + +
25D MET* 4.9 0.4 - - + -
44D PHE* 3.1 14.8 + - + +
45D ASP* 3.7 10.5 - - - +
47D ALA* 1.3 76.0 - - - +
49D GLU* 1.3 58.4 + - - +
51D TYR* 3.3 6.1 + - - +
52D GLU* 3.1 29.9 + - - +
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Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASP 3.1 14.6 + - - +
46D HIS* 3.6 13.5 - - - +
47D ALA 3.2 0.2 - - - -
48D ALA* 1.3 76.0 - - - +
50D GLU* 1.3 65.6 + - - +
52D GLU* 3.3 19.7 + - - +
53D HIS* 3.0 40.8 + - - +
56D LYS* 5.4 3.8 + - - -
126D GLU* 4.1 7.1 - - - +
130D GLU* 3.9 21.1 - - - +
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLU* 3.5 39.6 - - - +
20D SER* 3.8 16.2 + - - -
21D SER 4.0 4.5 - - - +
24D TYR* 4.0 13.9 - - + -
46D HIS* 3.1 34.5 + - - +
47D ALA 3.2 6.9 + - - +
49D GLU* 1.3 75.9 - - - +
51D TYR* 1.3 61.5 + - - +
53D HIS* 3.2 16.7 + - - +
54D ALA 3.0 17.5 + - - -
94D GLU* 3.4 5.2 - - - +
97D ILE* 5.5 1.6 - - - +
130D GLU* 3.1 15.8 - - - +
1006D FE 3.8 0.2 - - - -
1007D FE 2.5 24.0 - - - -
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Residues in contact with TYR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C SER* 2.8 23.5 + - - -
25C MET* 3.6 16.6 - - + +
47C ALA 3.7 8.5 + - - -
48C ALA* 3.8 4.6 - - - -
51C TYR* 3.3 64.4 - + + +
17D GLU 5.2 0.4 - - - -
18D MET* 3.8 35.7 - - + -
21D SER* 4.2 6.0 - - - +
47D ALA 3.3 3.2 + - - +
48D ALA 3.3 8.2 + - - +
49D GLU 3.2 0.6 - - - -
50D GLU* 1.3 79.8 - - - +
52D GLU* 1.3 60.2 + - - +
54D ALA* 3.2 7.0 + - - +
55D LYS* 2.9 61.7 + - + +
1008D GOL 4.0 5.2 - - - -
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLU* 4.7 7.8 - - - +
55C LYS* 4.9 4.2 + - - -
48D ALA 3.1 16.2 + - - +
49D GLU* 3.3 30.7 + - - +
51D TYR* 1.3 78.1 - - - +
53D HIS* 1.3 63.0 + - - +
55D LYS* 2.7 39.9 + - - +
56D LYS* 3.1 39.1 + - - +
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Residues in contact with HIS 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLU* 4.0 12.3 + - - -
49D GLU* 3.0 32.6 + - - +
50D GLU* 3.3 20.2 + - - +
52D GLU* 1.3 71.5 - - - +
54D ALA* 1.3 66.4 + - - +
56D LYS* 3.3 4.9 + - + +
57D LEU* 3.1 29.1 + - - +
122D TRP* 3.7 25.5 - + - -
123D TYR* 4.0 15.9 - + + -
126D GLU* 3.4 22.6 + - + +
130D GLU* 2.8 29.4 + - - -
1006D FE 3.1 23.5 - - - -
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D VAL* 4.3 8.0 - - + +
17D GLU* 3.8 23.8 - - + +
18D MET* 3.8 33.7 - - + +
50D GLU 3.0 8.6 + - - +
51D TYR* 3.3 9.6 - - - +
53D HIS* 1.3 75.1 - - - +
55D LYS* 1.3 58.1 + - - +
57D LEU* 3.3 8.8 + - - +
58D ILE* 3.0 34.1 + - - +
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C MET* 4.0 14.8 - - + -
44C PHE* 3.8 19.0 - - + -
48C ALA* 3.9 26.9 + - + +
52C GLU* 5.0 6.3 + - - -
51D TYR* 2.9 44.2 + - + +
52D GLU* 2.7 48.1 + - - +
54D ALA* 1.3 77.6 - - + +
56D LYS* 1.3 59.4 + - + +
58D ILE* 3.3 7.7 + - - +
59D ILE* 2.9 35.8 + - + +
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 5.4 4.3 + - - -
52D GLU* 3.1 28.6 + - - +
53D HIS* 3.9 1.3 - - - +
54D ALA 3.3 0.2 - - - -
55D LYS* 1.3 73.9 - - + +
57D LEU* 1.3 64.6 + - - +
59D ILE* 3.6 15.0 + - + +
60D PHE 3.2 15.4 + - - -
119D PHE* 3.4 15.4 - - + -
122D TRP* 3.6 45.9 - - + -
126D GLU* 4.9 10.9 + - - -
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 4.5 14.1 - - + +
13D GLN* 3.9 32.5 - - + +
14D VAL* 3.9 21.5 - - + +
17D GLU* 4.4 5.8 - - + -
53D HIS 3.1 19.4 + - - +
54D ALA* 3.6 6.5 - - - +
56D LYS* 1.3 74.8 - - - +
58D ILE* 1.3 63.2 + - - +
60D PHE* 3.1 7.3 + - + +
61D LEU* 3.0 26.8 + - + +
119D PHE* 3.9 24.5 - - + -
120D LEU* 4.5 7.0 - - + -
122D TRP* 4.8 4.3 - - + -
123D TYR* 4.2 31.0 - - + +
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C MET* 4.1 30.1 - - + +
28C SER* 6.5 0.2 - - - -
44C PHE* 3.7 15.0 - - + -
14D VAL* 3.9 26.7 - - + -
18D MET* 4.0 18.6 - - + -
54D ALA 3.0 20.0 + - - +
55D LYS 3.6 6.7 - - - +
57D LEU* 1.3 73.8 - - - +
59D ILE* 1.3 60.4 + - - +
61D LEU* 3.2 9.2 + - - +
62D ASN* 2.8 45.8 + - - +
68D VAL* 4.1 26.5 - - + -
70D LEU* 4.6 1.6 - - + -
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Residues in contact with ILE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PHE* 3.5 30.3 - - + -
55D LYS* 2.9 26.4 + - + +
56D LYS* 3.7 15.0 - - + +
58D ILE* 1.3 75.7 - - - +
60D PHE* 1.3 58.0 + - - +
62D ASN* 3.3 10.2 + - + +
63D GLU* 2.9 52.3 + - + +
119D PHE* 6.5 0.9 - - + -
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 3.9 19.1 - - + -
10D LEU* 4.1 19.7 - - + -
56D LYS 3.2 2.4 + - - -
57D LEU* 3.1 10.6 + - + +
59D ILE* 1.3 78.4 - - - +
61D LEU* 1.3 62.1 + - - +
63D GLU* 3.5 14.3 + - - -
64D ASN* 2.7 53.6 + - - -
115D ALA* 4.7 6.5 - - + -
116D THR* 3.7 38.6 - - + -
119D PHE* 3.5 60.6 - + + -
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 4.3 6.5 - - + -
7D ILE* 5.1 2.5 - - - +
10D LEU* 3.9 34.3 - - + -
11D ASN* 3.6 31.0 - - - +
14D VAL* 4.0 22.4 - - + -
57D LEU* 3.0 16.4 + - + +
58D ILE* 3.2 6.5 + - - +
60D PHE* 1.3 73.1 - - + +
62D ASN* 1.3 63.8 + - - +
64D ASN* 3.2 5.8 + - - -
66D VAL* 2.8 62.5 + - + +
68D VAL* 4.1 14.4 - - + -
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Residues in contact with ASN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 4.4 2.2 + - - -
29C SER* 4.0 11.8 + - - -
32C TYR* 3.3 61.7 - - + +
33C THR* 6.1 0.8 - - - +
44C PHE* 4.1 11.3 - - - -
58D ILE* 2.8 37.8 + - - +
59D ILE* 3.4 11.4 - - + +
61D LEU* 1.3 72.9 - - - +
63D GLU* 1.3 62.4 + - + +
65D ASN* 3.2 18.9 + - - +
66D VAL 4.6 3.7 - - - +
68D VAL* 3.7 17.0 - - - +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TYR* 6.5 0.7 - - + -
1D MET* 4.2 9.2 - - - +
59D ILE* 2.9 37.3 + - + +
60D PHE* 3.8 18.7 - - - +
61D LEU 3.2 0.2 - - - -
62D ASN* 1.3 78.6 - - + +
64D ASN* 1.3 62.8 + - - +
65D ASN* 3.3 6.3 + - - +
119D PHE* 5.9 1.0 - - - -
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D PRO* 3.5 0.2 - - - +
1D MET* 2.8 52.9 + - + +
2D LEU* 3.4 29.7 - - + +
60D PHE* 2.7 50.5 + - - +
61D LEU 3.2 0.2 + - - -
62D ASN 3.2 0.6 - - - -
63D GLU* 1.3 82.5 - - - +
65D ASN* 1.3 63.2 + - - +
66D VAL* 3.2 17.4 + - + +
115D ALA* 6.1 1.4 - - - +
----------------------------------------------------------
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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).
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