Contacts of the helix formed by residues 30 - 68 (chain B) in PDB entry 3VBB
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 PRO 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 3.3 61.6 + - - +
23B GLN* 4.0 12.1 - - + -
24B GLU* 3.9 24.7 - - + +
28B LYS 3.0 11.9 - - - +
29B ASP* 1.3 85.2 - - - +
31B GLY* 1.3 61.7 + - - +
32B LEU 3.2 1.1 - - - -
33B VAL* 3.2 11.8 + - - +
34B ASP* 3.7 0.7 - - - +
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 4.0 2.6 - - - +
29B ASP* 3.0 17.5 + - - -
30B PRO* 1.3 75.8 - - - +
32B LEU* 1.3 62.6 + - - +
33B VAL 2.9 6.3 - - - -
34B ASP* 2.9 29.4 + - - +
35B GLN* 2.9 23.5 + - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 4.5 6.1 - - + +
28B LYS* 6.2 0.2 - - + -
29B ASP* 3.3 37.6 + - + +
30B PRO 3.2 0.4 - - - -
31B GLY* 1.3 76.5 - - - +
33B VAL* 1.3 59.7 + - - +
35B GLN* 4.2 10.1 - - - +
36B LEU* 3.4 7.6 + - - +
131B ASN* 3.0 50.9 + - - +
134B GLU* 3.5 45.8 - - + +
135B ILE* 4.1 10.7 - - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 4.2 11.4 - - + -
16B PRO* 3.8 23.3 - - + +
19B ILE* 3.8 27.1 - - + +
20B ARG* 3.9 18.6 - - + -
23B GLN* 4.6 7.9 - - + -
30B PRO 3.3 14.4 - - - +
31B GLY 2.9 1.2 - - - -
32B LEU* 1.3 76.9 - - - +
34B ASP* 1.3 62.2 + - - +
35B GLN 3.2 0.2 - - - -
36B LEU* 3.1 5.1 + - - +
37B VAL* 2.9 39.9 + - + +
135B ILE* 4.0 15.0 - - + -
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Residues in contact with ASP 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 2.9 45.9 + - - +
31B GLY* 2.9 20.5 + - - +
33B VAL* 1.3 76.1 - - - +
35B GLN* 1.3 58.8 + - + +
37B VAL* 3.4 6.5 + - - +
38B LYS* 3.0 30.1 + - - +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 4.1 14.6 + - - -
31B GLY* 2.9 22.3 + - - +
32B LEU* 4.2 8.7 - - - +
34B ASP* 1.3 78.3 - - + +
36B LEU* 1.3 58.6 + - - +
38B LYS* 3.8 7.7 - - - +
39B ALA* 3.0 31.2 + - - +
127B GLU* 4.5 10.5 - - - +
131B ASN* 3.4 25.8 + - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.6 7.6 - - + -
8B PHE* 3.4 40.6 - - + -
32B LEU 3.4 12.7 + - - +
33B VAL 3.1 9.0 + - - +
35B GLN* 1.3 76.9 - - - +
37B VAL* 1.3 60.3 + - - +
39B ALA* 3.5 2.4 + - - +
40B ASP* 2.8 32.4 + - + +
127B GLU 5.5 0.7 - - - -
128B ARG* 3.1 51.4 - - + +
131B ASN* 3.5 9.2 - - + +
132B LEU* 3.5 25.8 - - + -
135B ILE* 4.2 6.1 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.9 33.9 - - + +
16B PRO* 4.2 15.0 - - + -
33B VAL* 2.9 29.5 + - + +
34B ASP* 3.9 6.5 - - - +
36B LEU* 1.3 76.0 - - - +
38B LYS* 1.3 53.4 + - - +
40B ASP* 3.1 7.4 + - + +
41B SER* 2.8 46.6 + - - +
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASP 3.0 18.9 + - - +
35B GLN* 3.8 7.2 - - - +
37B VAL* 1.3 77.2 - - - +
39B ALA* 1.3 63.9 + - + +
41B SER* 3.1 8.0 + - - -
42B GLU* 3.0 50.0 + - + +
45B ARG* 5.5 0.2 + - - -
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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
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35B GLN 3.0 19.4 + - - +
36B LEU* 4.1 3.6 - - - +
38B LYS* 1.3 78.9 - - + +
40B ASP* 1.3 58.5 + - - +
42B GLU* 4.5 4.3 - - - -
43B TRP* 2.9 28.1 + - - +
124B LEU* 3.6 30.6 - - + +
127B GLU* 4.0 23.3 - - + +
128B ARG* 5.1 11.2 - - - +
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.1 12.8 - - + +
8B PHE* 5.4 1.9 - - + +
9B ARG* 2.7 53.6 + - - +
36B LEU 2.8 21.1 + - - +
37B VAL* 3.5 6.3 - - - +
39B ALA* 1.3 77.5 - - - +
41B SER* 1.3 57.4 + - - +
43B TRP* 3.1 5.2 + - - +
44B ARG* 2.9 32.7 + - - +
128B ARG* 2.9 33.8 + - + +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 2.8 33.9 + - - +
38B LYS* 3.1 7.1 + - - -
40B ASP* 1.3 72.1 + - - +
42B GLU* 1.3 59.5 + - - +
44B ARG* 3.1 15.6 + - - +
45B ARG* 2.9 56.4 + - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 3.0 52.1 + - + +
39B ALA* 3.9 1.4 - - - +
41B SER* 1.3 71.4 - - - +
43B TRP* 1.3 68.1 + - - +
45B ARG* 3.3 23.6 + - - +
46B CYS* 3.1 28.9 + - - -
123B LYS* 5.1 4.9 + - - -
124B LEU* 3.6 27.4 - - + +
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Residues in contact with TRP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 4.5 5.6 - - - -
39B ALA 2.9 16.6 + - - +
40B ASP* 3.2 13.0 - - - +
42B GLU* 1.3 79.0 - - - +
44B ARG* 1.3 76.9 + - + +
46B CYS* 3.4 6.5 + - - +
47B ARG* 3.3 53.0 + - - -
121B ARG* 3.3 59.2 + - + +
124B LEU* 3.3 13.8 - - + +
125B GLU* 3.1 37.2 + - + +
128B ARG* 3.4 32.8 - - - +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 3.9 37.5 - - - +
11B ASP* 2.9 41.0 + - - -
12B LYS* 4.3 13.1 - - - +
40B ASP* 2.9 17.6 + - - +
41B SER* 3.1 14.3 + - - +
43B TRP* 1.3 97.2 - - + +
45B ARG* 1.3 64.8 + - + +
47B ARG* 3.7 17.8 + - - +
48B PHE* 3.4 19.1 + - - +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 2.9 37.7 + - - +
42B GLU* 3.7 33.9 - - - +
44B ARG* 1.3 75.1 - - + +
46B CYS* 1.3 56.1 + - - +
48B PHE* 3.0 12.5 + - + +
49B ARG* 2.7 37.3 + - + +
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Residues in contact with CYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 3.1 19.5 + - - -
43B TRP* 3.5 9.9 - - - +
45B ARG* 1.3 73.9 - - - +
47B ARG* 1.3 59.3 + - - +
49B ARG* 4.4 3.4 - - - +
50B ALA* 2.8 35.3 + - - +
117B CYS* 4.1 20.9 - - - -
120B GLU* 4.1 28.9 - - - -
121B ARG* 3.8 21.8 - - + -
124B LEU* 5.1 1.1 - - - -
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 5.7 1.6 - - - +
43B TRP* 3.3 39.9 + - - +
44B ARG* 4.0 20.4 + - - +
45B ARG 3.4 0.2 - - - -
46B CYS* 1.3 77.8 - - - +
48B PHE* 1.3 61.9 + - + +
50B ALA* 4.3 3.2 - - - +
51B ASP* 3.5 20.1 + - + +
121B ARG* 3.2 34.3 - - - +
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG 3.4 11.0 + - - +
45B ARG* 3.0 14.6 + - + +
47B ARG* 1.3 80.0 - - + +
49B ARG* 1.3 70.3 + - + +
51B ASP* 3.2 14.9 + - + +
52B ASN* 3.4 36.7 + - - -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 2.7 20.7 + - + +
46B CYS* 4.1 1.8 - - - +
48B PHE* 1.3 78.0 - - + +
50B ALA* 1.3 61.1 + - - +
52B ASN* 2.9 31.8 + - - +
53B LEU* 3.1 30.0 + - + +
87B PHE* 4.6 13.3 - - - -
113B ALA* 4.0 23.0 + - - +
117B CYS* 3.9 18.8 - - - -
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Residues in contact with ALA 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B CYS 2.8 22.8 + - - +
47B ARG* 4.5 4.0 - - - +
49B ARG* 1.3 75.6 - - - +
51B ASP* 1.3 59.6 + - - +
53B LEU* 3.7 10.2 + - - +
54B ASN* 3.4 20.3 + - - +
114B ILE* 4.4 17.1 - - + +
117B CYS* 3.7 24.2 - - + -
118B ASP* 5.1 3.8 - - - +
121B ARG* 5.5 2.5 - - - +
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ARG 3.5 16.3 + - - +
48B PHE* 3.2 8.8 + - + +
49B ARG 3.1 1.2 - - - -
50B ALA* 1.3 77.6 - - - +
52B ASN* 1.3 63.7 + - - +
54B ASN* 3.6 14.3 + - - +
55B LYS* 3.1 49.5 + - - +
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Residues in contact with ASN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.4 44.8 + - - +
49B ARG* 2.9 12.3 + - - +
51B ASP* 1.3 80.3 - - - +
53B LEU* 1.3 67.2 + - + +
54B ASN 3.2 0.2 - - - -
55B LYS* 3.1 23.2 + - - +
56B LEU* 3.1 17.8 + - + +
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 3.1 41.4 + - + +
50B ALA* 3.9 7.0 - - - +
51B ASP 3.4 0.2 - - - -
52B ASN* 1.3 77.2 - - + +
54B ASN* 1.3 57.4 + - - +
56B LEU* 3.3 14.3 + - + -
57B LYS* 2.8 26.7 + - - +
87B PHE* 4.3 24.9 - - + -
110B ILE* 3.4 19.7 - - + +
113B ALA* 3.8 24.2 - - + +
114B ILE* 3.4 30.3 - - + +
117B CYS* 5.0 0.4 - - - -
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Residues in contact with ASN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 3.4 11.2 + - - +
51B ASP* 3.6 17.2 + - - +
52B ASN 3.2 0.2 - - - -
53B LEU* 1.3 78.4 - - - +
55B LYS* 1.3 60.5 + - + +
57B LYS* 3.6 9.4 + - - +
58B ASN* 3.0 44.5 + - - +
114B ILE* 3.5 20.2 - - - +
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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
----------------------------------------------------------
51B ASP* 3.1 44.2 + - - +
52B ASN* 3.4 14.8 - - - +
54B ASN* 1.3 79.7 - - + +
56B LEU* 1.3 59.7 + - + +
58B ASN* 3.3 9.7 + - - +
59B LEU* 3.0 29.3 + - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN* 3.1 15.6 + - + +
53B LEU* 3.7 16.4 - - + +
55B LYS* 1.3 75.7 - - + +
57B LYS* 1.3 64.9 + - - +
59B LEU* 3.5 6.2 + - + +
60B CYS* 3.0 26.3 + - - +
87B PHE* 3.6 44.2 - - + +
90B LEU* 4.0 33.6 - - + +
110B ILE* 3.5 17.3 - - + -
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU 2.8 20.3 + - - +
54B ASN* 3.8 9.9 - - - +
56B LEU* 1.3 73.3 - - - +
58B ASN* 1.3 70.6 + - - +
60B CYS* 3.1 9.1 + - - +
61B SER* 2.8 39.2 + - - +
107B ARG* 4.2 12.3 - - + +
110B ILE* 3.7 11.5 - - + +
111B ASP* 3.0 41.1 - - - +
114B ILE* 4.6 9.6 - - + -
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Residues in contact with ASN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASN* 3.0 32.1 + - - +
55B LYS* 3.5 10.2 - - - +
56B LEU 3.3 0.2 - - - -
57B LYS* 1.3 89.7 + - - +
59B LEU* 1.3 63.7 + - - +
61B SER* 3.1 5.7 + - - +
62B LYS* 2.8 55.5 + - - +
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Residues in contact with LEU 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 16.6 + - - +
56B LEU* 3.8 8.5 - - + +
58B ASN* 1.3 73.1 - - - +
60B CYS* 1.3 62.6 + - - +
62B LYS* 3.9 9.3 - - - +
63B THR* 3.0 28.6 + - - -
90B LEU* 5.2 4.5 - - + -
91B THR 6.1 0.2 - - - -
92B ALA* 5.5 11.9 - - + +
95B LEU* 4.4 12.1 - - + +
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Residues in contact with CYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU 3.0 16.3 + - - +
57B LYS* 3.2 10.8 - - - +
59B LEU* 1.3 76.1 - - - +
61B SER* 1.3 56.7 + - - +
63B THR* 3.3 1.4 + - - -
64B ILE* 2.8 34.3 + - - +
90B LEU* 4.5 2.5 - - - -
95B LEU* 4.2 17.0 - - - +
103B ILE* 3.7 19.5 - - + +
106B VAL* 3.7 30.1 - - - -
107B ARG* 4.0 23.8 - - + -
110B ILE* 4.3 4.0 - - - -
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 2.8 28.4 + - - +
58B ASN* 3.9 4.7 - - - -
60B CYS* 1.3 69.4 - - - +
62B LYS* 1.3 60.4 + - - +
63B THR 3.4 0.2 - - - -
64B ILE* 3.8 3.0 - - - +
65B GLY* 3.0 21.1 + - - -
107B ARG* 2.5 45.9 + - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 2.8 49.9 + - - +
59B LEU* 3.9 7.0 - - - +
61B SER* 1.3 77.2 - - - +
63B THR* 1.3 59.0 + - - +
65B GLY* 3.1 3.2 + - - -
66B GLU* 3.0 24.9 + - - +
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU 3.0 18.2 + - - -
60B CYS 3.9 1.8 - - - -
62B LYS* 1.3 74.4 - - - +
64B ILE* 1.3 56.1 + - - +
65B GLY 2.9 4.5 - - - -
66B GLU* 3.2 14.5 + - - +
67B LYS* 3.0 40.0 + - - +
92B ALA* 4.4 3.8 + - - +
95B LEU* 3.2 34.4 - - + +
96B ALA* 4.4 3.1 - - + +
103B ILE* 3.5 22.4 - - + -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS 2.8 18.4 + - - +
61B SER* 3.8 5.8 - - - +
63B THR* 1.3 72.5 - - - +
65B GLY* 1.3 60.0 + - - +
67B LYS* 3.9 6.7 - - - +
68B MET* 3.5 32.9 + - - +
100B VAL* 3.9 19.7 - - + +
103B ILE* 3.2 30.5 - - + +
104B LYS* 3.4 49.8 - - + +
107B ARG* 4.3 21.5 - - - +
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B SER 3.0 16.2 + - - -
62B LYS* 3.1 8.5 + - - -
63B THR 2.9 1.2 - - - -
64B ILE* 1.3 79.9 - - - +
66B GLU* 1.3 58.8 + - - +
67B LYS 3.6 0.2 + - - -
68B MET* 3.6 5.3 + - - +
69B LYS* 3.6 23.1 + - - +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS 3.0 9.8 + - - +
63B THR* 3.3 23.0 - - - +
65B GLY* 1.3 74.4 - - - +
67B LYS* 1.3 91.0 + - - +
68B MET 3.4 0.2 - - - -
69B LYS* 3.2 47.5 + - - +
70B LYS* 4.3 8.8 + - - +
96B ALA* 5.1 4.9 - - - +
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 3.0 20.1 + - - +
64B ILE* 4.4 2.9 - - - +
65B GLY 3.3 0.4 - - - -
66B GLU* 1.3 95.1 + - - +
68B MET* 1.3 58.3 + - - +
69B LYS 3.2 4.9 - - - -
70B LYS* 3.6 19.6 + - - +
96B ALA* 3.0 43.0 + - - +
98B LEU 2.9 29.6 - - - +
99B LYS* 5.3 0.2 - - - -
100B VAL* 3.2 33.7 - - + +
103B ILE* 3.9 12.1 - - + -
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.5 24.7 + - - +
65B GLY* 3.6 5.8 + - - +
66B GLU 3.4 0.2 - - - -
67B LYS* 1.3 75.8 - - - +
69B LYS* 1.3 56.1 + - - +
70B LYS 3.2 12.1 + - - +
77B ASP* 6.2 0.4 - - - +
100B VAL* 4.4 15.9 - - + -
104B LYS* 4.4 25.8 - - - +
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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) + - + + + + + -
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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