Contacts of the helix formed by residues 23 - 61 (chain F) in PDB entry 2RAX
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 SER 23 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F MET 4.6 13.2 + - - -
20F LYS 3.4 17.0 + - - -
21F LEU* 3.0 2.8 + - - +
22F ALA* 1.3 72.4 - - - +
24F PHE* 1.3 67.2 + - - +
25F LEU 3.2 1.6 - - - +
26F LYS* 3.4 18.1 + - - +
27F ASP* 3.2 25.1 + - - +
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Residues in contact with PHE 24 (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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53B LEU* 3.5 31.2 - - + -
57B GLU* 3.4 33.4 - - + -
60B ARG* 4.9 4.5 - - - -
21F LEU* 3.2 25.6 + - + +
22F ALA* 4.1 4.7 - - + -
23F SER* 1.3 81.8 + - - +
25F LEU* 1.3 79.6 + - + +
27F ASP* 3.0 16.0 + - + +
28F PHE* 3.0 20.7 + - + +
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TRP* 3.8 34.8 - - + -
102A LEU* 3.6 30.1 - - + -
105A ASP* 4.2 0.4 - - - +
53B LEU* 5.2 8.5 - - + -
54B TYR* 3.6 31.2 - - + +
57B GLU* 4.4 14.4 - - + -
22F ALA* 4.8 13.5 - - + +
23F SER* 3.2 1.2 - - - +
24F PHE* 1.3 100.5 - - + +
26F LYS* 1.3 65.3 + - - +
28F PHE* 2.7 21.5 + - + +
29F ASP* 2.7 14.0 + - - +
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Residues in contact with LYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 5.1 17.5 - - + -
9A ALA* 6.3 2.7 - - + -
10A TRP* 5.5 2.8 - - - -
23F SER* 3.4 22.0 + - - +
24F PHE 3.4 0.6 - - - -
25F LEU* 1.3 75.6 - - - +
27F ASP* 1.3 65.1 + - - +
29F ASP* 3.3 11.0 + - - +
30F ARG* 3.2 18.2 + - - +
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Residues in contact with ASP 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F SER* 3.2 12.2 + - - +
24F PHE* 3.0 17.3 + - + +
26F LYS* 1.3 78.1 - - - +
28F PHE* 1.3 62.8 + - - +
30F ARG* 3.0 12.3 + - - +
31F GLU* 3.0 18.6 + - - +
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Residues in contact with PHE 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 5.6 2.9 - - + -
46B LEU* 5.3 1.3 - - + -
49B GLU* 4.4 9.4 - - + -
50B VAL* 3.8 37.0 - - + -
53B LEU* 3.3 35.4 - - + -
54B TYR* 4.5 18.4 - + - -
24F PHE* 3.0 13.6 + - + +
25F LEU* 2.7 17.8 + - + +
27F ASP* 1.3 70.3 - - - +
29F ASP* 1.3 67.4 + - - +
31F GLU* 2.9 32.8 + - + +
32F VAL* 2.9 47.5 + - + +
35F ARG* 5.1 5.6 - - - -
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Residues in contact with ASP 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.1 22.3 - - + +
112A LYS* 3.8 20.9 + - - +
25F LEU 2.7 14.4 + - - +
26F LYS* 3.3 15.9 - - - +
28F PHE* 1.3 75.3 - - - +
30F ARG* 1.3 51.9 + - - +
32F VAL* 3.4 7.9 + - - +
33F GLU* 2.7 45.0 + - - +
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Residues in contact with ARG 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LYS 3.2 7.2 + - - +
27F ASP* 3.0 13.8 + - - +
29F ASP* 1.3 77.9 + - - +
31F GLU* 1.3 60.4 + - - +
33F GLU* 3.7 38.0 + - - +
34F ILE* 2.8 65.3 + - - +
37F LYS* 6.4 0.4 - - - +
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 4.5 2.1 - - - +
27F ASP 3.0 11.3 + - - +
28F PHE* 2.9 32.2 + - + +
30F ARG* 1.3 76.2 - - - +
32F VAL* 1.3 58.9 + - - +
34F ILE* 3.1 12.5 + - - +
35F ARG* 2.8 65.0 + - - +
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Residues in contact with VAL 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 5.3 6.3 - - + +
112A LYS* 5.1 9.4 - - + +
113A ILE* 3.3 30.7 - - + -
46B LEU* 4.3 13.0 - - + -
50B VAL* 4.5 5.2 - - + -
28F PHE* 2.9 47.6 + - + +
29F ASP* 3.4 9.9 - - - +
31F GLU* 1.3 73.1 - - + +
33F GLU* 1.3 68.3 + - - +
35F ARG* 2.8 7.9 + - - +
36F ILE* 2.8 36.3 + - + +
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Residues in contact with GLU 33 (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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112A LYS* 3.9 27.5 + - - +
116A GLU* 6.0 1.1 - - - +
29F ASP* 2.7 30.9 + - - +
30F ARG* 3.4 38.8 + - - +
32F VAL* 1.3 72.2 - - - +
34F ILE* 1.3 65.3 + - - +
36F ILE* 3.7 5.7 + - - +
37F LYS* 3.3 18.0 + - - +
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Residues in contact with ILE 34 (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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30F ARG* 2.8 54.7 + - - +
31F GLU* 3.2 11.7 - - + +
33F GLU* 1.3 73.3 - - - +
35F ARG* 1.3 71.7 - - + +
37F LYS* 3.0 19.8 + - - +
38F GLN* 3.2 13.2 + - + +
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Residues in contact with ARG 35 (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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42B ASP 5.4 0.6 + - - -
45B ASN* 5.0 3.2 - - - +
46B LEU* 3.6 44.7 - - + +
49B GLU* 3.0 42.0 + - - +
28F PHE* 5.1 2.6 - - - -
31F GLU* 2.8 56.1 + - + +
32F VAL 2.8 3.7 + - - +
34F ILE* 1.3 77.7 - - + +
36F ILE* 1.3 67.6 + - - +
38F GLN* 3.2 10.0 + - - +
39F ILE* 3.1 23.0 + - + +
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Residues in contact with ILE 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 4.0 10.8 - - + +
113A ILE* 3.4 53.8 - - + +
116A GLU* 3.4 44.2 - - + +
117A THR* 4.6 3.4 - - - +
46B LEU* 4.3 2.8 - - + +
32F VAL* 2.8 33.3 + - + +
33F GLU* 3.9 6.5 - - - +
35F ARG* 1.3 70.0 - - - +
37F LYS* 1.3 67.4 + - - +
39F ILE* 2.7 24.3 + - + +
40F GLU* 2.9 14.5 + - + -
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Residues in contact with LYS 37 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG* 6.4 0.4 - - - +
33F GLU 3.3 10.7 + - - +
34F ILE* 3.0 14.1 + - - +
36F ILE* 1.3 80.0 - - - +
38F GLN* 1.3 65.1 + - - +
40F GLU* 3.5 6.2 + - - +
41F SER* 3.1 23.1 + - - -
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Residues in contact with GLN 38 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASP* 6.0 1.3 - - - +
34F ILE* 3.2 10.6 + - + +
35F ARG* 3.4 12.6 - - - +
36F ILE 2.9 1.4 + - - -
37F LYS* 1.3 78.7 - - - +
39F ILE* 1.3 65.8 + - + +
41F SER* 2.7 29.4 + - - -
42F ASP* 2.9 31.1 + - - +
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Residues in contact with ILE 39 (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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113A ILE* 5.6 1.8 - - + -
117A THR* 4.0 26.7 - - + +
39B ILE* 3.9 22.6 - - + +
42B ASP* 4.1 22.4 - - + +
43B ARG* 3.9 32.3 - - + +
46B LEU* 3.9 20.4 - - + -
35F ARG* 3.1 13.9 + - + +
36F ILE* 2.7 14.9 + - + +
38F GLN* 1.3 73.2 - - + +
40F GLU* 1.3 57.8 + - - +
42F ASP* 3.1 9.1 + - - +
43F ARG* 2.8 28.0 + - + +
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Residues in contact with GLU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 3.1 28.2 + - + +
117A THR* 3.8 10.5 + - + -
118A ASN 4.8 0.5 + - - -
119A ASN* 4.9 9.8 + - - +
36F ILE* 2.9 17.6 + - + +
37F LYS* 4.0 7.2 - - + +
39F ILE* 1.3 72.8 - - - +
41F SER* 1.3 56.9 + - - +
43F ARG* 3.0 35.4 + - - +
44F GLN* 2.9 61.4 + - - +
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Residues in contact with SER 41 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LYS* 3.1 12.8 + - - -
38F GLN* 2.7 30.9 + - - -
40F GLU* 1.3 73.0 - - - +
42F ASP* 1.3 64.1 + - - +
44F GLN* 3.0 5.7 + - - +
45F ASN* 2.7 49.6 + - - -
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Residues in contact with ASP 42 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 5.6 1.0 + - - -
39B ILE* 4.0 20.1 - - + +
42B ASP* 4.7 10.0 - - - +
38F GLN* 2.9 29.2 + - - +
39F ILE* 3.1 10.3 + - - +
41F SER* 1.3 87.5 + - - +
43F ARG* 1.3 58.0 + - - +
45F ASN* 4.0 7.2 + - - +
46F LEU* 3.1 29.1 + - - +
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Residues in contact with ARG 43 (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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117A THR* 3.5 26.6 + - + -
118A ASN 4.2 4.0 + - - -
119A ASN 3.4 31.7 + - - -
39B ILE* 3.8 17.0 - - + +
113E ILE* 4.5 11.9 - - + -
114E ALA* 4.2 28.9 + - - +
117E THR* 3.6 28.5 - - + +
118E ASN* 4.4 3.0 - - - +
39F ILE 2.8 19.1 + - - +
40F GLU* 3.0 24.4 + - - +
42F ASP* 1.3 73.1 - - - +
44F GLN* 1.3 73.9 + - - +
46F LEU* 3.8 3.1 + - - +
47F LEU* 3.3 36.5 + - + +
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Residues in contact with GLN 44 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN 5.6 2.4 - - - -
40F GLU* 2.9 44.9 + - - +
41F SER* 3.6 5.8 - - - +
43F ARG* 1.3 95.5 - - - +
45F ASN* 1.3 67.3 + - - +
46F LEU 3.1 1.8 - - - -
47F LEU* 3.1 20.9 + - - +
48F LYS* 3.0 22.1 + - - +
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Residues in contact with ASN 45 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 5.3 2.9 - - - +
41F SER* 2.7 33.2 + - - +
42F ASP* 4.0 6.8 + - - +
44F GLN* 1.3 71.7 - - - +
46F LEU* 1.3 65.8 + - - +
48F LYS* 3.4 8.5 + - - +
49F GLU* 3.0 35.4 + - - +
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 5.2 1.1 - - + -
32B VAL* 4.4 14.8 - - + +
35B ARG* 3.5 58.5 - - + +
36B ILE* 3.7 18.6 - - + -
39B ILE* 4.2 12.6 - - + -
113E ILE* 3.5 32.8 - - + -
42F ASP 3.1 17.7 + - - +
43F ARG 3.8 5.6 - - - +
44F GLN 3.1 0.2 - - - -
45F ASN* 1.3 75.9 - - - +
47F LEU* 1.3 59.6 + - - +
49F GLU* 2.9 23.4 + - + +
50F VAL* 3.1 11.6 + - + +
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Residues in contact with LEU 47 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E LYS* 3.7 39.9 - - + +
113E ILE* 3.7 30.1 - - + -
114E ALA* 5.0 4.0 - - + +
43F ARG* 3.3 33.8 + - + +
44F GLN* 3.1 29.5 + - - +
46F LEU* 1.3 80.9 - - - +
48F LYS* 1.3 59.1 + - - +
50F VAL* 3.5 7.6 + - + +
51F ASP* 3.2 24.8 + - - +
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Residues in contact with LYS 48 (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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44F GLN 3.0 12.4 + - - +
45F ASN* 3.7 11.4 - - - +
46F LEU 3.3 0.2 - - - -
47F LEU* 1.3 75.3 - - - +
49F GLU* 1.3 57.1 + - - +
51F ASP* 3.3 9.6 + - - +
52F ASN* 2.8 42.1 + - - +
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Residues in contact with GLU 49 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PHE* 4.2 11.8 - - + -
31B GLU* 4.6 1.2 - - - +
35B ARG* 2.7 45.4 + - - +
45F ASN* 3.0 19.3 + - - +
46F LEU* 2.9 12.1 + - + +
48F LYS* 1.3 77.9 - - - +
50F VAL* 1.3 56.6 + - - +
52F ASN* 3.8 7.9 - - + +
53F LEU* 2.9 31.4 + - - +
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Residues in contact with VAL 50 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PHE* 3.5 28.0 - - + -
32B VAL* 4.1 12.3 - - + -
106E ARG* 3.8 13.0 - - + +
109E ALA* 3.8 15.0 - - + -
110E LYS* 3.7 23.8 - - + -
113E ILE* 4.2 16.8 - - + -
46F LEU 3.1 11.5 + - - +
47F LEU* 3.6 8.3 - - - +
49F GLU* 1.3 73.0 - - - +
51F ASP* 1.3 66.9 + - - +
52F ASN 3.0 1.2 + - - -
53F LEU* 3.1 10.4 + - - -
54F TYR* 3.2 27.5 + - + +
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Residues in contact with ASP 51 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ARG* 3.3 19.3 + - - +
110E LYS* 3.2 42.4 + - - +
47F LEU 3.2 8.3 + - - +
48F LYS* 3.4 12.5 - - - +
50F VAL* 1.3 78.0 - - - +
52F ASN* 1.3 62.9 + - - +
55F ASN* 2.8 39.9 + - - +
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Residues in contact with ASN 52 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LYS* 2.8 28.5 + - - +
49F GLU* 3.8 7.3 + - + +
51F ASP* 1.3 79.4 + - - +
53F LEU* 1.3 56.1 + - - +
55F ASN* 3.1 8.5 + - - +
56F ILE* 2.8 43.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.4 39.0 - - + -
25B LEU* 6.4 0.9 - - + -
28B PHE* 3.3 53.4 - - + -
49F GLU 2.9 18.5 + - - +
50F VAL 3.1 2.9 + - - +
52F ASN* 1.3 77.3 - - - +
54F TYR* 1.3 62.9 + - + +
56F ILE* 3.4 9.4 + - + +
57F GLU* 3.1 23.3 + - + +
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Residues in contact with TYR 54 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.5 32.7 - - + +
28B PHE* 4.3 19.7 - + - -
102E LEU* 3.5 29.6 - - + -
105E ASP* 2.5 28.4 + - + -
106E ARG* 3.3 49.6 - - + +
109E ALA* 4.3 7.7 - - + +
50F VAL* 3.2 26.4 + - + +
53F LEU* 1.3 76.4 - - + +
55F ASN* 1.3 68.2 + - - +
57F GLU* 3.1 8.8 + - + +
58F ILE* 2.9 30.0 + - + +
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Residues in contact with ASN 55 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ARG* 2.9 34.5 + - - +
51F ASP* 2.8 28.8 + - - +
52F ASN* 3.1 11.3 + - - +
54F TYR* 1.3 76.0 - - - +
56F ILE* 1.3 62.2 + - + +
58F ILE* 3.0 9.0 + - - +
59F LEU* 2.8 27.3 + - - +
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Residues in contact with ILE 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ASN* 2.8 27.0 + - + +
53F LEU* 3.4 13.9 - - + +
54F TYR 3.3 0.2 - - - -
55F ASN* 1.3 71.0 - - - +
57F GLU* 1.3 70.4 + - - +
59F LEU* 3.4 14.2 + - + +
60F ARG* 3.1 51.1 + - + +
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Residues in contact with GLU 57 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 5.7 1.5 - - - +
24B PHE* 3.8 33.0 - - + -
25B LEU* 5.1 9.0 - - + -
102E LEU* 4.4 14.4 - - + -
53F LEU* 3.1 15.8 + - + +
54F TYR* 3.1 12.6 + - + +
56F ILE* 1.3 82.3 - - - +
58F ILE* 1.3 63.8 + - - +
60F ARG* 3.1 50.5 + - - +
61F LEU* 3.3 24.3 + - + +
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Residues in contact with ILE 58 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E GLY* 4.6 8.5 - - - +
102E LEU* 3.6 29.2 - - + +
103E LYS* 3.6 48.9 - - + +
106E ARG* 4.9 3.1 - - - +
54F TYR* 2.9 25.3 + - + +
55F ASN* 3.6 12.1 - - - +
57F GLU* 1.3 75.6 - - - +
59F LEU* 1.3 61.7 + - - +
61F LEU* 3.9 10.6 + - - +
66F ARG* 3.9 25.5 - - - +
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Residues in contact with LEU 59 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ASN 2.8 16.1 + - - +
56F ILE* 3.7 15.5 - - + +
58F ILE* 1.3 80.5 - - - +
60F ARG* 1.3 61.1 + - - +
61F LEU 3.6 5.4 + - - +
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Residues in contact with ARG 60 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 5.6 5.7 - - - -
56F ILE* 3.1 33.6 + - + +
57F GLU* 3.1 36.9 + - - +
59F LEU* 1.3 76.1 - - - +
61F LEU* 1.3 66.4 + - + +
62F PRO* 3.4 7.1 - - - +
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E LEU* 3.4 35.4 - - + -
99E GLY* 4.8 2.0 - - - +
102E LEU* 4.0 21.1 - - + -
57F GLU* 3.3 19.7 + - + +
58F ILE* 4.1 6.3 - - - +
59F LEU 3.4 7.1 - - - +
60F ARG* 1.3 78.4 - - + +
62F PRO* 1.3 74.8 - - + +
63F LYS 3.9 0.5 + - - -
65F LEU* 4.8 5.6 - - + -
66F ARG* 3.8 39.2 - - + +
73F TYR* 4.9 9.6 - - - +
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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