Contacts of the helix formed by residues 22 - 50 (chain A) in PDB entry 1U5T
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 LYS 22 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.4 3.3 - - - +
21A ASN* 1.3 91.7 + - - +
23A THR* 1.3 65.9 + - - +
24A ILE* 3.7 2.1 - - - +
25A LEU* 3.7 18.5 - - - +
26A GLU* 3.4 16.3 - - - +
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Residues in contact with THR 23 (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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22A LYS* 1.3 76.1 - - - +
24A ILE* 1.3 54.6 + - - +
25A LEU 2.5 20.4 + - - -
26A GLU* 3.1 31.6 + - + +
27A LYS* 2.8 47.3 - - + +
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Residues in contact with ILE 24 (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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20A VAL 5.7 2.5 - - - +
21A ASN* 3.9 27.4 - - - +
22A LYS 3.7 2.1 - - - +
23A THR* 1.3 74.3 - - - +
25A LEU* 1.3 58.6 + - + +
27A LYS* 4.2 21.4 - - + +
28A GLN* 3.2 19.4 + - - +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 3.4 25.8 - - - +
22A LYS* 3.7 20.4 - - - +
23A THR 2.5 7.3 + - - -
24A ILE* 1.3 81.5 - - + +
26A GLU* 1.3 61.2 + - + +
27A LYS 2.6 15.7 + - - -
28A GLN* 2.7 32.3 + - - +
29A SER* 3.2 10.1 + - - -
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.4 17.2 - - - +
23A THR* 3.1 39.7 + - + +
25A LEU* 1.3 83.6 - - + +
27A LYS* 1.3 62.0 + - - +
29A SER* 3.4 23.0 - - - -
30A VAL* 4.3 8.5 + - - +
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 2.8 47.6 - - + +
24A ILE* 4.2 17.8 - - + +
25A LEU 2.6 2.0 + - - +
26A GLU* 1.3 77.2 - - + +
28A GLN* 1.3 62.8 + - + +
29A SER 3.0 1.9 + - - -
30A VAL* 2.8 33.2 - - + +
31A GLU* 3.9 2.1 + - - +
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Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.2 25.3 + - - +
25A LEU* 2.7 22.2 + - + +
27A LYS* 1.3 75.2 - - + +
29A SER* 1.3 67.1 + - - +
31A GLU* 3.5 5.3 + - - +
32A LEU* 2.7 26.4 + - + +
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU 3.2 7.5 + - - -
26A GLU* 3.4 22.1 + - - -
27A LYS 3.0 0.4 - - - -
28A GLN* 1.3 76.1 - - - +
30A VAL* 1.3 56.9 + - - -
32A LEU* 2.4 34.5 + - - +
33A ARG* 2.8 13.0 + - - -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLU 4.6 7.2 - - - +
27A LYS* 2.8 28.3 - - - +
29A SER* 1.3 77.2 - - - +
31A GLU* 1.3 67.5 + - + +
33A ARG* 3.4 24.2 - - - +
34A ASP* 3.5 11.4 + - - +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS 4.8 2.5 - - - +
28A GLN* 3.5 7.1 + - - +
29A SER 2.9 1.6 + - - -
30A VAL* 1.3 85.7 - - + +
32A LEU* 1.3 67.9 + - - +
34A ASP* 2.7 38.7 + - - +
35A GLN* 2.8 7.8 + - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN* 2.7 17.5 + - + +
29A SER* 2.4 29.7 + - - +
31A GLU* 1.3 68.4 - - - +
33A ARG* 1.3 66.0 + - - +
35A GLN* 2.6 45.7 + - + +
36A LEU* 3.0 22.5 + - + -
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER 2.8 12.5 + - - +
30A VAL* 3.4 18.2 - - - +
32A LEU* 1.3 72.6 - - - +
34A ASP* 1.3 52.1 + - - +
36A LEU* 3.1 7.5 + - - +
37A MET* 2.6 49.1 + - + +
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL 3.7 10.2 - - - +
31A GLU* 2.7 38.0 + - - +
33A ARG* 1.3 73.8 - - - +
35A GLN* 1.3 47.7 + - - +
36A LEU 2.5 1.6 + - - -
37A MET* 2.4 16.9 + - - +
38A VAL* 2.4 45.8 + - + +
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Residues in contact with GLN 35 (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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31A GLU 2.8 9.1 + - - +
32A LEU* 2.6 34.3 + - + +
34A ASP* 1.3 71.0 - - - +
36A LEU* 1.3 59.5 + - + +
38A VAL* 3.1 12.0 - - + +
39A PHE* 2.8 28.9 + - - +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.0 25.5 + - + +
33A ARG* 3.5 7.6 - - - +
34A ASP 2.5 4.0 + - - -
35A GLN* 1.3 75.1 - - + +
37A MET* 1.3 54.6 + - - +
38A VAL 2.6 14.7 + - - -
39A PHE* 3.0 15.4 + - + +
40A GLN* 3.0 29.8 + - - +
71A ILE* 4.1 35.9 - - + +
73A ILE* 5.2 0.7 - - - +
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Residues in contact with MET 37 (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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33A ARG* 2.6 29.4 + - + +
34A ASP* 2.4 20.9 + - - +
36A LEU* 1.3 70.9 - - - +
38A VAL* 1.3 48.5 + - + +
40A GLN* 4.1 14.7 - - - +
41A GLU* 2.8 51.5 + - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 2.4 49.8 + - + +
35A GLN* 3.1 13.0 - - + +
37A MET* 1.3 70.8 - - - +
39A PHE* 1.3 54.7 + - - +
40A GLN 2.4 18.8 + - - -
41A GLU* 2.7 19.7 + - + +
42A ARG* 2.6 41.1 + - + +
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Residues in contact with PHE 39 (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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35A GLN 2.8 14.9 + - - +
36A LEU* 3.7 18.2 - - + +
38A VAL* 1.3 79.1 - - - +
40A GLN* 1.3 50.1 + - - +
42A ARG* 3.0 26.4 - - + +
43A LEU* 2.6 64.0 + - + +
67A MET* 5.0 12.3 - - + -
71A ILE* 3.7 26.9 - - + -
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Residues in contact with GLN 40 (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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36A LEU* 3.0 17.6 + - - +
37A MET* 4.1 14.9 - - - +
38A VAL 2.4 10.9 + - - -
39A PHE* 1.3 68.4 - - - +
41A GLU* 1.3 57.2 + - - +
42A ARG 2.4 14.5 + - - -
43A LEU* 2.5 18.7 + - - +
44A VAL* 2.7 16.2 + - + +
73A ILE* 3.0 46.7 - - + +
78A LEU* 4.0 17.3 - - + +
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Residues in contact with GLU 41 (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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37A MET* 2.8 41.8 + - - +
38A VAL* 2.7 24.1 + - + +
40A GLN* 1.3 77.2 - - - +
42A ARG* 1.3 55.9 + - - +
44A VAL* 2.6 27.9 - - - +
45A GLU* 3.8 11.3 + - - +
81A ARG* 4.0 20.2 + - - +
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Residues in contact with ARG 42 (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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38A VAL* 2.6 27.1 + - + +
39A PHE* 3.0 34.4 - - + +
40A GLN 2.4 5.8 + - - -
41A GLU* 1.3 72.8 - - - +
43A LEU* 1.3 55.8 + - + +
45A GLU* 2.5 55.7 + - + +
46A PHE* 3.4 5.1 + - + -
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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
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39A PHE* 2.6 58.3 + - + +
40A GLN* 2.5 14.0 + - - +
42A ARG* 1.3 73.1 - - + +
44A VAL* 1.3 61.7 + - - +
45A GLU 3.2 0.7 + - - -
46A PHE* 3.5 9.6 + - + +
47A ALA* 3.3 21.8 + - - +
64A PHE* 3.4 30.7 - - + -
67A MET* 3.9 25.1 - - + -
68A CYS* 4.3 9.6 - - - -
71A ILE* 3.5 16.6 - - + -
73A ILE* 5.3 1.3 - - + -
78A LEU* 3.9 17.0 - - + -
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Residues in contact with VAL 44 (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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40A GLN* 2.7 16.9 + - + +
41A GLU* 2.6 41.7 - - - +
43A LEU* 1.3 72.9 - - - +
45A GLU* 1.3 52.0 + - + +
47A ALA* 3.4 6.5 - - - +
48A LYS* 2.4 41.5 + - + +
78A LEU* 3.6 42.8 - - + +
81A ARG* 3.9 34.3 - - + +
85A LEU* 4.4 4.7 - - + +
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Residues in contact with GLU 45 (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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41A GLU 3.8 10.6 - - - +
42A ARG* 2.5 51.5 + - + +
44A VAL* 1.3 71.4 - - + +
46A PHE* 1.3 54.5 + - + +
47A ALA 2.4 7.6 + - - -
48A LYS* 2.4 34.9 + - + +
49A LYS* 2.7 14.6 + - - +
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Residues in contact with PHE 46 (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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42A ARG* 3.4 7.0 + - + +
43A LEU* 3.5 16.6 + - + +
45A GLU* 1.3 80.9 - - + +
47A ALA* 1.3 55.6 + - - +
49A LYS* 5.0 1.1 - - - -
50A HIS* 2.7 42.2 + + - -
60A PHE* 3.2 42.4 - + - -
63A LYS* 4.4 13.7 - - - -
64A PHE* 4.8 9.9 - + + -
67A MET* 4.0 36.6 - - + -
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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
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43A LEU 3.3 10.8 + - - +
44A VAL* 3.4 9.4 - - - +
45A GLU 2.4 3.4 + - - -
46A PHE* 1.3 75.8 - - - +
48A LYS* 1.3 55.1 + - - +
49A LYS 2.6 17.2 + - - -
50A HIS* 3.0 22.0 + - - +
51A ASN 3.7 0.9 + - - -
54A LEU* 4.3 15.0 - - + +
60A PHE* 6.2 0.4 - - - -
64A PHE* 4.0 24.4 - - + -
85A LEU* 4.1 22.1 - - + +
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Residues in contact with LYS 48 (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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44A VAL* 2.4 30.3 + - + +
45A GLU* 2.4 30.0 + - + +
47A ALA* 1.3 68.3 - - - +
49A LYS* 1.3 53.1 + - - +
51A ASN* 2.5 34.0 + - - +
81A ARG* 6.3 1.6 - - + -
82A ASP* 2.9 47.0 - - + +
84A HIS* 3.7 22.4 - - - +
85A LEU* 4.5 16.6 - - + +
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Residues in contact with LYS 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 GLU 2.7 12.8 + - - +
46A PHE* 4.5 0.7 - - - -
47A ALA 2.6 4.4 + - - -
48A LYS* 1.3 68.3 - - - +
50A HIS* 1.3 78.1 + - + +
51A ASN* 2.4 35.4 + - - +
53A GLU* 4.3 12.3 + - - +
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Residues in contact with HIS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 2.7 38.4 + + - +
47A ALA* 3.0 8.5 + - - +
49A LYS* 1.3 89.7 - - + +
51A ASN* 1.3 53.1 + - - +
52A SER 2.7 17.5 + - - -
53A GLU* 2.8 29.4 - - + +
54A LEU* 3.0 21.2 + - + +
60A PHE* 3.0 42.0 - + + -
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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