Contacts of the helix formed by residues 55 - 81 (chain B) in PDB entry 6VW1
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 THR 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B TYR* 4.2 1.6 - - - -
53B ASN* 2.9 29.3 + - - +
54B ILE* 1.3 81.1 - - - +
56B GLU* 1.3 62.2 + - - +
57B GLU* 3.8 8.7 + - - +
58B ASN* 3.0 28.1 + - - +
59B VAL* 2.9 29.0 + - - +
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Residues in contact with GLU 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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55B THR* 1.3 73.8 - - - +
57B GLU* 1.3 67.8 + - + +
59B VAL* 3.1 20.3 - - - +
60B GLN* 2.9 49.9 + - - +
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Residues in contact with GLU 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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55B THR* 3.4 7.4 - - - +
56B GLU* 1.3 78.1 - - + +
58B ASN* 1.3 61.8 + - - +
60B GLN* 3.8 6.5 - - - +
61B ASN* 2.9 41.9 + - - +
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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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46B ALA 4.3 2.1 - - - +
49B ASN* 3.1 29.7 + - - +
50B TYR* 3.8 12.0 - - - +
53B ASN* 2.5 46.4 + - - +
55B THR* 3.0 18.3 + - - +
56B GLU 3.2 0.8 - - - -
57B GLU* 1.3 78.3 - - - +
59B VAL* 1.3 59.4 + - - +
61B ASN* 3.4 9.2 + - - +
62B MET* 2.9 30.0 + - - +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 3.5 33.6 - - + +
55B THR 2.9 13.0 + - - +
56B GLU* 3.1 38.8 - - - +
58B ASN* 1.3 76.1 - - - +
60B GLN* 1.3 60.5 + - + +
62B MET* 3.4 16.6 + - + +
63B ASN* 2.9 41.6 + - - +
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Residues in contact with GLN 60 (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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56B GLU* 2.9 41.7 + - - +
57B GLU* 3.8 6.5 - - - +
59B VAL* 1.3 83.2 - - + +
61B ASN* 1.3 57.8 + - - +
63B ASN* 3.4 7.1 + - - +
64B ASN* 2.9 39.0 + - - +
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Residues in contact with ASN 61 (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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46B ALA* 3.7 10.6 - - + +
49B ASN* 6.5 0.7 - - + -
57B GLU* 2.9 30.9 + - - +
58B ASN* 3.8 9.0 + - - +
60B GLN* 1.3 74.8 - - - +
62B MET* 1.3 66.6 + - - +
64B ASN* 3.3 13.2 + - - +
65B ALA* 3.0 25.8 + - - +
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Residues in contact with MET 62 (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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43B SER* 5.3 1.7 + - - +
46B ALA* 3.5 19.4 - - - +
47B SER* 3.6 33.4 - - - +
50B TYR* 3.8 27.6 - - + -
51B ASN* 4.6 2.7 - - - -
58B ASN 2.9 17.6 + - - +
59B VAL* 3.6 23.6 - - + +
60B GLN 3.3 0.2 - - - -
61B ASN* 1.3 77.9 - - - +
63B ASN* 1.3 73.8 + - - +
65B ALA* 3.4 1.6 + - - +
66B GLY* 2.9 26.3 + - - -
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Residues in contact with ASN 63 (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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59B VAL* 2.9 33.9 + - - +
60B GLN* 3.9 6.1 - - - +
62B MET* 1.3 86.2 - - - +
64B ASN* 1.3 62.4 + - - +
66B GLY* 3.8 1.5 - - - +
67B ASP* 2.9 44.4 + - - +
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Residues in contact with ASN 64 (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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60B GLN* 2.9 25.2 + - - +
61B ASN* 3.5 16.1 + - - +
63B ASN* 1.3 78.5 - - - +
65B ALA* 1.3 63.3 + - - +
67B ASP* 3.7 7.8 - - - +
68B LYS* 3.0 24.0 + - - +
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Residues in contact with ALA 65 (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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39B LEU 5.3 0.7 - - - +
42B GLN* 4.0 8.7 - - + +
43B SER* 3.6 30.2 + - - +
46B ALA* 3.8 12.6 - - + -
61B ASN 3.0 16.5 + - - +
62B MET 3.9 0.9 - - - +
64B ASN* 1.3 76.0 - - - +
66B GLY* 1.3 58.8 + - - +
68B LYS* 3.3 8.2 + - - +
69B TRP* 2.9 29.6 + - - +
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Residues in contact with GLY 66 (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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43B SER* 4.1 11.8 + - - -
62B MET 2.9 17.3 + - - -
63B ASN* 3.8 1.8 - - - -
65B ALA* 1.3 77.7 - - - +
67B ASP* 1.3 58.7 + - - +
69B TRP* 3.4 5.8 + - - +
70B SER* 2.8 35.1 + - - -
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Residues in contact with ASP 67 (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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63B ASN* 2.9 34.9 + - - +
64B ASN* 3.7 7.4 + - - +
66B GLY* 1.3 74.8 - - - +
68B LYS* 1.3 65.7 + - - +
70B SER* 3.3 6.1 + - - -
71B ALA* 2.9 26.2 + - - +
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Residues in contact with LYS 68 (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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39B LEU* 3.9 33.5 - - + +
64B ASN 3.0 13.8 + - - +
65B ALA* 3.7 10.5 - - - +
67B ASP* 1.3 78.3 - - - +
69B TRP* 1.3 57.5 + - - +
71B ALA* 3.3 5.7 + - - +
72B PHE* 3.0 28.1 + - - +
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Residues in contact with TRP 69 (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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32B PHE* 5.1 0.4 - + - -
36B ALA* 3.6 33.9 - - + -
39B LEU* 3.8 13.0 - - + +
40B PHE* 3.7 36.7 - + + -
43B SER* 4.4 18.2 - - - -
65B ALA 2.9 18.3 + - - +
66B GLY* 3.7 6.3 - - - +
67B ASP 3.3 0.2 - - - -
68B LYS* 1.3 77.4 - - - +
70B SER* 1.3 63.9 + - - +
72B PHE* 3.3 17.1 + + - +
73B LEU* 2.9 60.8 + - + +
390B PHE* 3.6 32.1 - + - -
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Residues in contact with SER 70 (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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66B GLY 2.8 22.4 + - - -
67B ASP* 3.8 7.4 + - - -
69B TRP* 1.3 81.9 - - - +
71B ALA* 1.3 58.2 + - - +
73B LEU* 3.2 8.5 + - - +
74B LYS* 2.9 29.6 + - - +
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Residues in contact with ALA 71 (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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67B ASP 2.9 18.2 + - - +
68B LYS* 3.7 6.5 - - + +
70B SER* 1.3 73.7 - - - +
72B PHE* 1.3 65.4 + - - +
74B LYS* 3.3 5.4 + - - +
75B GLU* 2.9 26.5 + - - +
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Residues in contact with PHE 72 (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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32B PHE* 3.6 29.8 - + - -
35B GLU* 3.9 35.2 - - + -
36B ALA* 3.6 20.4 - - + -
39B LEU* 3.6 22.4 - - + -
68B LYS 3.0 14.6 + - - +
69B TRP* 3.5 25.8 - + - +
71B ALA* 1.3 75.8 - - - +
73B LEU* 1.3 61.5 + - + +
75B GLU* 3.4 12.7 + - - +
76B GLN* 2.9 67.7 + - + +
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Residues in contact with LEU 73 (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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32B PHE* 4.3 23.1 - - + -
69B TRP* 2.9 57.6 + - + +
70B SER* 3.2 8.3 + - - +
72B PHE* 1.3 80.1 - - + +
74B LYS* 1.3 57.6 + - - +
76B GLN* 3.4 3.0 + - - +
77B SER* 2.9 29.1 + - - -
100B LEU* 4.6 9.1 - - + +
390B PHE* 6.1 0.2 - - + -
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Residues in contact with LYS 74 (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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70B SER 2.9 15.8 + - - +
71B ALA* 3.9 5.4 - - - +
73B LEU* 1.3 72.7 - - - +
75B GLU* 1.3 67.3 + - - +
77B SER* 3.2 9.5 + - - -
78B THR* 3.0 47.4 + - + +
81B GLN* 5.2 1.0 + - - +
103B ASN* 4.3 8.5 + - - -
106B SER* 3.5 39.8 + - - +
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Residues in contact with GLU 75 (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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71B ALA 2.9 17.3 + - - +
72B PHE* 3.7 14.6 - - - +
74B LYS* 1.3 76.9 - - - +
76B GLN* 1.3 73.6 + - - +
78B THR* 2.7 24.2 + - - +
79B LEU* 3.0 24.1 + - + +
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Residues in contact with GLN 76 (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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28B PHE* 3.2 31.7 - - + -
31B LYS* 6.0 3.1 - - - +
32B PHE* 3.7 27.3 - - + +
35B GLU* 6.0 0.8 - - - +
72B PHE* 2.9 58.1 + - + +
73B LEU 3.9 3.4 - - - +
75B GLU* 1.3 90.4 + - - +
77B SER* 1.3 57.1 + - - +
79B LEU* 3.7 12.5 - - - +
80B ALA* 2.8 32.4 + - - +
100B LEU* 4.4 5.8 - - + -
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Residues in contact with SER 77 (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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73B LEU 2.9 18.9 + - - -
74B LYS* 3.5 15.1 + - - +
76B GLN* 1.3 74.1 - - - +
78B THR* 1.3 65.9 + - - +
80B ALA* 3.3 1.3 + - - +
81B GLN* 3.0 44.7 + - - +
100B LEU* 3.4 27.8 + - - +
101B GLN 4.3 0.2 + - - -
102B GLN 3.9 11.2 + - - -
103B ASN* 4.5 3.3 + - - -
106B SER* 5.3 0.7 + - - -
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Residues in contact with THR 78 (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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74B LYS* 3.0 42.9 + - + +
75B GLU* 2.7 25.1 + - - +
77B SER* 1.3 75.7 - - - +
79B LEU* 1.3 66.6 + - - +
81B GLN* 3.9 20.1 + - - +
82B MET* 3.4 21.0 - - - +
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Residues in contact with LEU 79 (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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28B PHE* 3.9 24.7 - - + -
75B GLU* 3.0 28.4 + - + +
76B GLN* 3.7 16.6 - - - +
77B SER 3.1 0.2 - - - -
78B THR* 1.3 80.8 + - - +
80B ALA* 1.3 60.0 + - - +
82B MET* 3.0 39.8 + - + +
83B TYR* 4.2 5.9 - - - -
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Residues in contact with ALA 80 (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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28B PHE* 3.5 24.9 - - + -
76B GLN 2.8 21.1 + - - +
77B SER 4.0 2.9 - - - +
79B LEU* 1.3 68.5 - - - +
81B GLN* 1.3 62.6 + - - +
82B MET 3.0 6.9 + - - -
83B TYR* 3.4 16.6 + - - -
97B LEU* 4.0 10.2 - - + +
100B LEU* 3.9 22.9 - - + -
101B GLN* 3.2 20.4 + - + -
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Residues in contact with GLN 81 (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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74B LYS* 5.2 1.5 + - - +
77B SER* 3.0 33.0 + - - +
78B THR* 4.1 17.0 + - - +
79B LEU 3.2 0.8 - - - -
80B ALA* 1.3 76.4 - - - +
82B MET* 1.3 60.0 + - + +
83B TYR 3.3 5.1 + - - +
101B GLN* 3.5 36.7 + - + +
103B ASN* 2.9 31.7 + - - +
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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
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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