Contacts of the helix formed by residues 48 - 71 (chain a) in PDB entry 5GJQ
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 48 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47a GLY* 1.3 72.0 - - - -
49a ALA* 1.3 65.7 + - - +
50a ALA* 3.5 11.3 + - - +
51a ASP* 3.1 34.4 + - - -
52a THR* 3.1 24.9 + - - +
95a MET* 2.7 32.0 + - - +
116b HIS* 5.9 0.3 - - - +
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Residues in contact with ALA 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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20a THR* 5.4 12.6 - - + -
45a ARG* 5.2 2.2 - - - +
47a GLY 3.3 5.4 + - - +
48a SER* 1.3 70.3 + - - +
50a ALA* 1.3 66.3 + - - +
52a THR* 3.1 7.3 + - - -
53a GLN* 3.0 36.5 + - - +
118b SER* 3.5 24.7 - - - +
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Residues in contact with ALA 50 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48a SER* 3.3 8.2 + - - +
49a ALA* 1.3 78.6 - - - +
51a ASP* 1.3 67.2 + - - +
53a GLN* 3.9 1.7 - - - +
54a ALA* 3.0 27.5 + - - +
88b PHE* 3.8 13.8 - - + -
116b HIS* 3.3 41.9 - - + +
117b GLY 4.7 2.6 - - - +
118b SER* 4.0 11.9 - - - +
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Residues in contact with ASP 51 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48a SER* 3.1 25.9 + - - +
49a ALA 3.2 0.2 - - - -
50a ALA* 1.3 84.1 - - - +
52a THR* 1.3 63.6 + - - +
54a ALA* 3.8 0.9 - - - +
55a VAL* 2.9 30.8 + - - +
93a ASP 3.8 6.6 - - - +
94a LEU* 3.5 25.9 - - + +
95a MET* 2.9 24.7 + - - +
96a ALA* 4.3 14.8 - - + -
88b PHE* 3.3 24.2 - - - -
91b GLN* 5.0 2.1 - - - +
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Residues in contact with THR 52 (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 ARG* 3.3 31.2 + - - +
46a SER 3.2 33.6 - - - +
47a GLY 5.0 0.5 + - - -
48a SER 3.1 16.0 + - - +
49a ALA* 3.1 8.0 + - - -
51a ASP* 1.3 76.9 - - - +
53a GLN* 1.3 59.9 + - - +
55a VAL* 4.1 3.0 - - - +
56a ALA* 2.9 31.9 + - - +
96a ALA* 3.7 19.1 - - + -
98a ILE* 3.8 13.1 - - + +
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Residues in contact with GLN 53 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31a THR* 6.3 1.0 - - - +
45a ARG* 3.5 28.0 - - - +
49a ALA* 3.0 25.2 + - - +
50a ALA* 3.9 2.5 - - - +
52a THR* 1.3 75.0 + - - +
54a ALA* 1.3 67.7 + - - +
56a ALA* 3.4 4.9 + - - +
57a ASP* 3.0 31.0 + - - +
84b LYS* 3.5 24.1 + - - +
117b GLY 5.2 0.7 - - - +
118b SER* 3.1 15.5 - - - -
119b THR 2.9 45.4 + - - +
120b ASP* 4.5 4.6 + - - -
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Residues in contact with ALA 54 (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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103B TYR* 5.3 0.7 + - - -
50a ALA 3.0 17.6 + - - +
51a ASP 3.8 2.2 - - - +
53a GLN* 1.3 78.2 - - - +
55a VAL* 1.3 63.9 + - + +
57a ASP* 3.2 8.0 + - - +
58a ALA* 3.0 23.7 + - - +
86a MET* 5.4 1.3 - - + -
84b LYS* 5.9 1.1 - - - +
88b PHE* 4.2 33.4 - - + -
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Residues in contact with VAL 55 (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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51a ASP 2.9 22.7 + - - +
52a THR* 4.1 3.6 - - - +
54a ALA* 1.3 77.0 - - + +
56a ALA* 1.3 64.3 + - - +
58a ALA* 3.2 1.1 + - - +
59a VAL* 2.9 28.2 + - + +
83a PHE* 3.5 28.3 - - + -
86a MET* 3.9 37.0 - - + -
87a CYS* 4.4 10.8 - - - -
94a LEU* 4.1 26.9 - - + -
96a ALA* 5.5 1.3 - - + -
98a ILE* 5.8 1.8 - - + -
88b PHE* 6.1 1.3 - - + -
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Residues in contact with ALA 56 (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 THR* 4.3 16.2 - - + -
37a ILE* 4.1 2.2 - - + +
43a CYS* 4.2 22.9 - - - -
45a ARG* 4.4 5.6 - - - -
52a THR 2.9 20.0 + - - +
53a GLN* 3.6 5.2 - - - +
55a VAL* 1.3 78.1 - - - +
57a ASP* 1.3 58.2 + - - +
59a VAL* 3.4 1.2 + - - +
60a THR* 2.8 34.0 + - - -
83a PHE* 3.8 14.3 - - + -
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Residues in contact with ASP 57 (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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103B TYR* 4.3 6.9 - - + -
53a GLN* 3.0 22.2 + - - +
54a ALA* 3.6 6.6 - - - +
56a ALA* 1.3 78.6 - - - +
58a ALA* 1.3 63.1 + - - +
60a THR* 3.2 9.2 + - - +
61a TYR* 3.0 22.0 + - - +
81b ARG* 2.8 45.7 + - - +
84b LYS* 4.4 14.9 + - - +
85b GLN* 5.4 5.9 + - - +
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Residues in contact with ALA 58 (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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103B TYR* 3.8 25.7 + - + +
54a ALA 3.0 16.6 + - - +
55a VAL 3.5 4.3 - - - +
57a ASP* 1.3 76.4 - - - +
59a VAL* 1.3 62.6 + - - +
61a TYR* 3.2 4.9 - - - +
62a GLN* 3.0 31.0 + - - +
86a MET* 3.7 29.4 - - + -
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Residues in contact with VAL 59 (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 ILE* 4.1 10.8 - - + -
55a VAL* 2.9 25.3 + - + +
56a ALA 3.9 1.6 - - - +
58a ALA* 1.3 78.3 - - + +
60a THR* 1.3 64.1 + - - +
62a GLN* 3.9 8.1 - - - +
63a LEU* 2.9 25.2 + - + +
79a ALA* 4.0 4.7 - - - +
82a LEU* 4.0 24.7 - - + +
83a PHE* 3.5 59.0 - - + +
86a MET* 5.1 3.6 - - + -
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Residues in contact with THR 60 (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 THR* 5.5 0.9 - - - +
36a PRO 4.1 4.7 + - - +
37a ILE* 3.7 42.8 + - - +
38a HIS* 5.6 0.2 - - - -
56a ALA* 2.8 25.3 + - - +
57a ASP* 3.2 11.8 + - - -
59a VAL* 1.3 76.6 - - - +
61a TYR* 1.3 56.9 + - - +
63a LEU* 3.9 0.5 - - - +
64a GLY* 2.9 27.9 + - - -
81b ARG* 6.1 1.8 - - - +
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Residues in contact with TYR 61 (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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96B TYR* 3.3 20.4 + + - -
99B ALA* 3.9 25.5 - - + +
100B ASN* 2.7 34.5 + - - -
103B TYR* 3.0 48.2 - + + -
57a ASP 3.0 6.0 + - - +
58a ALA* 3.2 8.3 - - + +
60a THR* 1.3 77.3 - - - +
62a GLN* 1.3 84.7 + - + +
64a GLY* 3.2 2.8 + - - -
65a PHE* 3.1 26.9 + + + +
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Residues in contact with GLN 62 (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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102X PHE* 5.2 6.6 - - + -
58a ALA* 3.0 19.0 + - - +
59a VAL* 4.0 7.9 - - - +
61a TYR* 1.3 98.1 - - + +
63a LEU* 1.3 57.6 + - - +
65a PHE* 3.4 6.6 + - - +
66a HIS* 2.9 28.0 + - - +
82a LEU* 3.8 38.7 - - + +
86a MET* 4.3 20.4 - - - +
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Residues in contact with LEU 63 (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 ILE* 3.5 28.9 - - + +
38a HIS* 4.4 18.9 - - + -
41a ILE* 4.4 6.3 - - + -
59a VAL* 2.9 16.1 + - + +
60a THR 4.1 2.0 - - - +
62a GLN* 1.3 76.0 - - - +
64a GLY* 1.3 61.5 + - - +
66a HIS* 3.6 7.4 + - - +
67a SER* 2.9 28.8 + - - -
74a PRO* 4.1 18.2 - - + -
78a THR* 3.6 31.0 - - + -
79a ALA* 3.7 22.2 - - + +
82a LEU* 3.8 13.0 - - + +
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Residues in contact with GLY 64 (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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102B LYS* 6.1 3.8 - - - -
38a HIS* 4.5 10.7 - - - -
60a THR 2.9 19.7 + - - -
61a TYR 3.7 1.1 - - - -
63a LEU* 1.3 73.2 - - - +
65a PHE* 1.3 65.1 + - - +
67a SER* 2.9 21.6 + - - -
68a ILE* 3.0 16.2 + - - +
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Residues in contact with PHE 65 (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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92B GLN* 4.0 21.8 - - - -
95B ARG* 3.8 25.1 - - + -
96B TYR* 3.7 37.7 - + + -
99B ALA* 4.4 16.3 - - + +
114X ARG* 5.7 4.7 - - - -
61a TYR* 3.1 18.6 + + + +
62a GLN* 3.7 9.6 - - - +
64a GLY* 1.3 74.3 - - - +
66a HIS* 1.3 59.1 + - - +
68a ILE* 3.4 7.1 + - + +
69a GLU* 2.9 53.8 + - + +
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Residues in contact with HIS 66 (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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98X PHE* 3.3 28.7 - + - -
102X PHE* 4.2 20.3 - + + -
104X TYR* 3.0 28.7 + - - -
110X HIS* 4.8 7.4 - + - -
62a GLN 2.9 17.9 + - - +
63a LEU* 3.6 11.8 - - + +
64a GLY 3.2 0.2 - - - -
65a PHE* 1.3 78.0 - - - +
67a SER* 1.3 66.7 + - - +
69a GLU* 3.3 5.4 + - - +
70a LEU* 3.0 43.3 + - + +
74a PRO* 5.2 7.7 - - + +
75a LEU 6.1 0.4 - - - -
78a THR* 4.0 23.6 - - + +
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Residues in contact with SER 67 (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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74B GLU* 5.1 2.9 + - - -
38a HIS* 3.3 26.5 + - - -
63a LEU 2.9 13.9 + - - -
64a GLY* 2.9 15.1 + - - -
66a HIS* 1.3 81.9 + - - +
68a ILE* 1.3 60.4 + - - +
70a LEU* 3.4 2.0 + - - -
71a ASN* 2.8 29.5 + - - -
72a GLU 3.5 21.7 + - - +
74a PRO* 4.0 12.8 - - - -
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Residues in contact with ILE 68 (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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71B LYS* 3.8 32.5 - - + +
72B ILE 3.9 11.2 - - - +
73B THR* 4.4 6.7 - - + -
74B GLU* 3.8 37.7 - - + +
95B ARG* 3.6 37.6 + - + +
102B LYS* 6.0 3.4 - - - +
64a GLY 3.0 14.6 + - - +
65a PHE* 3.7 10.1 - - + +
67a SER* 1.3 81.9 + - - +
69a GLU* 1.3 65.0 + - - +
71a ASN* 3.2 15.5 + - - +
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Residues in contact with GLU 69 (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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92B GLN* 3.8 34.2 + - - +
95B ARG* 4.0 15.0 + - - +
110X HIS* 2.8 42.9 + - + +
113X ASP* 4.9 14.1 - - - +
114X ARG* 3.8 18.0 + - - +
65a PHE* 2.9 40.1 + - + +
66a HIS* 3.3 6.9 + - - +
68a ILE* 1.3 77.3 - - - +
70a LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 70 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104X TYR* 3.6 10.5 - - - +
107X PRO* 4.0 16.6 - - + -
109X LYS* 6.1 1.3 - - + -
110X HIS* 3.3 50.7 - - + +
66a HIS* 3.0 48.7 + - + +
67a SER* 4.2 2.2 - - - +
69a GLU* 1.3 78.2 - - - +
71a ASN* 1.3 70.2 + - - +
72a GLU* 3.3 33.3 + - + +
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Residues in contact with ASN 71 (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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71B LYS* 4.8 32.0 + - - +
95B ARG* 6.2 0.2 - - - +
229B ILE* 6.1 3.2 - - - +
67a SER 2.8 13.4 + - - -
68a ILE* 3.2 11.3 + - - +
70a LEU* 1.3 80.1 - - - +
72a GLU* 1.3 61.1 + - - +
73a PRO* 4.7 0.7 - - - +
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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