Contacts of the helix formed by residues 73 - 101 (chain A) in PDB entry 3E8G
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 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.6 27.1 - - + +
46A GLU* 2.7 23.5 + - - +
71A PRO* 4.5 0.2 - - - +
72A GLN* 1.3 82.9 - - + +
74A ASP* 1.3 59.9 + - - +
75A PHE* 3.6 4.6 + - - -
76A GLY* 2.8 14.9 + - - -
77A LYS* 2.9 31.3 + - - +
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Residues in contact with ASP 74 (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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72A GLN 5.0 0.5 - - - +
73A THR* 1.3 71.8 - - - +
75A PHE* 1.3 65.2 + - - +
77A LYS* 3.2 23.9 + - - +
78A ILE* 2.9 38.2 + - + +
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.7 18.2 - + - -
45A VAL* 3.9 32.1 - - + -
73A THR* 3.9 7.6 - - - +
74A ASP* 1.3 79.5 - - - +
76A GLY* 1.3 57.5 + - - +
78A ILE* 3.4 10.2 + - + +
79A PHE* 2.9 35.7 + + + +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.6 20.1 - - - -
42A TYR* 5.2 0.2 - - - -
46A GLU* 3.4 20.4 - - - -
71A PRO* 3.7 8.5 - - - -
73A THR* 2.8 11.1 + - - -
75A PHE* 1.3 77.4 - - - +
77A LYS* 1.3 53.9 + - - +
79A PHE* 3.9 0.7 - - - +
80A THR* 2.7 37.8 + - - -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 3.2 37.7 - - + -
72A GLN* 3.9 14.0 + - - +
73A THR 2.9 17.4 + - - +
74A ASP* 3.2 24.4 + - - +
76A GLY* 1.3 74.8 - - - +
78A ILE* 1.3 66.7 + - + +
80A THR* 3.4 3.2 + - - -
81A ILE* 3.1 32.8 + - + +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 2.9 29.3 + - + +
75A PHE* 3.9 9.6 - - + +
77A LYS* 1.3 76.3 - - + +
79A PHE* 1.3 64.8 + - - +
81A ILE* 3.2 14.8 + - + +
82A LEU* 3.1 38.1 + - + +
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 4.5 10.8 - - - -
38A GLY* 4.4 4.9 - - - -
41A PHE* 3.4 60.3 - + + -
42A TYR* 3.5 18.2 - + - -
75A PHE* 2.9 24.7 + + + +
78A ILE* 1.3 79.5 - - - +
80A THR* 1.3 55.0 + - - +
82A LEU* 3.1 8.4 + - - +
83A TYR* 2.6 74.4 + + - +
503A MPD 3.1 32.8 - - + -
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 2.7 33.1 + - - +
56A PHE* 4.3 10.3 - - + -
60A THR* 4.1 13.0 - - + -
71A PRO* 3.8 13.4 - - + +
76A GLY 2.7 23.4 + - - -
77A LYS* 3.7 4.7 - - - -
78A ILE 3.3 0.2 - - - -
79A PHE* 1.3 76.6 - - - +
81A ILE* 1.3 58.6 + - + +
83A TYR* 3.6 2.6 - - + +
84A ILE* 2.9 54.1 + - + +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.1 23.0 + - + +
78A ILE* 3.5 13.2 - - + +
79A PHE 3.2 0.2 - - - -
80A THR* 1.3 78.0 - - - +
82A LEU* 1.3 69.2 + - + +
84A ILE* 3.4 8.4 + - + +
85A PHE* 3.3 47.2 + - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.1 29.4 + - + +
79A PHE* 3.7 8.5 - - - +
81A ILE* 1.3 81.0 - - + +
83A TYR* 1.3 65.8 + - - +
84A ILE 3.3 0.2 + - - -
85A PHE* 3.3 7.0 + - + +
86A ILE* 3.1 35.4 + - + +
503A MPD 4.2 42.2 - - + +
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 2.8 46.5 + - + -
35A LEU* 3.6 3.5 - - - -
37A SER* 4.9 3.6 - - - -
38A GLY* 3.6 13.1 - - - -
42A TYR* 3.9 17.9 - + - -
57A SER* 3.5 35.2 - - - -
60A THR* 4.8 7.2 - - + -
61A LEU* 3.5 36.8 - - + +
79A PHE* 2.6 44.6 + + + +
80A THR* 3.6 4.0 - - - +
82A LEU* 1.3 72.6 - - - +
84A ILE* 1.3 56.5 + - - +
86A ILE* 5.0 0.7 - - + -
87A GLY* 2.8 31.2 + - - -
503A MPD 4.1 13.2 - - + +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.6 31.9 - - + +
61A LEU* 4.0 6.3 - - + -
63A THR* 6.4 2.5 - - + -
80A THR* 2.9 39.3 + - + +
81A ILE* 3.6 8.7 - - + +
82A LEU 3.2 0.2 - - - -
83A TYR* 1.3 76.4 - - - +
85A PHE* 1.3 72.8 + - + +
88A ILE* 3.0 38.7 + - + +
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Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.3 40.1 + - + +
82A LEU* 3.3 8.3 + - + +
84A ILE* 1.3 87.1 - - + +
86A ILE* 1.3 63.5 + - + +
88A ILE* 4.2 10.3 - - + +
89A GLY* 5.0 1.9 + - - -
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 6.4 1.1 - - + -
82A LEU* 3.1 23.3 + - + +
83A TYR* 4.2 1.6 - - + +
85A PHE* 1.3 81.2 - - + +
87A GLY* 1.3 60.4 + - - +
88A ILE 3.8 0.2 - - - -
89A GLY* 4.6 2.2 + - - -
90A LEU* 4.5 12.3 + - - +
503A MPD 3.8 32.3 - - + -
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 4.6 10.5 - - - -
61A LEU* 4.0 19.5 - - - -
83A TYR* 2.8 22.0 + - - -
86A ILE* 1.3 74.4 - - - +
88A ILE* 1.3 64.3 + - - +
89A GLY 3.4 2.5 - - - -
90A LEU* 3.3 5.9 + - - +
91A VAL* 3.0 26.7 + - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.8 19.5 - - - +
63A THR* 4.7 9.9 - - + -
84A ILE* 3.0 29.6 + - + +
85A PHE* 4.2 10.5 - - + +
87A GLY* 1.3 70.0 - - - +
89A GLY* 1.3 77.6 + - - +
90A LEU 3.2 0.2 + - - -
91A VAL 3.2 0.5 + - - -
92A PHE* 2.9 49.5 + - + -
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE 5.0 2.0 + - - -
86A ILE 4.6 3.5 + - - -
87A GLY 3.4 0.6 - - - -
88A ILE* 1.3 93.2 - - - +
90A LEU* 1.3 57.3 + - - +
92A PHE* 3.5 2.2 + - - +
93A GLY* 3.0 25.1 + - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.8 22.9 - - + +
30A LEU* 3.5 41.5 - - + +
31A THR* 4.0 13.0 - - - +
34A THR* 3.1 33.7 - - + +
86A ILE 4.5 8.9 + - - +
87A GLY* 3.3 9.5 + - - +
88A ILE 3.2 0.6 - - - -
89A GLY* 1.3 72.8 - - - +
91A VAL* 1.3 67.7 + - + +
93A GLY* 2.9 13.1 + - - -
94A PHE* 2.9 10.7 + - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 4.5 23.8 - - + -
34A THR* 5.3 2.9 - - + -
35A LEU* 5.4 3.1 - - + -
61A LEU* 3.7 37.7 - - + +
62A THR* 3.8 29.4 - - + -
87A GLY 3.0 21.0 + - - +
88A ILE 3.9 2.2 - - - +
90A LEU* 1.3 79.0 - - + +
92A PHE* 1.3 59.7 + - + +
94A PHE* 3.4 5.1 + - + +
95A ILE* 3.0 34.4 + - + +
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 3.6 20.9 - - - -
62A THR* 3.3 29.8 - - - -
63A THR* 4.0 9.2 - - + -
88A ILE* 2.9 43.7 + - + +
89A GLY* 4.2 2.7 - - - +
91A VAL* 1.3 75.9 - - + +
93A GLY* 1.3 61.1 + - - +
94A PHE 3.1 0.7 - - - -
95A ILE* 3.9 22.5 - - + +
96A HIS* 2.9 30.1 + - - +
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Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.0 10.1 - - - -
89A GLY 3.0 11.7 + - - -
90A LEU* 2.9 8.9 + - - -
92A PHE* 1.3 77.4 - - - +
94A PHE* 1.3 58.4 + - - +
96A HIS* 3.5 5.5 - - - +
97A LYS* 3.0 36.0 + - - +
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.5 33.0 - + - -
27A LEU* 3.8 19.9 - - + +
28A PHE* 3.7 50.3 - + + -
31A THR* 3.5 31.6 - - + +
90A LEU 2.9 8.4 + - - +
91A VAL* 3.6 9.6 - - + +
93A GLY* 1.3 74.7 - - - +
95A ILE* 1.3 68.2 + - + +
96A HIS 3.1 1.6 - - - -
97A LYS* 3.9 0.7 - - - +
98A LEU* 2.8 52.2 + - + +
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Residues in contact with ILE 95 (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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62A THR* 4.0 15.9 - - + -
91A VAL* 3.0 37.7 + - + +
92A PHE* 3.9 26.9 - - + +
94A PHE* 1.3 84.5 - - + +
96A HIS* 1.3 63.5 + - - +
98A LEU* 3.6 11.5 - - + +
99A ALA* 3.2 26.4 + - + +
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Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE 2.9 20.2 + - - +
93A GLY* 3.5 7.0 - - - +
95A ILE* 1.3 80.1 - - - +
97A LYS* 1.3 92.8 + - + +
99A ALA* 4.0 1.3 - - - +
100A VAL* 3.0 56.7 + - + +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 3.6 19.3 + - - +
24A PHE* 4.5 15.0 - - + -
27A LEU* 3.4 22.2 - - + -
93A GLY* 3.0 19.2 + - - +
94A PHE 3.4 2.7 + - - +
96A HIS* 1.3 102.3 + - + +
98A LEU* 1.3 59.6 + - - +
100A VAL* 4.5 0.9 - - + -
101A ASN* 2.7 59.3 + - + +
102A VAL* 3.5 1.9 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.4 35.6 - - + -
94A PHE* 2.8 39.0 + - + +
95A ILE* 3.6 13.2 - - + +
97A LYS* 1.3 77.9 - - - +
99A ALA* 1.3 60.0 + - + +
102A VAL* 3.0 34.5 - - + +
103A GLN* 3.2 9.1 + - + +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.2 16.4 + - + +
96A HIS* 4.3 1.8 - - - +
98A LEU* 1.3 80.7 - - + +
100A VAL* 1.3 59.3 + - + +
103A GLN* 3.4 14.3 - - + +
104A LEU* 2.7 32.1 + - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A HIS* 3.0 44.9 + - + +
97A LYS* 4.3 2.0 - - + +
99A ALA* 1.3 81.3 - - + +
101A ASN* 1.3 73.1 + - - +
102A VAL 3.4 0.2 - - - -
104A LEU* 3.0 39.7 - - + +
105A PRO* 3.3 7.3 - - - +
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 4.1 16.7 + - - -
24A PHE* 5.7 4.5 - - + +
97A LYS* 2.7 50.4 + - + +
100A VAL* 1.3 86.8 - - - +
102A VAL* 1.3 64.4 + - + +
105A PRO* 4.3 10.6 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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