Contacts of the helix formed by residues 72 - 99 (chain A) in PDB entry 5OQN
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 GLU 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 4.0 30.6 - - + +
69A LYS* 3.4 48.5 + - - +
70A LYS 3.0 4.7 + - - +
71A ASN* 1.3 75.1 - - - +
73A ILE* 1.3 69.2 + - - +
74A ILE* 2.9 15.4 + - + +
75A GLY 3.1 7.8 + - - -
76A ASP* 3.1 12.5 - - - +
136A ARG* 3.4 5.7 + - - +
457B LYS* 4.8 11.6 + - - -
459B LEU* 4.7 15.2 - - + +
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.9 7.6 - - - +
71A ASN 3.1 7.8 + - - +
72A GLU* 1.3 74.5 + - - +
74A ILE* 1.3 82.0 + - + +
76A ASP* 3.7 8.6 + - + +
77A ARG* 3.1 61.7 + - + +
458B VAL* 5.3 13.0 - - + -
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 3.5 47.8 - - + +
65A ILE* 5.3 1.1 - - + -
68A LEU* 4.1 15.7 - - + -
72A GLU* 2.9 10.6 + - + -
73A ILE* 1.3 94.0 - - + +
75A GLY* 1.3 68.5 + - - +
77A ARG* 3.2 12.1 + - - +
78A ILE* 3.3 16.2 + - + +
458B VAL* 5.0 1.1 - - + -
459B LEU* 3.3 53.4 - - + +
461B ILE* 4.5 9.9 - - + -
463B PHE* 5.5 0.4 - - + -
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Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.8 7.2 - - - -
68A LEU* 3.8 15.7 - - - +
72A GLU 3.1 7.5 + - - -
74A ILE* 1.3 77.5 - - - +
76A ASP* 1.3 64.7 + - - +
78A ILE* 2.8 10.4 + - - +
79A VAL* 2.8 29.9 + - - +
136A ARG* 3.9 16.8 - - - -
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Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.0 14.6 - - - +
71A ASN* 4.0 12.8 - - - +
72A GLU 3.1 19.4 - - - +
73A ILE* 3.9 11.0 - - + +
74A ILE 3.4 0.8 - - - -
75A GLY* 1.3 72.1 - - - +
77A ARG* 1.3 58.5 + - - +
79A VAL* 3.2 7.2 + - - +
80A LYS* 2.8 48.2 + - + +
136A ARG* 4.0 12.4 + - - +
139A GLN* 4.4 12.6 + - - +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 3.7 13.5 - - - +
25A GLN* 2.8 26.4 + - - +
26A GLY 3.3 18.4 + - - -
27A SER* 3.6 22.5 - - - +
28A TYR* 3.4 41.8 - - + +
31A HIS* 3.2 12.6 + - + -
73A ILE* 3.1 53.9 + - - +
74A ILE* 3.6 4.7 - - - +
75A GLY 3.0 0.8 + - - -
76A ASP* 1.3 74.5 - - - +
78A ILE* 1.3 64.0 + - - +
80A LYS* 3.4 0.6 + - - +
81A LEU* 3.0 19.8 + - - +
458B VAL* 5.9 4.9 - - - +
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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
----------------------------------------------------------
21A PHE* 3.4 46.2 - - + +
24A ALA* 4.3 5.2 - - + -
25A GLN* 3.6 39.3 - - + +
61A LEU 5.4 0.2 - - - +
62A VAL* 5.4 1.6 - - + -
65A ILE* 3.8 36.8 - - + -
74A ILE* 3.4 15.3 - - + +
75A GLY 2.8 4.8 + - - +
77A ARG* 1.3 74.9 - - - +
79A VAL* 1.3 58.2 + - - +
81A LEU* 3.1 7.3 + - + +
82A VAL* 2.8 37.6 + - + +
463B PHE* 4.5 2.9 - - + -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.2 9.9 - - + -
75A GLY 2.8 24.3 + - - +
76A ASP* 3.6 7.6 - - - +
78A ILE* 1.3 75.9 - - - +
80A LYS* 1.3 68.0 + - + +
82A VAL* 3.2 4.2 + - - +
83A ALA* 2.8 22.9 + - - +
136A ARG* 4.2 14.4 - - + +
139A GLN* 4.4 22.0 - - + +
140A LEU* 3.6 34.3 - - + -
143A VAL* 4.1 22.8 - - + +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.5 21.5 - - + +
31A HIS* 4.2 12.6 - - + +
76A ASP* 2.8 42.6 + - - +
77A ARG* 3.7 6.3 - - - +
79A VAL* 1.3 75.5 - - + +
81A LEU* 1.3 58.1 + - - +
83A ALA* 3.6 6.2 - - - +
84A ALA* 2.8 31.5 + - - +
139A GLN* 6.1 1.2 - - - +
143A VAL* 5.7 7.1 - - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.4 14.1 - - + -
21A PHE* 4.8 20.6 - - + -
24A ALA* 3.5 30.1 - - + -
31A HIS* 3.8 17.2 + - + +
34A HIS* 4.4 10.8 - - + +
35A ILE* 3.4 25.4 - - + +
38A LEU* 4.0 18.8 - - + -
58A PHE* 6.2 0.2 - - + -
77A ARG 3.0 14.5 + - - +
78A ILE* 3.4 10.1 - - - +
80A LYS* 1.3 76.3 - - - +
82A VAL* 1.3 61.8 + - + +
84A ALA* 3.1 3.4 + - - -
85A PHE* 2.8 27.3 + - + +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 4.3 5.4 - - + -
58A PHE* 4.2 22.0 - - + -
62A VAL* 4.1 24.7 - - + -
78A ILE* 2.8 35.3 + - + +
79A VAL* 3.7 5.6 - - - +
81A LEU* 1.3 72.2 - - + +
83A ALA* 1.3 63.0 + - - +
85A PHE* 3.2 7.6 + - - +
86A ILE* 3.0 33.7 + - + +
118A PHE* 4.0 30.5 - - + -
140A LEU* 5.4 6.3 - - + -
144A ILE* 4.9 4.7 - - + -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL 2.8 17.6 + - - +
80A LYS* 3.6 6.7 - - - +
82A VAL* 1.3 77.2 - - - +
84A ALA* 1.3 57.3 + - - +
86A ILE* 3.2 4.0 + - - +
87A ALA* 2.9 30.7 + - - +
143A VAL* 3.6 33.9 - - + +
144A ILE* 4.1 13.4 - - + +
147A ASN* 4.5 2.5 - - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 5.6 4.0 - - + -
35A ILE* 3.5 22.6 - - + +
80A LYS 2.8 20.6 + - - +
81A LEU* 3.1 2.2 + - - +
83A ALA* 1.3 73.7 - - - +
85A PHE* 1.3 56.3 + - - +
87A ALA* 3.8 6.0 - - - +
88A SER* 2.8 33.1 + - - -
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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
----------------------------------------------------------
35A ILE* 3.2 19.6 - - + +
38A LEU* 3.3 43.5 - - + -
39A LYS* 3.7 22.9 - - + -
42A GLN* 3.4 23.1 - - - -
54A PHE* 4.0 17.0 - + - -
58A PHE* 4.0 20.2 - + + -
81A LEU 2.8 20.3 + - - +
82A VAL* 3.5 7.4 - - - +
84A ALA* 1.3 70.0 - - - +
86A ILE* 1.3 67.1 + - + +
88A SER* 3.8 1.0 - - - -
89A LEU* 3.0 46.7 + - + +
114A PHE* 4.2 19.7 - + - -
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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
----------------------------------------------------------
58A PHE* 5.5 0.4 - - + -
82A VAL* 3.0 21.2 + - + +
83A ALA 3.7 5.2 - - - +
85A PHE* 1.3 77.5 - - + +
87A ALA* 1.3 63.8 + - - +
89A LEU* 3.1 7.9 + - - +
90A GLU* 2.9 21.0 + - - +
111A PHE* 3.9 13.1 - - + -
114A PHE* 3.4 36.1 - - + -
115A VAL* 4.7 13.5 - - + -
118A PHE* 4.9 11.2 - - + -
144A ILE* 4.1 28.0 - - + +
147A ASN* 3.7 27.6 - - + +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 2.9 15.2 + - - +
84A ALA* 3.8 7.0 - - - +
86A ILE* 1.3 78.0 - - - +
88A SER* 1.3 57.8 + - - +
90A GLU* 3.0 3.7 + - - +
91A ARG* 2.8 32.8 + - + +
147A ASN* 3.3 33.1 + - - +
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.7 17.3 - - - +
39A LYS* 2.9 32.1 + - - -
84A ALA 2.8 23.4 + - - -
85A PHE 3.8 2.5 - - - -
87A ALA* 1.3 72.2 - - - +
89A LEU* 1.3 62.7 + - - +
91A ARG* 3.3 8.3 + - - +
92A GLU* 3.1 26.5 + - - +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 4.0 20.0 - - + -
42A GLN* 3.5 24.0 - - - +
85A PHE* 3.0 54.7 + - + +
86A ILE* 3.1 9.6 + - - +
88A SER* 1.3 74.9 - - - +
90A GLU* 1.3 66.2 + - - +
92A GLU* 3.4 14.9 + - - +
93A LEU* 3.3 17.8 + - - +
111A PHE* 3.9 25.3 - - + +
114A PHE* 4.8 8.5 - - + -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE 2.9 13.1 + - - +
87A ALA 3.4 7.4 - - - +
89A LEU* 1.3 75.9 - - - +
91A ARG* 1.3 54.8 + - - +
93A LEU* 2.7 33.8 + - - +
94A ILE* 2.9 40.1 + - + +
97A LYS* 4.8 8.0 + - - -
111A PHE* 3.0 30.7 - - + -
146A ASP 5.7 0.2 - - - +
147A ASN* 3.8 33.2 - - + +
149A GLY* 3.7 20.2 - - - -
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 2.8 20.3 + - + +
88A SER* 3.6 9.4 - - - +
89A LEU 3.2 0.2 - - - -
90A GLU* 1.3 72.1 - - - +
92A GLU* 1.3 64.1 + - - +
93A LEU 2.9 1.0 + - - -
94A ILE* 3.0 24.6 + - + +
95A LEU* 3.4 29.4 + - - +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 2.9 41.9 + - - +
88A SER* 3.1 15.1 + - - +
89A LEU* 3.6 17.2 - - - +
91A ARG* 1.3 75.6 - - - +
93A LEU* 1.3 59.0 + - - +
95A LEU* 4.1 12.8 - - - +
96A ALA* 3.8 18.9 + - - +
103A LEU* 4.9 8.6 - - + +
107A GLU* 6.2 0.2 - - - +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU 3.3 8.9 + - - +
90A GLU* 2.7 25.4 + - - +
92A GLU* 1.3 74.7 - - - +
94A ILE* 1.3 60.4 + - - -
96A ALA* 3.9 5.3 - - + +
97A LYS* 3.2 43.0 + - + +
103A LEU* 6.1 4.5 - - + -
107A GLU* 4.9 4.9 - - + +
108A GLU* 3.8 51.4 - - + +
111A PHE* 4.2 26.5 - - + -
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 2.9 43.9 + - + +
91A ARG* 3.0 14.7 + - + +
93A LEU* 1.3 74.5 - - - +
95A LEU* 1.3 60.0 + - - +
96A ALA 3.0 2.2 - - - -
97A LYS* 2.7 39.8 + - + +
98A LYS* 2.9 19.8 + - + +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 3.4 29.4 + - - +
92A GLU* 4.1 10.8 - - - +
94A ILE* 1.3 78.3 - - - +
96A ALA* 1.3 64.7 + - + +
98A LYS* 3.4 19.5 + - - +
99A GLN* 2.8 37.8 + - - +
100A ASN* 5.7 2.9 - - + +
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU 3.8 14.9 + - - +
93A LEU* 3.9 8.5 - - + +
94A ILE 2.9 1.0 + - - -
95A LEU* 1.3 85.9 - - + +
97A LYS* 1.3 61.0 + - + +
98A LYS 2.9 1.0 + - - -
99A GLN 2.9 0.7 + - - -
100A ASN* 2.4 47.5 + - - +
103A LEU* 3.4 35.0 - - + -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 4.8 9.7 + - - -
93A LEU* 3.2 47.4 + - + +
94A ILE* 2.7 21.5 + - + +
96A ALA* 1.3 76.4 - - + +
98A LYS* 1.3 61.7 + - - +
99A GLN* 3.2 2.5 + - - -
100A ASN 4.2 2.5 - - - -
101A TYR* 5.7 3.6 - - - -
108A GLU* 4.9 16.1 + - - +
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 2.9 23.7 + - + +
95A LEU* 3.4 19.1 - - - +
96A ALA 2.9 0.8 + - - -
97A LYS* 1.3 78.2 - - - +
99A GLN* 1.3 76.2 + - - +
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Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 2.8 26.7 + - - +
96A ALA 2.9 0.8 + - - -
97A LYS 3.2 2.2 - - - -
98A LYS* 1.3 90.4 - - - +
100A ASN* 1.3 83.4 + - + +
101A TYR* 3.6 12.4 + - - +
----------------------------------------------------------
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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