Contacts of the helix formed by residues 81 - 111 (chain A) in PDB entry 5C5B
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 VAL 81 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 1.3 81.3 - - + +
82A MET* 1.3 68.8 + - + +
83A SER 3.1 0.9 + - - -
84A SER* 3.2 8.7 + - - -
85A THR* 3.1 38.1 + - + +
232A SER* 4.3 18.8 - - - +
236A VAL* 5.5 6.5 - - + -
193B GLN* 3.3 23.8 - - - +
197B MET* 4.8 6.1 - - + -
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU 3.3 6.4 - - - +
81A VAL* 1.3 84.2 - - + +
83A SER* 1.3 58.1 + - - +
85A THR* 2.6 21.7 + - - +
86A LEU* 2.9 40.8 + - + +
192B LYS* 4.0 28.0 - - + +
193B GLN* 3.9 33.0 - - + +
196B MET* 3.6 42.4 - - + -
197B MET* 5.7 5.8 - - + -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 4.2 21.4 - - - +
80A GLU* 3.6 21.1 + - - -
81A VAL 3.1 0.4 + - - -
82A MET* 1.3 75.4 - - - +
84A SER* 1.3 60.2 + - - +
86A LEU* 3.3 7.5 + - - +
87A GLN* 2.9 39.2 + - - +
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU 4.0 5.4 + - - -
81A VAL* 3.2 8.5 + - - -
83A SER* 1.3 75.9 - - - +
85A THR* 1.3 66.4 + - - +
87A GLN* 3.2 12.6 + - - +
88A GLN* 2.9 44.2 + - - +
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.1 24.2 + - + +
82A MET* 2.6 27.4 + - - +
84A SER* 1.3 76.9 - - - +
86A LEU* 1.3 65.2 + - - +
88A GLN* 3.3 16.3 + - - +
89A PHE* 2.9 28.1 + - - +
225A PHE* 3.8 1.2 - - - -
228A ASN* 6.2 0.9 - - + -
229A ILE* 3.6 19.3 - - + -
232A SER* 4.4 6.3 - - - +
197B MET* 3.7 27.5 - - + +
200B MET* 3.8 7.0 - - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 4.2 18.5 - - + +
68A TYR* 5.1 4.0 - - + +
69A GLU* 3.8 27.5 - - + +
82A MET* 2.9 48.2 + - + +
83A SER* 3.6 4.7 - - - +
85A THR* 1.3 88.9 + - - +
87A GLN* 1.3 56.5 + - - +
89A PHE* 3.7 6.3 - - - +
90A SER* 2.9 26.9 + - - -
36B TYR* 4.6 22.4 - - + +
196B MET* 5.1 8.5 - - + -
197B MET* 5.9 1.1 - - + -
200B MET* 4.0 20.2 - - - -
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 3.2 29.8 + - - +
83A SER* 2.9 24.1 + - - +
84A SER* 3.2 10.3 + - - +
86A LEU* 1.3 73.9 - - - +
88A GLN* 1.3 66.3 - - - +
89A PHE 3.2 0.2 - - - -
90A SER* 2.7 22.6 + - - +
91A LYS* 2.9 13.2 + - - +
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 2.9 41.5 + - - +
85A THR* 3.5 12.2 - - - +
87A GLN* 1.3 73.5 - - - +
89A PHE* 1.3 58.4 + - - +
91A LYS* 3.1 14.3 + - - +
92A VAL* 3.0 33.5 + - + +
225A PHE* 3.9 23.2 - - + -
228A ASN* 3.6 33.9 + - - +
229A ILE* 4.2 5.7 - - - +
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 5.2 2.2 - - + -
65A LEU* 3.4 28.7 - - + -
85A THR 2.9 16.9 + - - +
86A LEU* 3.7 5.8 - - - +
88A GLN* 1.3 74.0 - - - +
90A SER* 1.3 64.6 + - - +
92A VAL* 3.1 9.9 - - + +
93A ILE* 2.9 51.7 + - + +
222A LEU* 6.4 0.2 - - + -
225A PHE* 3.4 27.7 - + + -
40B LEU* 6.5 0.2 - - + -
44B MET* 5.7 6.5 - - + -
111B MET* 5.7 2.9 - - - -
199B PRO 5.0 0.2 - - - -
200B MET* 3.4 46.2 - - + -
203B PHE* 3.6 33.2 - + + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER* 3.5 4.7 + - - -
65A LEU* 3.7 21.2 - - - +
66A LYS* 3.9 34.6 - - - +
69A GLU* 5.0 0.7 - - - -
86A LEU 2.9 14.9 + - - -
87A GLN* 2.7 28.1 + - - +
89A PHE* 1.3 75.8 - - - +
91A LYS* 1.3 55.6 + - - +
93A ILE* 3.4 2.1 + - - +
94A ASP* 2.6 37.6 + - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 5.7 1.8 - - - +
87A GLN 2.9 17.5 + - - +
88A GLN* 3.1 10.9 + - - +
90A SER* 1.3 78.5 + - - +
92A VAL* 1.3 70.4 + - - +
94A ASP* 3.2 8.3 + - - +
95A GLU* 3.0 26.5 + - - +
221A GLN* 3.1 42.8 + - - +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 3.0 19.0 + - + +
89A PHE* 3.1 33.0 - - + +
91A LYS* 1.3 95.2 - - - +
93A ILE* 1.3 59.3 + - + +
95A GLU* 3.2 6.2 + - - +
96A LEU* 3.0 24.9 + - - +
218A LEU* 3.6 10.3 - - + +
221A GLN* 3.9 30.5 - - + +
222A LEU* 4.3 23.1 - - + +
225A PHE* 4.4 12.6 - - + -
203B PHE* 5.4 1.8 - - + -
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.2 39.0 - - + +
61A THR* 3.6 21.5 - - + -
62A SER* 3.6 12.8 - - - +
65A LEU* 3.9 3.6 - - + -
89A PHE* 2.9 53.7 + - + +
90A SER* 3.7 3.8 - - - +
92A VAL* 1.3 79.2 - - - +
94A ASP* 1.3 56.8 + - - +
96A LEU* 3.3 5.9 + - - +
97A SER 2.9 23.4 + - - -
44B MET* 5.8 0.2 - - + -
203B PHE* 3.8 26.9 - - + -
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 3.8 24.3 + - - -
62A SER* 2.1 32.3 + - - -
66A LYS* 3.4 21.7 + - - +
90A SER 2.6 19.6 + - - +
91A LYS* 3.2 6.5 + - - +
93A ILE* 1.3 74.3 - - - +
95A GLU* 1.3 62.6 + - - +
97A SER* 3.4 7.4 + - - -
98A SER* 2.9 26.5 + - - -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 3.0 17.9 + - - +
92A VAL 3.2 7.6 + - - +
94A ASP* 1.3 75.5 - - - +
96A LEU* 1.3 64.5 + - - +
98A SER* 3.2 10.7 + - - -
99A CYS* 3.0 27.0 + - - -
213A MET* 5.1 2.4 - - + +
217A ASN* 3.9 19.3 - - + +
218A LEU* 3.8 13.3 + - + -
221A GLN* 2.4 46.8 + - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 4.0 12.6 - - + +
92A VAL 3.0 12.9 + - - +
93A ILE* 3.5 8.3 - - - +
95A GLU* 1.3 77.3 - - - +
97A SER* 1.3 62.2 + - - +
99A CYS* 3.0 8.1 + - + +
100A HIS* 2.9 47.3 + - + +
218A LEU* 3.4 16.9 - - + +
203B PHE* 3.4 33.9 - - + -
207B GLN* 3.7 17.0 - - + +
211B PHE* 3.6 35.0 - - + -
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 3.1 22.6 + - - -
58A THR* 3.7 19.9 - - - +
59A HIS* 3.6 20.2 + - - +
93A ILE 2.9 16.6 + - - -
94A ASP* 3.5 10.3 - - - -
96A LEU* 1.3 76.9 - - - +
98A SER* 1.3 57.4 + - - +
100A HIS* 3.4 5.8 + - - +
101A ALA* 2.9 29.2 + - - +
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP 2.9 14.5 + - - -
95A GLU* 3.3 16.2 - - - +
97A SER* 1.3 73.8 - - - +
99A CYS* 1.3 65.7 + - - +
101A ALA* 3.2 7.9 + - - +
102A VAL* 2.9 24.8 + - - +
213A MET* 3.9 13.8 - - - +
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Residues in contact with CYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 3.0 17.2 + - - -
96A LEU* 3.0 16.7 + - + +
98A SER* 1.3 76.7 - - - +
100A HIS* 1.3 64.1 + - - +
102A VAL* 3.1 6.6 - - - +
103A LEU* 3.0 23.7 + - - +
210A PHE* 3.7 21.4 - - + -
213A MET* 3.6 37.9 - - - -
214A GLY* 4.1 19.7 - - - -
217A ASN* 6.3 0.7 - - - -
218A LEU* 4.8 8.1 - - - -
211B PHE* 4.7 2.5 - - + -
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Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 2.8 29.8 + - - +
54A LEU* 3.9 30.9 - - + +
55A SER* 3.7 22.4 - - - +
58A THR* 4.0 15.2 + - - -
96A LEU* 2.9 50.6 + - + +
97A SER 3.7 2.7 - - - +
99A CYS* 1.3 76.2 - - - +
101A ALA* 1.3 57.3 + - - +
103A LEU* 3.5 0.4 + - - -
104A SER* 2.9 30.8 + - - -
210A PHE* 3.9 21.4 - + - -
51B GLN* 5.2 5.9 + - - -
100B HIS* 5.9 2.2 - + - -
103B LEU* 6.3 1.1 - - + -
207B GLN* 5.2 3.0 + - - -
210B PHE* 5.5 6.7 - + - -
211B PHE* 5.3 0.4 - + - -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 3.9 11.2 - - - -
97A SER 2.9 17.5 + - - +
98A SER* 3.4 9.4 - - - +
99A CYS 3.1 0.2 - - - -
100A HIS* 1.3 75.9 - - - +
102A VAL* 1.3 59.8 + - - +
104A SER* 3.0 8.9 + - - -
105A THR* 2.9 31.1 + - - -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 2.9 14.2 + - - +
99A CYS 3.1 18.8 - - - +
101A ALA* 1.3 75.2 - - - +
103A LEU* 1.3 58.5 + - + +
105A THR* 3.4 7.1 + - - +
106A GLN* 3.0 36.8 + - + +
209A SER* 5.8 2.9 - - - +
210A PHE* 5.4 5.2 - - + -
213A MET* 3.5 32.5 - - + -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 3.4 33.0 - - + +
99A CYS 3.0 17.5 + - - +
100A HIS 3.6 5.2 - - - +
102A VAL* 1.3 79.9 - - - +
104A SER* 1.3 56.3 + - - +
106A GLN* 3.8 4.2 - - + +
107A LEU* 2.9 39.2 + - + +
206A ALA* 3.4 43.3 - - + +
207A GLN* 3.8 18.4 - - - +
209A SER* 5.8 0.7 - - - -
210A PHE* 3.5 37.7 - - + +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 3.4 11.0 - - - -
51A GLN* 3.1 25.5 + - - +
52A ASN* 3.0 37.7 + - - -
55A SER* 4.4 1.4 + - - -
100A HIS 2.9 12.7 + - - -
101A ALA* 3.0 12.5 + - - -
103A LEU* 1.3 77.0 - - - +
105A THR* 1.3 57.8 + - - +
107A LEU* 3.2 6.9 + - - +
108A ALA 2.9 23.7 + - - -
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA 2.9 13.4 + - - -
102A VAL* 3.8 11.3 - - - -
104A SER* 1.3 75.7 - - - +
106A GLN* 1.3 63.6 + - - +
108A ALA* 3.0 9.8 + - + +
109A ASP* 3.0 36.2 + - - +
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 3.0 24.0 + - + +
103A LEU* 4.0 4.8 - - - +
105A THR* 1.3 78.4 - - - +
107A LEU* 1.3 57.4 + - - +
109A ASP* 4.6 3.4 - - - +
110A ALA* 2.9 43.6 + - + +
202A GLY 5.5 0.2 + - - -
205A GLN* 4.3 8.3 + - - +
206A ALA* 3.9 24.8 - - + +
209A SER* 2.6 35.0 + - - -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 4.3 18.4 - - + -
48A TYR* 4.1 13.0 - - + -
51A GLN* 4.0 30.5 - - + +
103A LEU* 2.9 32.6 + - + +
104A SER* 3.3 7.0 - - - +
106A GLN* 1.3 74.8 - - - +
108A ALA* 1.3 60.1 + - - +
111A MET* 2.8 43.2 + - + +
112A MET 3.0 9.4 + - - -
203A TYR* 3.5 34.3 - - + -
206A ALA* 4.0 16.2 - - + -
207A GLN* 5.0 1.1 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 3.4 35.1 - - + +
104A SER 2.9 7.8 + - - +
105A THR* 3.0 13.2 + - + +
107A LEU* 1.3 75.9 - - - +
109A ASP* 1.3 63.7 + - - +
112A MET* 3.6 9.4 - - + +
113A PHE* 3.1 27.9 + - - +
----------------------------------------------------------
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 3.0 28.0 + - - +
106A GLN* 4.5 2.6 - - - +
108A ALA* 1.3 83.5 - - - +
110A ALA* 1.3 61.5 + - - +
113A PHE* 3.4 26.3 - - - +
114A PRO* 3.6 4.0 - - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLN* 2.9 31.9 + - + +
109A ASP* 1.3 75.3 - - - +
111A MET* 1.3 58.6 + - + +
114A PRO* 3.2 18.3 - - - +
198A GLU* 4.2 1.9 - - - +
199A PRO* 4.0 4.0 - - - +
202A GLY* 3.9 33.5 - - - +
----------------------------------------------------------
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Residues in contact with MET 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 3.4 52.5 - - - +
47A ILE* 4.7 3.1 - - + -
48A TYR* 4.3 5.8 - - + +
107A LEU* 2.8 42.7 + - + +
110A ALA* 1.3 78.7 - - - +
112A MET* 1.3 87.1 + - + +
113A PHE 3.3 1.1 - - - -
114A PRO* 3.2 9.8 - - - +
115A ILE* 3.7 5.0 + - - +
199A PRO* 3.5 34.2 - - - +
202A GLY 4.8 0.2 - - - -
203A TYR* 3.8 31.6 - - + +
61B LEU* 6.3 0.9 - - - -
----------------------------------------------------------
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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