Contacts of the helix formed by residues 56 - 90 (chain A) in PDB entry 2L5G
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 MET 56 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 4.4 29.2 - - + +
54A LYS 3.1 9.1 - - - +
55A GLU* 1.3 76.5 - - - +
57A GLU* 1.3 68.4 + - - +
58A GLU 3.1 2.2 - - - -
59A ARG* 3.0 22.3 + - + +
60A MET* 3.2 33.1 + - + +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A MET* 1.3 80.9 - - - +
58A GLU* 1.3 68.1 + - + +
60A MET* 3.4 17.8 + - + +
61A SER* 3.3 15.5 + - - +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 3.5 36.3 - - - +
56A MET 3.1 0.6 - - - -
57A GLU* 1.3 82.8 - - + +
59A ARG* 1.3 65.1 + - + +
61A SER* 3.4 16.7 + - - -
62A LEU* 3.4 12.0 + - - +
203B GLU 5.2 3.4 - - - +
204B ALA* 4.5 31.9 - - + +
206B LYS 5.6 2.5 - - - +
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU 3.8 18.3 + - - +
56A MET* 3.0 15.4 + - + +
58A GLU* 1.3 79.6 - - + +
60A MET* 1.3 62.6 + - + +
62A LEU* 3.4 14.8 + - - +
63A GLU* 3.3 19.4 + - - +
201B GLU 5.0 1.8 + - - -
204B ALA* 3.5 33.5 + - - +
205B ALA* 3.6 18.6 - - - +
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Residues in contact with MET 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A MET* 3.3 35.7 - - + +
57A GLU* 3.5 15.0 - - + +
58A GLU 3.2 0.4 - - - -
59A ARG* 1.3 80.2 - - + +
61A SER* 1.3 61.4 + - - +
63A GLU* 3.4 26.9 + - - +
64A GLU* 3.7 12.1 + - - +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.3 14.0 + - - +
58A GLU* 3.7 10.0 - - - -
59A ARG 3.3 0.2 - - - -
60A MET* 1.3 76.6 - - - +
62A LEU* 1.3 65.4 + - - +
64A GLU* 3.3 24.0 + - - +
65A THR* 3.3 15.0 + - - -
200B LEU* 4.8 4.3 - - - -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU 3.4 8.3 + - - +
59A ARG* 3.4 18.1 + - - +
60A MET 3.3 0.4 - - - -
61A SER* 1.3 79.7 - - - +
63A GLU* 1.3 64.4 + - - +
65A THR* 3.3 2.1 + - - -
66A LYS* 3.1 46.1 + - + +
197B GLN* 4.5 2.5 - - - +
200B LEU* 3.7 28.7 - - + +
201B GLU* 3.4 43.3 - - + +
204B ALA* 4.1 11.2 - - + -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG 3.3 8.9 + - - +
60A MET* 3.5 21.7 - - - +
61A SER 3.2 0.4 - - - -
62A LEU* 1.3 83.3 - - - +
64A GLU* 1.3 60.8 + - + +
66A LYS* 3.5 10.4 + - + +
67A GLU* 3.5 18.0 + - - +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET 3.7 6.6 + - - +
61A SER* 3.3 22.3 + - - +
62A LEU 3.2 0.2 - - - -
63A GLU* 1.3 79.8 - - + +
65A THR* 1.3 64.7 + - - +
67A GLU* 3.3 19.7 + - - +
68A GLN* 3.7 5.5 + - - +
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A SER 3.3 11.3 + - - -
62A LEU 3.3 8.8 + - - -
64A GLU* 1.3 78.9 - - - +
66A LYS* 1.3 63.1 + - - +
68A GLN* 3.3 13.3 + - + +
69A ILE* 3.1 23.1 + - + +
193B LEU* 5.3 1.8 - - + -
196B LYS* 3.2 36.3 + - - +
197B GLN* 3.5 14.1 - - - +
200B LEU* 3.4 15.7 - - + +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.1 29.2 + - + +
63A GLU* 3.6 10.5 - - + +
64A GLU 3.2 0.2 - - - -
65A THR* 1.3 76.9 - - - +
67A GLU* 1.3 59.1 + - - +
69A ILE* 3.3 8.4 + - + +
70A LEU* 2.9 36.0 + - + +
197B GLN* 3.1 28.3 - - - +
201B GLU* 3.3 21.9 + - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU 3.5 9.4 + - - +
64A GLU* 3.3 14.7 + - - +
65A THR 3.2 0.4 - - - -
66A LYS* 1.3 80.5 - - - +
68A GLN* 1.3 61.2 + - - +
70A LEU* 3.6 11.4 + - + +
71A LYS* 3.3 26.3 + - - +
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.7 5.3 + - - +
65A THR* 3.3 13.2 + - + +
66A LYS 3.2 0.6 - - - -
67A GLU* 1.3 80.1 - - - +
69A ILE* 1.3 65.8 + - + +
71A LYS* 3.6 13.6 + - - +
72A LEU* 3.5 23.3 + - - +
193B LEU* 5.0 18.6 - - + +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 3.1 17.3 - - + +
66A LYS* 3.3 7.1 + - + +
68A GLN* 1.3 74.1 - - - +
70A LEU* 1.3 66.6 + - - +
72A LEU* 3.4 25.0 - - + +
73A GLU* 3.8 9.4 + - - +
190B ILE* 5.4 3.4 - - + +
193B LEU* 3.4 29.4 - - + +
194B LYS* 4.0 36.8 - - + +
197B GLN* 2.8 56.3 - - + +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 2.9 20.4 + - + +
67A GLU* 3.9 12.8 - - + +
68A GLN 3.3 0.2 - - - -
69A ILE* 1.3 77.3 - - - +
71A LYS* 1.3 64.1 + - - +
73A GLU* 3.1 37.2 + - + +
74A GLU* 3.8 13.7 + - + +
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.3 23.4 + - - +
68A GLN* 3.7 18.2 - - - +
70A LEU* 1.3 80.5 - - - +
72A LEU* 1.3 63.6 + - - +
74A GLU* 3.1 41.6 + - - +
75A LYS* 3.1 26.2 + - + +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 3.5 17.2 + - + +
69A ILE* 3.4 14.3 + - + +
71A LYS* 1.3 81.0 - - - +
73A GLU* 1.3 56.5 + - - +
75A LYS* 3.1 16.4 + - + +
76A LEU* 2.7 33.1 + - - +
186B VAL* 4.7 8.5 - - + +
189B GLN* 4.9 6.1 - - + -
190B ILE* 3.4 48.8 - - + +
193B LEU* 3.4 36.6 - - + -
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 3.9 9.9 - - - +
70A LEU* 3.2 28.5 - - + +
71A LYS 3.1 0.2 - - - -
72A LEU* 1.3 78.4 - - + +
74A GLU* 1.3 57.3 + - + +
76A LEU* 3.9 6.6 - - - +
77A LEU* 3.1 43.8 + - + +
190B ILE* 5.3 5.6 - - + -
194B LYS* 4.6 14.5 + - - +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.7 13.4 - - - +
71A LYS* 3.1 36.6 + - - +
73A GLU* 1.3 79.3 - - + +
75A LYS* 1.3 59.7 + - - +
77A LEU* 4.0 8.2 - - + +
78A ALA* 3.1 27.5 + - - +
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Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 3.1 27.4 + - + +
72A LEU* 3.6 22.0 - - + +
74A GLU* 1.3 78.4 - - - +
76A LEU* 1.3 61.7 + - - +
78A ALA* 3.6 5.5 + - + +
79A LEU* 3.3 33.9 + - + +
186B VAL* 4.4 10.0 - - + +
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU 2.7 17.4 + - - +
73A GLU* 3.9 6.5 - - - +
75A LYS* 1.3 77.6 - - - +
77A LEU* 1.3 65.2 + - + +
79A LEU* 3.5 11.9 + - + +
80A GLN* 3.5 18.8 + - + +
183B ILE* 4.3 12.7 - - + +
186B VAL* 4.2 7.4 - - + +
187B GLU* 3.7 46.9 - - + +
190B ILE* 3.5 22.2 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 3.1 31.4 + - + +
74A GLU* 4.0 8.3 - - + +
76A LEU* 1.3 78.2 - - + +
78A ALA* 1.3 64.6 + - - +
80A GLN* 3.4 12.2 + - + +
81A GLU* 3.2 26.8 + - + +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU 3.1 19.0 + - - +
75A LYS* 3.8 8.5 - - + +
77A LEU* 1.3 78.1 - - - +
79A LEU* 1.3 66.5 + - + +
81A GLU* 3.3 9.8 + - - +
82A GLU* 3.2 24.1 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 3.3 21.7 + - + +
76A LEU* 3.6 12.1 - - - +
78A ALA* 1.3 84.7 - - + +
80A GLN* 1.3 63.0 + - - +
82A GLU* 3.2 26.3 + - + +
83A LYS 3.5 4.0 + - - -
179B VAL* 4.9 3.5 - - + +
182B GLU* 4.0 24.5 - - + +
183B ILE* 3.6 46.7 - - + +
186B VAL* 4.2 23.8 - - + -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 3.5 13.5 + - + +
77A LEU* 3.4 16.6 + - + +
78A ALA 3.3 0.4 - - - -
79A LEU* 1.3 80.2 - - - +
81A GLU* 1.3 62.9 + - + +
83A LYS* 3.4 4.9 + - - +
84A HIS* 3.2 19.4 + - - +
183B ILE* 4.1 25.3 - - + +
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.2 15.9 + - + +
78A ALA* 3.4 13.5 - - - +
79A LEU 3.2 0.2 - - - -
80A GLN* 1.3 80.5 - - + +
82A GLU* 1.3 63.1 + - - +
84A HIS* 3.2 19.1 + - - +
85A GLN* 3.2 19.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA 3.2 10.5 + - - +
79A LEU* 3.2 19.9 + - + +
81A GLU* 1.3 81.3 - - - +
83A LYS* 1.3 63.9 + - - +
85A GLN* 3.1 33.5 + - - +
86A LEU* 3.6 5.4 + - - +
179B VAL* 4.5 11.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 3.5 1.6 + - - -
80A GLN* 3.4 8.3 + - - +
81A GLU 3.3 0.2 - - - -
82A GLU* 1.3 79.4 - - - +
84A HIS* 1.3 63.2 + - - +
86A LEU* 3.1 20.6 + - - +
87A PHE* 3.5 17.8 + - + -
176B MET* 4.0 35.4 - - + +
179B VAL* 3.8 17.8 - - + +
180B ASP* 3.2 43.3 + - + +
183B ILE* 4.2 13.8 - - + +
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Residues in contact with HIS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN 3.2 10.9 + - - +
81A GLU* 3.3 24.5 + - - +
82A GLU 3.1 0.2 - - - -
83A LYS* 1.3 81.6 - - - +
85A GLN* 1.3 63.1 + - - +
87A PHE* 3.2 27.0 + - + +
88A LEU* 3.6 21.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU 3.2 8.0 + - - +
82A GLU* 3.1 25.3 + - - +
84A HIS* 1.3 82.9 - - - +
86A LEU* 1.3 68.1 + - - +
88A LEU* 3.2 22.6 + - + +
89A GLN* 3.2 37.6 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU 3.6 3.0 + - - +
83A LYS* 3.1 13.6 + - - +
85A GLN* 1.3 88.2 - - - +
87A PHE* 1.3 52.1 + - - +
89A GLN* 3.0 13.6 + - - +
90A LEU* 2.6 35.3 + - - +
172B LEU* 3.1 38.8 - - + +
175B ASN* 3.8 15.3 - - + +
176B MET* 3.5 28.7 - - + -
179B VAL* 3.5 35.2 - - + -
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Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 3.5 24.8 + - + -
84A HIS* 3.2 21.7 + + + +
86A LEU* 1.3 80.4 - - - +
88A LEU* 1.3 65.8 + - + +
89A GLN 3.1 0.7 + - - -
90A LEU* 3.2 21.3 + - + +
176B MET* 3.2 39.0 - - + +
----------------------------------------------------------
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A HIS* 4.1 27.4 - - + +
85A GLN* 3.2 17.6 + - + +
86A LEU 3.1 0.2 - - - -
87A PHE* 1.3 83.1 - - + +
89A GLN* 1.3 64.2 + - + +
90A LEU* 4.6 1.2 - - - +
----------------------------------------------------------
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLN* 3.2 36.7 + - - +
86A LEU* 3.0 15.9 + - - +
88A LEU* 1.3 81.2 - - + +
90A LEU* 1.3 70.2 + - - +
166B GLY* 4.5 10.6 + - - -
172B LEU* 3.4 25.1 - - + +
----------------------------------------------------------
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU 2.6 17.4 + - - +
87A PHE* 3.2 19.0 + - + +
88A LEU 4.6 1.4 - - - +
89A GLN* 1.3 78.8 - - - +
169B LYS* 3.4 31.9 + - - +
172B LEU* 3.5 34.0 - - + +
173B ILE* 3.0 37.7 - - + -
176B MET* 3.3 35.7 - - + -
----------------------------------------------------------
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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
------------------------------------------------------------
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