Contacts of the helix formed by residues 64 - 85 (chain B) in PDB entry 1EZF
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 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP 3.5 0.2 + - - -
63B GLY* 1.3 71.4 - - - -
65B MET* 1.3 63.2 + - - +
66B ARG 3.1 0.6 + - - -
67B ASN* 3.6 5.9 + - - +
68B ALA* 3.2 24.4 + - - +
135B LEU* 5.4 0.9 - - - +
136B ALA* 5.0 7.6 - - - +
138B LYS* 4.2 8.8 + - - -
139B TYR* 2.6 46.3 + - + +
190B SER* 5.1 3.1 - - - -
192B PHE* 4.5 5.3 - - + -
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Residues in contact with MET 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.0 17.5 - - + -
62B ASP 3.1 11.3 + - - +
64B GLU* 1.3 75.5 - - - +
66B ARG* 1.3 67.1 + - - +
68B ALA* 4.3 2.7 - - + -
69B VAL* 2.9 48.3 + - + +
139B TYR* 4.8 5.4 - - - -
186B LEU* 3.6 28.9 - - + +
187B PHE* 3.4 32.1 - - + -
190B SER* 3.3 28.3 - - - +
192B PHE* 3.6 26.7 - - + -
285B VAL* 5.1 5.4 - - + -
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.1 29.7 + - - +
58B ILE* 4.0 11.9 - - - +
59B GLN* 3.0 23.2 + - - +
61B LEU* 3.6 25.0 - - - +
62B ASP 3.8 1.8 + - - -
63B GLY 3.2 15.1 + - - +
64B GLU 3.1 0.2 - - - -
65B MET* 1.3 82.2 - - - +
67B ASN* 1.3 62.6 + - - +
69B VAL 3.9 0.2 - - - -
70B CYS* 3.0 23.9 + - - +
339C TYR* 3.2 17.2 + - - -
366C ILE 4.1 0.2 + - - -
367C ARG 2.9 29.9 + - - -
368C THR 3.5 12.1 + - - -
369C GLN 4.6 0.4 - - - -
370C ASN* 2.8 55.4 + - - +
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.8 29.7 - - + +
44B TYR* 2.6 37.9 + - - -
64B GLU* 3.6 6.3 + - - +
66B ARG* 1.3 83.2 + - - +
68B ALA* 1.3 66.7 + - - +
70B CYS* 3.6 2.8 - - - +
71B ILE* 2.9 31.4 + - + +
135B LEU* 4.0 15.7 - - + -
368C THR 5.2 0.9 - - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU 3.2 21.2 + - - +
65B MET* 4.0 5.8 - - + +
67B ASN* 1.3 77.2 - - - +
69B VAL* 1.3 58.9 + - - +
71B ILE* 3.5 0.9 + - - +
72B PHE* 3.0 27.8 + - - +
135B LEU* 3.9 14.6 - - + +
139B TYR* 4.1 34.8 - - + -
143B ILE* 3.8 7.4 - - + +
186B LEU* 4.6 10.5 - - + -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.9 12.1 - - + -
61B LEU* 3.6 25.8 - - + -
65B MET* 2.9 44.2 + - + +
66B ARG 4.1 0.4 - - - +
68B ALA* 1.3 73.7 - - - +
70B CYS* 1.3 60.6 + - - +
72B PHE* 3.6 5.2 - - - +
73B TYR* 2.8 29.1 + - - +
183B LEU* 3.9 22.9 - - + -
186B LEU* 4.2 3.6 - - + -
187B PHE* 4.8 2.0 - - + -
288B PHE* 3.7 21.8 - - + -
992B IN0 4.5 4.0 - - + -
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Residues in contact with CYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 5.8 0.4 - - - -
43B CYS* 4.2 11.2 - - - -
44B TYR* 3.9 39.3 - - + +
47B LEU* 4.0 23.9 - - - +
58B ILE* 3.9 11.2 - - + +
66B ARG 3.0 19.1 + - - +
67B ASN* 3.3 6.0 + - - +
69B VAL* 1.3 75.9 - - - +
71B ILE* 1.3 64.4 + - - +
73B TYR* 3.4 3.3 + - - +
74B LEU* 3.1 38.3 + - - +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 5.0 4.9 - - + -
43B CYS* 3.8 23.1 - - + -
67B ASN* 2.9 23.5 + - + +
68B ALA 3.9 3.6 - - - +
70B CYS* 1.3 80.0 - - + +
72B PHE* 1.3 65.6 + - - +
74B LEU* 3.1 7.2 + - + +
75B VAL* 2.8 32.8 + - + +
128B ILE* 4.4 7.4 - - + +
131B GLU* 3.6 32.5 - - + +
132B PHE* 3.9 33.0 - - + +
135B LEU* 3.9 18.6 - - + -
143B ILE* 5.0 1.1 - - + -
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 3.0 18.6 + - - +
69B VAL* 3.3 6.9 + - - +
71B ILE* 1.3 75.2 - - - +
73B TYR* 1.3 57.7 + - - +
75B VAL* 3.2 4.4 + - + +
76B LEU* 2.9 65.5 + - + +
143B ILE* 3.7 38.6 - - + +
146B ILE* 4.0 29.6 - - + -
147B CYS* 5.2 0.7 - - - -
179B VAL* 3.8 11.7 - - + -
182B GLY* 3.9 12.3 - - - -
183B LEU* 3.7 44.0 - - + -
186B LEU* 3.9 8.5 - - + -
992B IN0 4.1 2.0 - - + -
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.5 21.8 - - + -
50B THR* 2.9 42.3 + - - -
51B SER* 3.5 23.3 + - - -
54B PHE* 4.8 2.5 - + - -
58B ILE* 3.9 15.7 - - + -
69B VAL 2.8 17.5 + - - +
70B CYS 3.5 4.5 - - - +
72B PHE* 1.3 76.9 - - - +
74B LEU* 1.3 59.6 + - + +
76B LEU* 3.3 6.4 + - - +
77B ARG* 2.8 46.6 + - - +
992B IN0 3.3 68.7 + + + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B CYS* 3.4 43.3 - - + +
46B TYR* 3.8 12.6 - - + -
47B LEU* 3.6 31.4 - - + +
50B THR* 3.9 10.5 - - - +
70B CYS* 3.1 18.8 + - - +
71B ILE* 3.1 8.7 + - + +
73B TYR* 1.3 80.5 - - + +
75B VAL* 1.3 57.2 + - - +
77B ARG* 3.1 6.6 - - + +
78B ALA* 2.9 28.4 + - - +
121B VAL* 4.1 12.7 - - + +
128B ILE* 4.2 26.6 - - + +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 2.8 33.7 + - + +
72B PHE* 3.5 6.3 - - + +
74B LEU* 1.3 75.5 - - - +
76B LEU* 1.3 63.5 + - + +
78B ALA* 3.2 9.6 + - - +
79B LEU* 3.1 18.5 + - - +
100B PHE* 3.5 13.9 - - + -
104B LEU* 3.7 24.5 - - + -
125B PHE* 4.2 3.6 - - + -
128B ILE* 4.2 13.2 - - + -
132B PHE* 5.0 1.1 - - + -
143B ILE* 4.2 9.6 - - + -
147B CYS* 3.1 36.1 - - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 2.9 53.4 + - + +
73B TYR 3.6 3.4 - - - +
75B VAL* 1.3 72.0 - - + +
77B ARG* 1.3 61.1 + - - +
79B LEU* 3.2 5.5 + - - +
80B ASP* 2.9 42.8 + - - +
146B ILE* 4.7 2.2 - - + -
147B CYS* 4.9 8.5 - - - -
150B MET* 3.7 36.3 - - + -
179B VAL* 3.9 15.3 - - + -
992B IN0 3.9 35.4 - - + -
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 3.4 44.0 + - + +
73B TYR* 2.8 37.2 + - - +
74B LEU* 3.1 14.8 - - - +
76B LEU* 1.3 77.2 - - - +
78B ALA* 1.3 60.2 + - - +
80B ASP* 3.8 20.1 + - - +
81B THR* 2.9 34.4 + - - -
84B ASP* 5.0 6.7 + - - -
118B ASP* 3.0 30.2 + - + +
121B VAL* 4.4 5.4 - - + -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU 2.9 10.2 + - - +
75B VAL 3.2 9.4 + - - +
77B ARG* 1.3 76.5 - - - +
79B LEU* 1.3 61.6 + - - +
81B THR* 3.2 4.5 + - - -
82B LEU* 3.0 26.4 + - - +
100B PHE* 3.8 15.7 - - + -
121B VAL* 3.5 25.7 - - + +
122B LEU* 3.6 16.1 - - + +
125B PHE* 3.8 12.1 - - + -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL 3.1 8.8 + - - +
76B LEU* 3.2 9.4 + - + +
78B ALA* 1.3 77.2 - - - +
80B ASP* 1.3 67.2 + - - +
82B LEU* 3.1 9.4 + - + +
83B GLU* 3.0 21.7 + - - +
97B LEU* 4.0 16.4 - - + +
100B PHE* 3.5 40.4 - - + -
147B CYS* 3.8 29.4 - - + +
150B MET* 3.8 28.3 - - + -
151B GLY 4.3 0.7 - - - +
154B MET* 3.3 26.3 - - + +
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 2.9 30.7 + - - +
77B ARG* 3.8 22.2 + - - +
79B LEU* 1.3 75.8 - - - +
81B THR* 1.3 57.5 + - - +
83B GLU* 3.2 10.5 + - - +
84B ASP* 2.8 44.6 + - - +
150B MET* 4.6 8.7 - - - +
154B MET* 4.5 9.5 - - - +
175B VAL* 4.4 18.9 - - - +
992B IN0 5.7 5.7 - - - +
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 2.9 24.7 + - - +
78B ALA 3.5 5.2 - - - -
79B LEU 3.2 0.2 - - - -
80B ASP* 1.3 78.6 - - - +
82B LEU* 1.3 62.3 + - - +
84B ASP* 3.9 6.4 - - - +
85B ASP* 3.1 24.6 + - - +
114B SER* 3.6 14.1 - - - +
116B GLU* 3.4 30.1 - - + +
118B ASP* 3.5 32.3 + - + +
122B LEU* 3.8 15.9 - - + +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA 3.0 18.3 + - - +
79B LEU* 3.1 13.7 + - + +
81B THR* 1.3 79.3 - - + +
83B GLU* 1.3 59.8 + - - +
85B ASP* 3.6 4.7 + - - +
88B ILE* 4.0 18.3 - - + +
93B LYS* 3.0 27.8 + - + +
96B LEU* 4.0 38.8 - - + +
97B LEU* 4.0 10.3 - - + -
100B PHE* 4.0 26.7 - - + -
109B TRP* 4.7 4.3 - - + -
111B PHE* 4.1 17.5 - - + -
114B SER* 5.8 0.9 - - - -
122B LEU* 4.0 17.5 - - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU 3.0 12.7 + - - +
80B ASP* 3.7 12.0 - - - +
82B LEU* 1.3 76.8 - - - +
84B ASP* 1.3 67.8 + - - +
86B MET* 3.7 8.1 - - - +
93B LYS* 2.8 24.2 + - - +
97B LEU* 4.1 6.2 - - + +
154B MET* 3.5 49.2 - - + +
157B PHE* 5.5 0.3 - - - +
158B LEU* 4.5 14.6 - - + +
171B TYR* 3.1 36.4 + - - -
175B VAL* 4.0 7.7 - - - +
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 5.0 6.6 + - - -
80B ASP* 2.8 32.2 + - - +
81B THR* 3.9 4.5 - - - +
83B GLU* 1.3 89.3 - - - +
85B ASP* 1.3 58.0 + - - +
86B MET* 2.9 25.6 + - - +
116B GLU* 3.3 27.2 - - + +
228B ARG* 5.3 12.6 + - - -
230B PHE* 5.8 3.5 - - - -
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR 3.1 18.7 + - - +
82B LEU 3.9 0.7 - - - +
83B GLU 3.4 1.2 - - - -
84B ASP* 1.3 72.4 - - - +
86B MET* 1.3 62.8 + - - +
87B THR* 2.6 33.7 + - - +
88B ILE* 3.2 23.6 + - + +
93B LYS* 2.8 23.2 + - - -
114B SER* 3.0 18.8 + - - -
115B LYS* 2.9 27.6 + - - +
116B GLU* 3.7 17.5 + - + +
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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