Contacts of the helix formed by residues 83 - 97 (chain B) in PDB entry 2E7Y
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 ASN 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B HIS* 3.9 3.4 - - - +
49B GLY* 3.3 27.2 + - - -
79B TYR* 3.9 9.3 - - + -
80B PRO* 3.0 19.8 + - + +
81B GLU 3.3 1.4 + - - -
82B GLY* 1.3 74.1 - - - +
84B ARG* 1.3 64.7 + - - +
85B ALA* 3.4 8.3 - - - +
86B VAL* 3.0 44.9 + - + +
87B GLU* 3.4 17.1 + - - +
139B VAL* 3.2 31.9 + - - +
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 5.6 1.6 + - - -
82B GLY 2.8 16.5 + - - +
83B ASN* 1.3 70.0 - - - +
85B ALA* 1.3 59.7 - - - +
87B GLU* 3.1 16.7 + - - +
88B GLU* 2.7 75.3 + - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TRP* 5.7 1.7 - - + -
92A PHE* 5.5 0.5 - - - -
96A ALA* 6.4 0.7 - - - -
97A ASN* 6.4 0.2 - - - +
49B GLY 3.2 26.7 - - - +
50B HIS* 6.1 1.3 - - + -
54B ILE* 4.1 2.8 - - + +
83B ASN* 3.3 10.0 - - - +
84B ARG* 1.3 78.9 - - - +
86B VAL* 1.3 61.6 + - - +
88B GLU* 3.6 11.5 + - - +
89B TYR* 3.1 25.6 + - - +
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.0 19.3 - - + -
48B HIS* 4.0 9.2 - - - +
49B GLY* 3.8 14.4 - - - -
54B ILE* 4.5 8.1 - - + -
77B VAL* 5.5 0.2 - - + -
79B TYR* 3.6 45.8 - - + -
83B ASN* 3.0 31.1 - - - +
85B ALA* 1.3 75.3 - - - +
87B GLU* 1.3 60.3 + - - +
89B TYR* 3.4 0.9 + - - +
90B THR* 2.9 45.4 + - + +
106B VAL* 5.0 1.3 - - + -
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 2.8 34.4 + - + +
82B GLY* 4.7 8.9 + - - +
83B ASN 3.4 15.7 - - - +
84B ARG* 3.1 22.3 + - - +
86B VAL* 1.3 77.4 - - - +
88B GLU* 1.3 58.1 + - + +
90B THR* 3.3 5.9 + - - -
91B GLU* 2.9 50.9 + - - +
106B VAL* 6.1 2.2 - - + -
108B PRO* 5.3 1.4 - - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.7 13.5 - - + -
95A ARG* 4.6 10.0 + - - +
96A ALA* 4.0 29.7 - - + +
84B ARG* 2.7 58.6 + - - +
85B ALA* 4.0 10.7 - - - +
87B GLU* 1.3 74.5 - - + +
89B TYR* 1.3 59.1 + - - +
91B GLU* 3.8 12.3 - - - +
92B PHE* 3.0 26.7 + - - +
95B ARG* 4.8 2.4 + - - -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 6.0 0.2 - - - +
58A TRP* 3.8 12.6 - + + -
89A TYR* 5.1 3.1 - + - -
92A PHE* 3.5 33.2 - + + -
54B ILE* 3.1 45.5 - - + -
55B ALA* 2.9 26.6 + - - -
57B LEU* 3.9 11.9 - - + -
58B TRP* 3.2 24.6 + + + +
85B ALA 3.1 15.8 + - - +
86B VAL 4.0 1.3 - - - +
88B GLU* 1.3 77.8 - - - +
90B THR* 1.3 61.5 + - + +
92B PHE* 3.1 14.6 + + - +
93B ILE* 2.9 55.6 + - + +
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.9 26.7 - - + -
77B VAL* 5.4 0.2 - - + -
86B VAL* 2.9 31.9 + - + +
87B GLU* 3.3 8.8 + - - -
89B TYR* 1.3 77.2 - - + +
91B GLU* 1.3 65.0 + - - +
93B ILE* 3.3 9.2 + - - +
94B LYS* 3.1 29.9 + - - +
104B PHE* 3.9 9.4 - - + -
106B VAL* 3.6 38.5 - - + +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 2.9 40.4 + - - +
88B GLU* 3.8 11.5 - - - +
90B THR* 1.3 79.6 + - - +
92B PHE* 1.3 57.0 + - - +
94B LYS* 3.4 5.9 + - - +
95B ARG* 2.9 41.1 + - - +
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Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA 5.4 0.9 - - - -
88A GLU* 3.7 6.7 - - + -
89A TYR* 3.6 52.9 - + + -
92A PHE* 3.6 30.3 - + + -
58B TRP* 3.9 28.5 - + - -
88B GLU 3.0 15.7 + - - +
89B TYR* 3.5 18.6 - + - +
91B GLU* 1.3 78.1 - - - +
93B ILE* 1.3 74.5 + - + +
95B ARG* 3.5 23.2 - - - +
96B ALA* 2.9 48.7 + - + +
97B ASN* 4.7 0.2 - - - -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.4 9.9 - - + +
58B TRP* 3.7 50.7 - - + +
61B VAL* 4.3 3.1 - - + -
89B TYR* 2.9 41.6 + - + +
90B THR* 3.3 12.3 + - - +
92B PHE* 1.3 88.9 - - + +
94B LYS* 1.3 58.1 + - - +
97B ASN* 2.8 37.8 + - - +
100B LEU* 4.2 12.3 - - + +
104B PHE* 3.9 24.9 - - + -
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 3.1 17.0 + - - +
91B GLU* 4.0 4.5 - - - +
93B ILE* 1.3 73.9 - - - +
95B ARG* 1.3 65.0 + - - +
97B ASN 3.7 12.7 - - - +
101B ARG* 2.8 63.3 + - + +
104B PHE* 2.8 60.6 + - + -
105B ASN* 3.8 12.9 + - - +
106B VAL* 5.1 3.7 - - - +
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 4.4 16.6 + - - +
95A ARG* 3.3 33.8 - - - +
88B GLU 4.8 1.4 + - - -
91B GLU* 2.9 22.1 + - - +
92B PHE* 3.5 35.7 + - - +
94B LYS* 1.3 77.5 - - - +
96B ALA* 1.3 59.4 + - - +
98B PRO* 4.4 1.7 - - - +
101B ARG* 3.0 24.2 + - - +
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 6.4 0.4 - - - -
88A GLU* 3.5 33.7 - - + +
92B PHE* 2.9 43.7 + - + +
95B ARG* 1.3 79.8 - - - +
97B ASN* 1.3 71.7 + - - +
98B PRO* 3.5 8.0 - - - +
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Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 6.1 3.2 - - - +
58B TRP* 3.7 40.0 + - - +
92B PHE* 4.7 0.7 - - - -
93B ILE* 2.8 27.4 + - - +
94B LYS 3.7 6.1 - - - +
95B ARG 3.4 0.2 - - - -
96B ALA* 1.3 93.3 + - - +
98B PRO* 1.3 57.7 - - - +
99B ASP* 3.1 13.7 + - - +
100B LEU* 2.8 38.7 + - + +
101B ARG 3.4 6.1 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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