Contacts of the strand formed by residues 82 - 88 (chain B) in PDB entry 1EX0
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 PHE 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ASN* 3.5 18.6 - - - +
64B HIS* 3.9 8.3 - - - +
74B LEU* 3.9 21.3 - - + -
76B VAL* 3.8 30.1 - - + -
80B GLN 4.0 8.3 - - - -
81B SER* 1.3 75.2 - - - +
83B TYR* 1.3 67.8 + - - +
84B VAL* 3.7 24.2 - - + -
103B TYR* 3.3 32.3 - + - -
130B TRP* 5.2 4.7 - + - -
145B SER* 3.6 1.4 - - - -
146B ILE* 2.9 61.7 + - + +
148B SER* 5.2 8.7 - - - -
180B THR* 5.0 2.0 - - + -
182B ILE* 6.0 1.8 - - + -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU 3.6 4.0 - - - +
53B PHE* 3.6 15.8 - - + -
59B THR* 4.4 15.3 - - - -
60B ASN* 2.8 41.8 + - - +
81B SER* 5.6 4.2 + - - -
82B PHE* 1.3 74.2 - - - +
84B VAL* 1.3 67.6 + - - +
135B VAL* 4.3 12.6 - - + -
143B ARG* 4.0 21.8 - - - +
144B LEU 3.2 13.0 - - - +
145B SER* 3.7 25.1 + - - -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 5.1 0.4 - - + -
51B HIS 3.3 9.9 - - - +
52B LEU* 3.5 29.2 - - + -
53B PHE* 3.7 5.4 - - - -
82B PHE* 3.7 25.5 + - + -
83B TYR* 1.3 80.6 - - - +
85B GLN* 1.3 62.2 + - - +
86B ILE* 4.7 6.1 - - + -
142B VAL 4.1 0.2 - - - +
143B ARG* 3.4 5.0 - - - +
144B LEU* 2.8 49.0 + - + -
146B ILE* 3.6 23.8 - - + -
159B MET* 4.5 10.8 - - + -
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 3.5 4.0 - - - +
51B HIS* 2.7 53.1 + - + +
53B PHE* 3.6 21.7 - - + -
84B VAL* 1.3 75.5 - - - +
86B ILE* 1.3 65.8 + - - +
87B ASP* 2.5 33.2 + - - +
136B MET* 4.0 4.8 - - - +
141B SER* 3.5 16.3 + - - -
142B VAL 3.4 11.4 - - - +
143B ARG* 3.3 22.0 + - - +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 4.3 13.9 - - + -
49B SER 3.7 6.3 - - - +
50B VAL* 4.7 7.4 - - + -
84B VAL* 4.7 7.0 - - + -
85B GLN* 1.3 78.8 - - - +
87B ASP* 1.3 64.0 + - - +
88B PHE* 3.5 34.4 + - + -
99B PHE* 3.9 17.5 - - + -
101B VAL* 4.2 5.2 - - + -
141B SER* 3.3 1.4 - - - -
142B VAL* 2.9 37.5 + - + -
144B LEU* 3.6 31.9 - - + -
159B MET* 5.5 0.4 - - + -
161B VAL* 4.0 22.0 - - + -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 3.7 2.3 - - - +
48B THR* 2.7 46.8 + - - +
49B SER* 2.9 25.3 + - - +
51B HIS* 3.2 21.7 + - - -
85B GLN* 2.5 34.7 + - - +
86B ILE* 1.3 70.9 - - - +
88B PHE* 1.3 53.7 + - - +
140B ARG* 3.5 7.4 - - + +
141B SER* 2.8 12.7 + - - +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.5 31.0 - - + -
46B ASN 3.2 21.8 - - - +
47B VAL* 3.9 15.0 - - + -
48B THR* 3.9 5.7 + - - +
86B ILE* 3.5 30.7 - - + -
87B ASP* 1.3 75.5 - - - +
89B SER* 1.3 66.2 + - - +
90B ARG 3.2 15.5 - - - +
92B TYR* 4.4 13.5 - - + -
99B PHE* 3.7 37.9 - + + -
140B ARG* 2.7 34.0 + - - +
142B VAL* 3.8 25.4 - - + -
161B VAL* 4.7 1.6 - - + -
163B VAL* 5.1 2.2 - - + -
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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