Contacts of the strand formed by residues 87 - 92 (chain A) in PDB entry 2EX4
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 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER 3.0 12.9 + - - +
65A CYS* 3.3 15.0 - - - +
66A ALA 3.1 21.5 + - - -
85A PHE* 3.7 3.2 - - - +
86A ARG* 1.3 89.6 - - + +
88A VAL* 1.3 68.4 + - - +
111A ARG* 3.5 16.3 - - + +
113A ARG* 3.4 41.6 + - + +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A CYS* 5.1 0.9 - - - -
66A ALA* 3.3 11.0 - - + +
77A THR* 3.8 27.1 - - + +
81A LEU* 3.9 35.9 - - + +
82A LEU* 3.9 30.1 - - + +
85A PHE* 4.4 5.4 - - + +
87A GLU* 1.3 82.0 - - - +
89A ASP* 1.3 73.9 + - - +
90A MET* 4.4 1.3 - - + -
111A ARG 3.3 5.3 + - - -
112A VAL* 3.2 10.5 - - + +
113A ARG* 2.8 27.4 + - - -
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A CYS* 4.8 0.9 - - - -
66A ALA 2.8 6.3 + - - -
67A LEU* 3.4 11.7 - - + -
68A ASP 2.8 26.2 + - - -
88A VAL* 1.3 76.7 - - - +
90A MET* 1.3 61.9 + - - +
113A ARG* 2.8 33.3 + - - +
114A ASN* 2.9 44.2 + - - +
116A PHE* 3.8 6.3 - - + -
130A TYR* 2.6 33.4 + - + +
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Residues in contact with MET 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.6 1.3 - - - -
68A ASP* 3.6 4.0 - - + -
71A ALA* 3.6 13.2 - - + -
72A GLY 3.6 18.8 - - - +
74A GLY* 3.6 30.5 - - - +
77A THR* 3.6 21.1 - - + +
88A VAL* 4.4 0.7 - - + -
89A ASP* 1.3 78.6 - - - +
91A VAL* 1.3 55.0 + - - +
98A LEU* 4.1 12.1 - - + +
101A ALA* 3.8 11.0 - - + -
105A LEU* 3.8 16.6 - - - -
112A VAL* 4.2 9.4 - - + -
114A ASN 3.0 9.3 + - - +
115A TYR* 3.6 24.8 - - + -
116A PHE* 2.7 36.3 + - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.0 14.1 - - + -
68A ASP 2.9 16.7 + - - +
69A CYS* 3.8 14.6 - - - -
70A GLY 2.9 26.2 + - - -
71A ALA* 3.1 7.2 + - - -
90A MET* 1.3 75.6 - - - +
92A ASP* 1.3 64.5 + - - +
98A LEU* 4.7 0.2 - - - -
116A PHE* 3.3 24.0 - - + +
118A CYS* 3.5 19.7 - - + +
120A LEU* 3.9 15.9 - - + -
123A PHE* 3.9 31.9 - - + -
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY 3.1 12.0 - - - -
72A GLY* 2.8 24.0 + - - +
91A VAL* 1.3 75.2 - - - +
93A ILE* 1.3 63.2 + - - +
94A THR* 2.9 23.9 + - - +
97A PHE* 3.9 1.1 - - - -
98A LEU* 3.7 22.6 - - + +
116A PHE 3.1 5.9 + - - -
117A CYS* 3.3 8.5 - - - -
118A CYS 3.0 21.9 + - - -
1401A SAH 2.7 52.9 + - - -
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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
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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