Contacts of the strand formed by residues 176 - 181 (chain B) in PDB entry 2J86
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 ASP 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B CYS 3.2 3.5 - - - +
115B ALA* 3.0 4.0 - - - -
116B HIS* 2.9 56.7 + - + -
135B SER* 5.1 5.9 - - - +
137B HIS* 3.1 25.1 + - - -
174B GLN* 3.2 26.4 + - - +
175B ILE* 1.3 67.4 - - - +
177B ILE* 1.3 60.6 + - - +
178B GLN* 5.0 5.3 - - + +
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Residues in contact with ILE 177 (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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69B VAL* 3.2 38.2 - - + +
72B LEU* 3.4 28.3 - - + -
73B ARG* 3.2 43.5 - - + +
113B TRP* 4.3 10.8 - - + -
114B CYS 3.2 3.6 - - - +
115B ALA* 3.9 9.9 - - + -
175B ILE* 3.1 18.6 + - + +
176B ASP* 1.3 75.1 - - - +
178B GLN* 1.3 67.3 + - - +
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Residues in contact with GLN 178 (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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112B ALA 3.9 0.3 - - - +
113B TRP* 4.1 2.5 - - - -
114B CYS* 2.8 48.1 + - + +
116B HIS* 6.2 1.3 - - + +
133B ILE* 3.0 39.5 - - - +
134B THR* 4.6 3.2 - - + +
176B ASP* 5.0 5.4 - - + +
177B ILE* 1.3 80.9 - - - +
179B PRO* 1.3 82.9 + - + +
180B ILE* 4.0 9.5 - - - +
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Residues in contact with PRO 179 (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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111B ARG* 5.7 4.5 - - + -
112B ALA 3.3 8.5 - - - +
113B TRP* 3.2 45.8 - - + -
177B ILE 4.8 0.7 - - - +
178B GLN* 1.3 90.4 + - + +
180B ILE* 1.3 72.0 + - - +
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Residues in contact with ILE 180 (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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103B ILE* 4.9 0.4 - - + -
111B ARG* 3.5 2.5 - - - +
112B ALA* 2.6 66.5 + - + +
114B CYS* 3.6 21.3 - - - -
122B ILE* 5.3 0.2 - - + -
124B ARG* 5.0 5.2 - - + -
133B ILE* 3.8 35.2 - - + -
178B GLN* 4.0 6.7 - - - +
179B PRO* 1.3 81.1 - - - +
181B ASP* 1.3 66.5 + - - +
188B LEU* 4.4 20.2 - - + -
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Residues in contact with ASP 181 (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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110B ASP 3.6 4.9 - - - +
111B ARG* 4.4 6.9 - - - +
126B ARG* 3.2 18.0 + - - +
179B PRO* 6.2 0.3 - - - +
180B ILE* 1.3 81.3 - - - +
182B LEU* 1.3 60.6 + - - +
183B GLU* 4.0 4.7 - - + -
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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
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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