Contacts of the strand formed by residues 177 - 181 (chain B) in PDB entry 2QNR
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 ILE 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B CYS* 3.5 7.0 - - + -
151B TYR* 4.1 15.7 - - + -
168B MSE 3.5 48.7 - - + +
171B ILE* 3.9 24.2 - - + -
172B HIS* 3.4 37.0 - - + -
175B VAL* 3.4 10.3 + - + +
176B ASN* 1.3 72.9 - - - +
178B VAL* 1.3 63.2 + - - +
179B PRO* 3.9 0.3 - - - +
208B ILE* 4.7 3.4 - - + -
209B LYS 4.2 4.4 + - - +
210B ILE* 3.5 17.2 - - + +
211B TYR* 3.1 27.8 + - - +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B CYS* 3.7 22.4 - - - -
149B CYS 2.8 7.9 + - - +
150B PHE* 3.2 31.6 - - + -
151B TYR 2.7 30.6 + - - -
176B ASN 3.4 1.5 + - - +
177B ILE* 1.3 75.0 - - - +
179B PRO* 1.3 68.7 - - + +
180B VAL* 3.8 2.3 + - + +
211B TYR* 4.3 21.8 - - + -
213B LEU* 6.0 1.1 - - + -
235B ILE* 6.5 0.2 - - + -
237B PHE* 4.5 7.2 - - + -
276B LEU* 4.1 7.9 - - + -
279B MSE 4.1 22.2 - - + -
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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
----------------------------------------------------------
151B TYR* 3.5 9.0 - - + +
153B ILE* 4.1 14.8 - - + -
168B MSE 4.1 15.5 - - + -
177B ILE 3.9 7.2 - - - +
178B VAL* 1.3 90.8 - - + +
180B VAL* 1.3 64.0 + - - +
199B ILE* 5.2 0.9 - - + -
200B LEU* 6.2 0.2 - - + -
203B ILE* 4.8 7.9 - - + -
210B ILE* 4.0 32.1 - - + -
235B ILE* 4.6 7.9 - - + -
236B PRO* 3.4 33.4 - - + +
237B PHE* 3.7 3.6 + - - -
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PHE* 4.5 11.9 - - + -
151B TYR 2.9 9.8 + - - +
152B PHE* 3.4 23.4 - - + -
153B ILE* 2.8 30.2 + - - +
178B VAL* 3.8 21.5 - - + +
179B PRO* 1.3 82.0 - - - +
181B ILE* 1.3 68.2 + - - +
236B PRO* 4.7 0.4 - - - -
237B PHE* 3.4 11.9 - - + +
239B VAL* 3.6 32.3 - - + -
276B LEU* 4.4 16.8 - - + -
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ILE* 3.6 7.0 - - + +
155B PRO* 4.1 5.8 - - + -
180B VAL* 1.3 73.2 - - - +
182B ALA* 1.3 70.8 + - - +
184B ALA* 4.4 1.1 - - - +
187B LEU* 3.8 25.8 - - + -
192B ARG* 4.9 2.0 - - + +
195B LEU* 3.8 18.4 - - + -
196B LYS* 3.7 31.9 - - + +
199B ILE* 3.8 24.0 - - + -
236B PRO* 3.8 21.7 - - + +
237B PHE 2.9 7.5 + - - +
238B SER* 4.0 14.8 - - - -
239B VAL 3.1 24.9 + - - -
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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