Contacts of the strand formed by residues 175 - 179 (chain A) in PDB entry 4LIR
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 TRP 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU 3.9 16.2 - - - -
172A ASP* 3.2 15.7 + - - +
173A ASP* 4.3 3.8 - - - +
174A SER* 1.3 77.1 + - - +
176A VAL* 1.3 66.8 + - - +
201A LYS* 3.9 28.3 - - + -
203A VAL* 4.7 2.0 - - + -
212A HIS* 3.8 33.2 - - + -
213A ILE 3.3 19.7 - - - -
214A ARG* 3.5 49.9 - - + +
242A PRO* 4.1 4.0 - - - +
243A CYS* 3.4 26.6 + - + -
248A VAL* 3.9 17.5 - - + -
249A MSE 3.6 50.5 + - + +
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Residues in contact with VAL 176 (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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175A TRP* 1.3 79.1 - - - +
177A THR* 1.3 62.3 + - - +
178A VAL* 4.2 15.9 + - + -
212A HIS* 3.4 4.2 - - - -
213A ILE* 2.8 43.7 + - + +
215A TYR* 3.8 24.7 - - + -
221A ALA* 3.7 33.9 - - + +
224A ALA* 4.3 1.8 - - + -
225A LEU* 3.8 20.2 - - + -
240A VAL* 4.1 11.0 - - + -
241A LYS 3.5 8.1 - - - +
242A PRO* 5.0 0.4 - - + -
243A CYS* 3.9 4.9 - - - +
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Residues in contact with THR 177 (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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176A VAL* 1.3 70.4 - - - +
178A VAL* 1.3 62.6 + - - +
179A PHE* 3.8 3.6 - - - -
210A TRP* 4.1 10.8 - - + -
211A MSE 3.3 11.0 - - - +
212A HIS* 3.0 32.0 + - + +
240A VAL* 3.4 4.7 - - - +
241A LYS* 2.8 61.0 + - - -
243A CYS* 3.4 17.4 - - - -
244A ILE 4.6 0.7 + - - -
237B MSE 4.1 17.9 - - + -
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Residues in contact with VAL 178 (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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176A VAL* 4.1 12.3 - - + -
177A THR* 1.3 73.7 - - - +
179A PHE* 1.3 63.4 + - - +
181A PHE* 3.4 6.5 - - + -
189A ILE* 3.6 30.7 - - + -
193A PHE* 3.8 40.2 - - + -
210A TRP* 3.2 3.3 - - - +
211A MSE 2.9 42.6 + - + -
213A ILE* 3.8 16.6 - - + -
238A ILE* 3.9 10.3 - - + -
239A GLY 3.4 2.9 - - - -
240A VAL* 4.2 3.6 - - + -
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Residues in contact with PHE 179 (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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177A THR 3.8 9.9 - - - -
178A VAL* 1.3 77.0 - - - +
180A GLY* 1.3 62.6 + - - +
181A PHE* 3.6 6.1 - - - -
209A ASN 3.3 13.5 - - - +
210A TRP* 3.6 11.4 - - + -
228A ASP* 4.5 2.0 - - - -
238A ILE* 3.4 9.9 - - - +
239A GLY* 2.8 60.8 + - - -
240A VAL 3.7 3.6 - - - -
241A LYS* 3.7 25.6 - - + -
179B PHE* 4.6 1.3 - + - -
228B ASP* 4.2 10.8 - - - -
229B GLY* 4.0 16.2 - - - -
237B MSE 3.5 35.2 - - + -
238B ILE 3.6 18.8 - - - -
239B GLY* 3.6 14.1 - - - -
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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