Contacts of the strand formed by residues 192 - 196 (chain F) in PDB entry 4O9U
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 GLN 192 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B TYR* 4.8 20.2 - - + +
353B ASP* 5.6 5.1 + - - -
167F PRO* 3.6 28.3 - - + +
168F ALA 3.2 5.5 + - - +
169F LYS* 3.3 34.8 - - + +
170F VAL* 2.8 26.5 + - - +
187F LYS* 5.8 1.8 - - - +
190F GLY 3.8 2.4 + - - -
191F ALA* 1.3 69.1 - - - +
193F VAL* 1.3 59.6 + - - +
194F PHE* 4.3 10.5 - - + -
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F VAL* 3.3 11.2 - - + +
172F VAL* 4.0 15.9 - - + -
183F ILE* 3.8 33.4 - - + +
186F ALA* 3.9 22.9 - - + -
187F LYS* 4.1 13.5 - - + +
191F ALA* 3.2 21.2 + - + +
192F GLN* 1.3 73.7 - - - +
194F PHE* 1.3 86.1 + - - +
211F ALA* 3.2 23.7 - - + +
212F LYS 3.8 3.6 + - - -
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Residues in contact with PHE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F LYS* 4.0 24.2 - - + -
170F VAL 2.7 16.0 + - - +
171F MET* 3.3 8.1 - - + -
172F VAL* 2.8 24.8 + - - -
192F GLN* 4.3 13.5 - - + -
193F VAL* 1.3 86.4 - - - +
195F ALA* 1.3 62.5 + - - +
211F ALA* 4.1 2.7 - - - -
212F LYS* 3.2 36.3 - - + +
213F PRO 5.4 0.2 - - - -
214F ILE* 3.7 28.0 - - + -
249F MET* 3.6 28.5 - - + -
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Residues in contact with ALA 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F VAL 3.5 4.9 - - - +
175F VAL* 3.8 12.7 - - + +
183F ILE* 3.7 29.6 - - + -
194F PHE* 1.3 77.2 - - - +
196F TYR* 1.3 62.1 + - - +
197F ASP 4.3 0.5 + - - -
203F LEU* 4.6 6.6 - - - +
206F ALA* 3.7 20.4 - - + +
211F ALA* 4.6 4.1 - - + +
212F LYS 4.2 4.8 + - - -
213F PRO* 4.0 8.3 - - + +
214F ILE* 3.8 19.0 + - - +
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Residues in contact with TYR 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F MET* 4.9 3.4 - - - +
172F VAL 3.4 7.7 + - - +
173F MET* 4.2 21.8 - - + -
174F GLY* 2.7 32.7 + - - -
175F VAL* 3.6 4.1 + - - +
195F ALA* 1.3 73.3 - - - +
197F ASP* 1.3 78.0 + - - +
198F VAL* 3.8 15.5 - - + +
203F LEU* 5.0 1.8 - - + -
214F ILE* 4.4 23.8 - - + -
216F LEU* 4.7 17.4 + - - -
218F ILE* 4.6 9.5 - - - +
238F GLN* 3.9 25.9 - - + +
242F LEU* 3.6 34.1 - - + -
266F LEU* 5.2 1.3 - - + -
500F NAD 3.6 27.8 - + - -
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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