Contacts of the strand formed by residues 169 - 173 (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 LYS 169 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166F ARG* 4.3 12.3 - - - +
167F PRO 3.3 7.0 + - - +
168F ALA* 1.3 69.3 - - - +
170F VAL* 1.3 60.4 + - - +
192F GLN* 3.3 32.8 - - + +
194F PHE* 4.0 20.1 - - + -
248F GLY* 3.3 36.8 + - - +
249F MET* 3.3 21.2 - - + +
250F ASP* 2.7 33.2 + - - +
251F VAL 3.0 5.8 + - - -
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Residues in contact with VAL 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F PHE* 3.8 12.3 - - + -
168F ALA 3.5 15.3 - - - +
169F LYS* 1.3 71.4 - - - +
171F MET* 1.3 65.4 + - - +
172F VAL* 4.2 14.1 - - + -
186F ALA* 4.5 6.1 - - + -
191F ALA* 3.7 15.9 - - + -
192F GLN 2.8 12.3 + - - +
193F VAL* 3.3 10.0 - - + +
194F PHE* 2.7 35.7 + - - -
249F MET* 3.7 2.5 - - - -
251F VAL* 3.5 39.3 - - + -
253F ILE* 4.4 9.0 - - + -
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Residues in contact with MET 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F VAL* 1.3 74.7 - - - +
172F VAL* 1.3 60.3 + - - +
173F MET* 3.8 30.9 + - + +
194F PHE* 3.3 13.2 - - + +
195F ALA 4.9 0.2 - - - +
196F TYR* 4.9 7.0 - - - +
214F ILE* 3.9 29.4 - - + -
242F LEU* 5.1 4.3 - - + -
245F HIS* 4.3 14.6 - - + -
246F VAL* 3.8 31.0 - - + -
249F MET* 3.6 20.4 - - + -
251F VAL 2.8 9.1 + - - -
252F LEU* 3.3 15.3 - - + -
253F ILE 2.7 32.9 + - - +
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Residues in contact with VAL 172 (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* 4.2 7.6 - - + -
171F MET* 1.3 76.0 - - - +
173F MET* 1.3 58.4 + - - +
175F VAL* 3.3 20.1 - - + +
179F GLY* 3.4 35.9 - - - +
182F ALA* 3.7 26.5 - - + +
183F ILE* 3.7 23.8 - - + -
193F VAL* 4.0 11.2 - - + -
194F PHE 2.8 10.7 + - - +
195F ALA* 3.5 0.9 - - - -
196F TYR 3.4 13.3 + - - -
253F ILE* 3.2 18.2 - - + +
255F THR* 4.7 2.2 - - + -
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Residues in contact with MET 173 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F MET* 3.8 32.5 - - + +
172F VAL* 1.3 68.1 - - - +
174F GLY* 1.3 63.0 + - - +
196F TYR* 3.8 16.6 - - + +
242F LEU* 3.7 40.2 - - + -
246F VAL* 4.9 2.0 - - + -
252F LEU* 4.4 12.1 - - + -
253F ILE 2.6 10.5 + - - +
254F THR* 3.3 27.6 - - + -
255F THR* 2.9 28.4 + - - +
256F ALA* 3.5 1.8 + - - +
266F LEU* 3.9 26.9 - - + +
267F LEU* 4.6 13.0 - - + -
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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