Contacts of the strand formed by residues 205 - 209 (chain F) in PDB entry 4LQL
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 THR 205 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175F HIS 6.2 0.9 - - - -
176F ILE 3.1 9.0 + - - -
177F LYS* 3.4 15.6 - - - +
178F ILE* 3.3 26.1 + - - +
199F GLN* 3.5 25.4 + - - +
203F GLY 3.0 6.2 + - - -
204F TRP* 1.3 71.6 - - - +
206F VAL* 1.3 58.4 + - - +
207F ASP* 3.8 15.2 + - - -
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Residues in contact with VAL 206 (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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187C ASP 5.8 0.3 + - - -
178F ILE* 3.9 9.4 - - - -
195F LYS* 5.8 4.9 - - - +
199F GLN* 5.0 3.3 + - - +
204F TRP 3.5 5.9 + - - -
205F THR* 1.3 71.9 + - - +
207F ASP* 1.3 66.1 + - - +
208F TYR* 5.7 1.1 - - - -
309F PHE* 6.1 7.0 - - - -
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Residues in contact with ASP 207 (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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186C ARG* 4.4 20.6 - - + +
187C ASP* 5.0 13.0 - - - -
178F ILE 3.1 16.6 + - - +
179F ALA* 3.3 3.5 - - - -
180F ARG* 2.8 31.7 + - - +
205F THR* 3.8 14.1 + - - -
206F VAL* 1.3 78.2 - - - +
208F TYR* 1.3 58.8 + - - +
209F TYR* 5.1 2.9 - - + -
272F TYR* 5.9 3.8 - - + -
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Residues in contact with TYR 208 (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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183C ASP* 4.4 25.6 - - + -
184C THR 5.3 6.4 + - - +
186C ARG* 4.1 18.5 + - - +
180F ARG* 3.3 30.5 - - + +
182F GLY 5.4 2.2 - - - -
183F ASP* 5.0 7.4 - - + -
206F VAL 5.7 1.3 - - - -
207F ASP* 1.3 76.0 - - - +
209F TYR* 1.3 68.3 + - - +
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Residues in contact with TYR 209 (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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179F ALA* 4.8 13.7 - - + -
180F ARG 3.3 17.3 + - - +
181F PHE* 4.3 2.6 - - - -
182F GLY* 3.7 9.0 + - - -
207F ASP* 5.0 2.7 - - + -
208F TYR* 1.3 84.4 - - - +
210F PRO* 1.3 70.2 - - - +
213F GLU* 5.1 9.6 - - + -
266F PHE* 4.6 25.4 - + + -
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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