Contacts of the strand formed by residues 239 - 243 (chain C) in PDB entry 2F4N
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 PHE 239 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C TYR* 3.7 16.6 - + - -
68C LEU* 3.8 24.2 - - + -
114C TYR* 6.0 4.3 - + - -
176C ILE* 3.6 24.5 - - + -
185C ILE* 3.9 9.6 - - + -
186C THR 3.4 17.0 - - - +
187C ASN 3.5 23.6 - - - -
188C ILE 3.5 3.6 - - - -
189C LYS* 4.3 8.7 - - + -
233C LEU 3.2 1.2 - - - +
234C ILE* 3.3 3.3 - - - -
235C ASN* 2.8 32.7 + - - +
237C GLU* 3.7 27.4 - - + -
238C GLY* 1.3 82.9 - - - +
240C LEU* 1.3 64.6 + - - +
241C GLU 3.3 0.7 + - - -
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C THR* 3.0 40.6 + - + +
188C ILE* 3.0 30.2 + - + +
189C LYS 5.2 1.5 - - - +
195C PHE* 4.4 11.2 - - + -
201C ILE* 6.2 0.2 - - + -
203C ILE* 5.2 6.5 - - + -
219C PHE* 4.2 15.9 - - + -
232C CYS* 4.0 32.8 - - + -
233C LEU 3.3 14.4 - - - +
234C ILE* 4.5 6.8 - - + +
239C PHE* 1.3 70.2 - - - +
241C GLU* 1.3 59.0 + - - +
242C ILE* 5.5 3.3 - - + +
261C ILE* 6.1 0.7 - - + -
263C ILE* 3.5 33.4 - - + -
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Residues in contact with GLU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASP* 3.6 6.8 - - - +
183C ASN* 2.9 37.6 + - + +
184C ILE 3.3 11.0 - - - +
185C ILE* 3.7 10.4 - - + +
223C TYR* 2.7 36.1 + - - -
232C CYS* 2.8 7.2 - - - -
233C LEU* 2.6 49.0 + - + +
235C ASN* 3.2 29.0 + - + +
239C PHE 4.2 4.5 - - - +
240C LEU* 1.3 75.3 - - - +
242C ILE* 1.3 65.9 + - - +
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ASN* 3.5 4.9 - - - -
184C ILE* 2.8 66.8 + - + +
186C THR* 5.7 5.4 - - - +
203C ILE* 4.1 38.1 - - + -
205C ILE* 4.3 14.1 - - + -
215C ILE* 4.1 21.5 - - + -
217C CYS* 4.2 3.8 - - - -
230C PHE* 4.7 7.9 - - + -
231C ILE 3.3 9.4 - - - +
232C CYS* 4.6 3.6 - - + -
240C LEU* 5.5 4.3 - - + +
241C GLU* 1.3 74.6 - - - +
243C SER* 1.3 65.6 + - - +
249C ALA* 3.7 5.2 - - + +
253C LEU* 5.0 0.7 - - + -
261C ILE* 5.0 5.2 - - + -
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Residues in contact with SER 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ASN* 2.8 28.6 + - - -
223C TYR* 3.6 27.1 - - - -
230C PHE* 3.7 4.8 - - - -
231C ILE* 2.8 48.1 + - - +
233C LEU* 4.6 2.9 - - - -
241C GLU* 4.0 1.5 + - - -
242C ILE* 1.3 73.4 - - - +
244C LYS* 1.3 75.8 + - - +
245C PHE* 4.4 1.6 + - - -
247C ASP 5.3 0.2 + - - -
249C ALA* 4.1 6.3 - - - -
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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