Contacts of the strand formed by residues 233 - 237 (chain C) in PDB entry 5FHK
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 ILE 233 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C LEU* 4.1 14.4 - - + -
165C VAL 3.4 9.2 - - - +
166C ALA* 4.2 6.1 - - + -
170C TYR* 3.7 19.7 - - + -
176C MET* 4.7 1.8 - - - -
177C PRO* 4.2 6.5 - - + -
183C LEU* 3.8 19.7 - - + -
186C HIS* 3.9 28.0 - - + +
187C PHE 2.9 11.0 + - - +
188C LEU* 3.4 8.5 - - + -
189C LEU* 2.8 25.4 + - - -
197C TRP* 3.5 5.4 - - + -
232C GLY* 1.3 74.2 - - - -
234C THR* 1.3 69.5 + - - +
253C ILE* 3.4 37.9 - - + -
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Residues in contact with THR 234 (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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163C ILE 3.6 0.3 - - - +
164C LEU* 3.2 6.9 - - - +
165C VAL* 3.0 52.2 + - + -
189C LEU* 2.8 23.7 + - - -
190C LYS* 4.9 0.3 - - - -
191C GLY 5.2 0.7 + - - -
197C TRP* 4.0 5.8 - - - -
223C VAL* 3.1 21.9 - - + +
224C ARG* 5.6 0.9 - - + -
227C CYS* 3.7 17.0 - - + -
232C GLY 4.0 0.2 + - - -
233C ILE* 1.3 74.8 - - - +
235C LEU* 1.3 65.3 + - - +
236C MET* 3.4 24.4 - - + +
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Residues in contact with LEU 235 (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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162C ASP* 3.7 17.3 - - + +
163C ILE 3.5 32.8 - - - +
164C LEU* 3.8 14.8 - - + +
191C GLY 5.9 0.5 + - - -
194C LEU* 3.9 28.8 - - + +
197C TRP* 3.6 54.8 + - + +
198C THR 5.0 0.2 - - - +
199C LEU* 4.1 8.5 - - + -
220C LEU* 4.5 4.2 - - - +
234C THR* 1.3 77.4 + - - +
236C MET* 1.3 71.9 + - - +
258C SER* 5.6 0.2 - - - -
259C ALA* 4.1 18.2 - - + -
260C ASN* 5.2 0.4 - - - +
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Residues in contact with MET 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ASP* 3.9 3.1 - - - -
163C ILE* 2.8 36.0 + - - +
165C VAL* 4.7 0.2 - - + -
220C LEU* 4.2 22.2 - - + +
223C VAL* 4.1 12.8 - - + -
224C ARG* 4.5 13.9 - - + +
234C THR* 3.4 34.8 - - + +
235C LEU* 1.3 85.4 - - - +
237C PRO* 1.3 73.1 - - + +
238C ASP 3.4 0.3 + - - -
240C MET* 3.9 22.0 - - + -
241C ILE* 3.4 42.6 - - + -
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Residues in contact with PRO 237 (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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100C ASN* 5.4 2.0 - - + -
101C LEU* 4.0 13.9 - - + -
160C VAL* 3.9 16.4 - - + -
161C LYS 3.7 1.3 - - - +
162C ASP* 3.1 24.9 - - - +
194C LEU* 4.2 5.8 - - + -
220C LEU* 4.0 15.0 - - + -
236C MET* 1.3 89.8 - - + +
238C ASP* 1.3 67.3 + - - +
239C VAL 4.6 0.7 - - - +
240C MET* 2.9 42.6 + - + +
241C ILE* 3.7 5.5 + - - +
262C ARG* 3.9 9.9 - - - +
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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