Contacts of the strand formed by residues 235 - 244 (chain C) in PDB entry 1REP
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 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A T 3.9 2.9 + - - -
185C ILE* 4.2 18.3 - - + +
201C MET* 4.2 20.3 - - - +
205C ARG* 3.1 7.4 + - - -
228C GLU* 2.6 40.2 + - + +
229C LYS 3.2 18.2 - - - +
230C LYS* 2.5 28.2 + - - +
234C GLN* 1.3 75.8 - - - +
236C THR* 1.3 61.1 + - - +
237C HIS 3.6 10.5 - - - +
238C ILE* 4.6 0.4 - - + -
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Residues in contact with THR 236 (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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184C LYS* 3.3 14.5 - - - +
185C ILE* 2.8 30.7 + - - +
229C LYS* 2.8 20.4 + - - +
230C LYS 3.9 0.9 - - - -
231C LYS* 3.2 45.1 - - + +
234C GLN* 3.5 8.5 - - + +
235C THR* 1.3 73.9 - - - +
237C HIS* 1.3 94.9 + - - +
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Residues in contact with HIS 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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182C SER* 3.5 23.6 - - - +
183C LEU* 2.9 10.5 - - - +
184C LYS* 3.3 43.9 - - + +
185C ILE* 4.2 0.9 - - - +
229C LYS* 3.1 42.7 + - + +
235C THR* 3.6 6.4 - - - +
236C THR* 1.3 112.3 + - - +
238C ILE* 1.3 68.4 + - - +
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Residues in contact with ILE 238 (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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181C VAL 3.6 0.5 - - - +
182C SER* 3.3 1.4 - - - -
183C LEU 2.7 34.8 + - - +
185C ILE* 4.1 22.7 - - + -
188C ILE* 4.9 4.7 - - + -
201C MET* 6.1 0.4 - - - -
204C PHE* 4.6 7.0 - - + -
209C LEU* 3.5 29.2 - - + -
226C TYR* 4.0 13.5 - - + -
227C ILE 3.6 1.6 - - - +
228C GLU* 3.7 27.4 - - + -
237C HIS* 1.3 76.3 - - - +
239C VAL* 1.3 64.2 + - - +
240C PHE* 3.3 46.3 + - + -
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Residues in contact with VAL 239 (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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180C ILE* 4.1 29.2 - - + -
181C VAL 3.5 7.2 - - - +
182C SER* 3.6 9.6 - - - +
226C TYR* 3.1 6.9 - - - -
227C ILE* 2.7 58.5 + - + +
229C LYS* 3.5 33.2 - - + +
238C ILE* 1.3 70.5 - - - +
240C PHE* 1.3 63.4 + - - +
241C SER* 4.0 3.1 + - - +
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Residues in contact with PHE 240 (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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165C LEU* 3.8 25.6 - - + -
169C LEU* 3.7 24.9 - - + -
180C ILE* 3.1 5.4 - - - +
181C VAL* 2.7 42.2 + - + +
183C LEU* 3.4 37.5 - - + -
188C ILE* 4.5 7.2 - - + -
208C PHE* 5.6 0.4 - + - -
209C LEU* 3.9 22.2 - - + -
213C VAL* 4.8 3.6 - - + -
224C LEU* 4.0 19.7 - - + -
225C SER 3.7 1.3 - - - +
226C TYR* 3.8 16.4 - + + -
238C ILE* 3.3 35.2 - - + -
239C VAL* 1.3 72.3 - - - +
241C SER* 1.3 61.3 + - - +
242C PHE* 4.3 2.3 - - + -
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Residues in contact with SER 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 GLY 3.5 4.9 - - - -
180C ILE* 3.0 29.6 - - - +
224C LEU* 3.3 2.9 - - - +
225C SER* 3.1 42.7 + - - -
239C VAL* 4.0 4.2 + - - +
240C PHE* 1.3 70.5 - - - +
242C PHE* 1.3 60.9 + - - +
243C ARG* 4.1 15.1 + - - -
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Residues in contact with PHE 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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169C LEU* 3.0 50.0 - - + -
172C TYR* 4.0 9.6 - - + -
173C ARG* 3.3 27.6 - - + -
177C GLY 4.6 2.0 - - - -
178C SER* 3.0 6.0 - - - -
179C GLY* 2.8 52.7 + - - -
180C ILE* 4.1 2.2 - - - -
181C VAL* 4.5 9.4 - - + -
222C MET* 3.4 30.3 - - + -
223C ARG 3.4 3.6 - - - -
224C LEU* 3.7 16.8 - - + -
240C PHE* 4.4 1.1 - - + -
241C SER* 1.3 79.8 - - - +
243C ARG* 1.3 90.4 + - - +
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Residues in contact with ARG 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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174C LYS* 5.3 1.0 - - - +
177C GLY 3.8 1.1 - - - -
178C SER* 3.4 19.3 + - - -
179C GLY* 2.6 36.6 + - - +
180C ILE* 4.6 6.1 - - - +
222C MET* 5.0 2.5 - - - -
223C ARG* 3.0 36.3 + - + +
241C SER* 4.1 17.4 + - - -
242C PHE* 1.3 104.4 + - - +
244C ASP* 1.3 67.3 + - - +
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Residues in contact with ASP 244 (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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150C ARG* 5.8 1.6 + - - -
153C GLU* 5.6 0.7 - - - +
173C ARG* 5.1 6.4 + - - -
176C ASP 4.9 2.9 - - - +
177C GLY* 3.0 31.2 + - - +
178C SER* 4.7 0.2 - - - -
221C PRO* 3.7 21.0 - - - +
222C MET* 4.9 1.8 - - - +
243C ARG* 1.3 76.2 - - - +
245C ILE* 1.3 66.8 + - - +
246C THR* 2.4 59.7 + - - +
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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