Contacts of the helix formed by residues 176 - 181 (chain C) in PDB entry 2PK9
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 ALA 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C TYR 3.8 0.6 + - - -
175C ARG* 1.3 76.1 - - - +
177C PRO* 1.4 63.6 - - - +
178C ASP* 3.2 9.9 - - - +
179C VAL* 2.9 23.6 + - + +
180C LEU* 3.0 9.7 + - - +
190C ILE* 4.5 20.8 + - + +
193C TRP* 3.5 16.0 - - + -
285C ARG* 2.9 31.2 - - - +
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Residues in contact with PRO 177 (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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175C ARG 3.6 1.1 - - - +
176C ALA* 1.4 85.2 - - + +
178C ASP* 1.3 57.8 + - - +
180C LEU* 3.2 14.8 + - + +
181C MET* 2.8 37.5 + - + +
193C TRP* 3.6 31.2 - - + -
218C LEU* 3.9 17.0 - - + -
221C ILE* 4.5 6.1 - - + -
222C PHE* 4.4 12.6 - - + -
233C TRP* 5.1 4.0 - - + -
280C LEU* 3.9 34.8 - - + +
285C ARG* 4.1 1.3 - - - +
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ALA* 3.3 22.8 - - - +
177C PRO* 1.3 76.0 - - - +
179C VAL* 1.3 59.5 + - - +
181C MET* 3.5 0.6 + - - -
182C GLY 3.4 4.2 + - - -
183C SER* 3.0 31.6 + - - -
186C TYR* 3.7 24.4 - - - +
189C SER* 4.8 1.7 + - - -
190C ILE* 5.8 1.6 + - - -
233C TRP* 4.0 25.3 - - + -
239C LEU* 3.5 18.7 - - + +
282C PRO* 3.5 23.9 - - + +
285C ARG* 3.3 12.6 + - - -
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C SER* 3.5 23.5 + - - +
175C ARG* 3.4 34.3 - - - +
176C ALA* 2.9 10.6 + - + +
178C ASP* 1.3 82.7 - - - +
180C LEU* 1.3 59.4 + - - +
181C MET 3.1 1.6 - - - -
182C GLY* 2.8 20.6 + - - -
183C SER 3.9 4.9 + - - +
186C TYR* 3.6 34.8 - - + -
190C ILE* 3.7 23.6 - - + -
241C LYS* 4.5 0.9 + - - -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 4.0 29.2 - - + -
175C ARG* 3.6 34.3 - - + +
176C ALA 3.0 9.9 + - - +
177C PRO* 3.4 13.5 - - + +
179C VAL* 1.3 76.8 - - - +
181C MET* 1.3 52.8 + - - +
182C GLY 3.1 0.2 - - - -
214C ASP* 4.3 21.4 - - + +
217C GLN* 3.8 24.0 - - + -
218C LEU* 4.0 24.4 - - + +
221C ILE* 3.9 14.8 - - + -
241C LYS* 2.8 26.5 + - - +
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Residues in contact with MET 181 (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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177C PRO 2.8 21.9 + - - +
178C ASP* 3.7 0.9 - - - -
179C VAL 3.1 0.4 - - - -
180C LEU* 1.3 74.1 - - - +
182C GLY* 1.3 60.0 + - - +
183C SER 3.6 2.0 - - - -
218C LEU* 3.7 26.5 - - + -
222C PHE* 4.0 26.9 - - + -
228C PRO* 5.0 1.8 - - + -
233C TRP* 5.3 2.5 - - - -
236C VAL* 4.4 13.2 - - - -
239C LEU* 3.6 27.9 - - + +
240C PRO 3.7 0.5 - - - -
241C LYS* 3.0 39.9 + - - +
242C TYR* 3.6 43.5 - - + -
243C ASN* 4.2 4.9 - - + +
246C ILE* 5.6 3.4 - - + -
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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
------------------------------------------------------------
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