Contacts of the helix formed by residues 178 - 182 (chain A) 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 ASP 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ALA* 3.3 18.5 - - - +
177A PRO* 1.3 78.2 - - - +
179A VAL* 1.3 64.7 + - - +
181A MET* 2.9 20.1 + - - +
183A SER* 3.3 32.5 + - - -
186A TYR* 4.2 13.2 - - - +
189A SER* 5.4 0.5 + - - -
233A TRP* 4.0 17.9 - - + -
239A LEU* 3.8 23.7 - - + +
280A LEU 4.6 0.4 - - - +
282A PRO* 3.5 23.5 - - + +
285A ARG* 3.5 11.6 + - - -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A SER* 3.7 24.8 + - - +
175A ARG* 3.7 30.1 - - - +
176A ALA* 3.1 17.7 + - + +
178A ASP* 1.3 81.7 - - - +
180A LEU* 1.3 57.5 + - - +
182A GLY* 2.9 21.5 + - - -
183A SER* 3.8 7.6 + - - +
186A TYR* 3.9 21.5 - - + -
190A ILE* 3.6 33.7 - - + -
241A LYS* 5.7 0.2 + - - -
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 4.1 31.0 - - + -
175A ARG* 3.4 45.8 - - + +
176A ALA 3.0 9.4 + - - +
177A PRO* 3.5 9.2 - - + +
178A ASP 3.2 0.2 - - - -
179A VAL* 1.3 73.7 - - - +
181A MET* 1.3 56.9 + - - +
182A GLY 3.3 1.3 - - - -
214A ASP* 5.0 13.0 - - + +
217A GLN* 3.8 25.1 - - + -
218A LEU* 4.0 21.6 - - + +
221A ILE* 3.9 12.1 - - + -
241A LYS* 3.5 19.7 - - - +
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO* 3.0 17.3 + - - +
178A ASP* 2.9 11.3 + - - +
180A LEU* 1.3 77.1 - - - +
182A GLY* 1.3 57.6 + - - +
183A SER 3.4 3.2 + - - -
218A LEU* 3.8 27.4 - - + -
222A PHE* 4.3 12.1 - - + -
228A PRO* 4.9 5.6 - - + -
233A TRP* 5.2 2.9 - - - -
236A VAL* 3.8 15.9 - - + -
239A LEU* 3.7 16.0 - - + +
240A PRO* 3.6 6.8 - - - +
241A LYS* 2.9 40.6 + - - +
242A TYR* 3.5 47.1 - - + -
243A ASN 4.6 1.8 - - - +
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Residues in contact with GLY 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL 2.9 10.1 + - - -
180A LEU 3.3 2.4 + - - -
181A MET* 1.3 76.0 - - - +
183A SER* 1.3 66.9 + - - +
184A ARG* 3.4 14.7 + - - +
240A PRO* 3.2 17.3 - - - +
241A LYS* 4.1 9.3 - - - +
294D MES 3.6 21.3 + - - -
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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