Contacts of the helix formed by residues 237 - 241 (chain B) in PDB entry 2ETK
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 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B ASP* 5.6 1.0 + - - +
200B LYS* 3.9 21.6 + - - +
235B VAL 4.0 1.0 + - - -
236B GLY* 1.3 83.5 + - - +
238B PRO* 1.3 67.9 - - - +
239B ASP* 3.1 22.8 + - - +
240B TYR* 4.3 7.1 + - - +
241B ILE* 3.6 8.7 - - - +
283B LEU* 4.4 15.1 - - + +
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Residues in contact with PRO 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 5.2 7.2 - - + +
236B GLY 3.9 0.4 - - - -
237B THR* 1.3 84.6 - - - +
239B ASP* 1.3 68.1 + - - +
240B TYR 3.3 1.3 - - - -
241B ILE* 3.1 26.0 + - + +
246B LEU* 4.1 21.1 - - + -
283B LEU* 3.7 39.5 - - + +
286B THR* 3.8 13.7 - - + -
287B TYR* 4.2 5.4 - - + +
290B ILE* 3.0 30.6 - - + +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B THR* 3.1 14.8 + - - +
238B PRO* 1.3 84.7 - - - +
240B TYR* 1.3 80.3 + - + +
241B ILE 4.7 0.7 - - - +
262B TRP* 5.1 0.3 + - - -
266B VAL* 3.5 18.6 - - - +
276B THR* 3.3 32.3 + - + +
278B PHE* 4.7 9.3 - - - +
279B TYR* 4.4 11.6 - - - -
283B LEU* 5.5 1.6 - - - +
286B THR* 4.0 23.4 + - - +
290B ILE* 4.7 4.0 - - - +
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Residues in contact with TYR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B VAL* 5.9 0.5 - - - +
198B ASP* 5.8 2.7 - - - +
199B VAL 3.4 22.7 - - - +
200B LYS* 3.6 28.5 - - + -
201B PRO* 3.5 25.1 - - + +
202B ASP* 4.8 5.3 + - - -
237B THR* 4.3 8.3 + - - +
238B PRO 3.3 0.2 - - - -
239B ASP* 1.3 88.7 - - + +
241B ILE* 1.3 63.5 + - + +
262B TRP* 3.5 8.4 - - - -
263B SER* 2.7 34.3 + - - +
266B VAL* 3.6 29.2 - - + -
267B PHE* 4.6 4.3 - - - -
270B GLU* 2.5 38.1 + - - -
276B THR* 4.0 6.8 - - + +
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ARG 4.6 15.5 - - - +
198B ASP* 5.2 9.0 - - - +
235B VAL* 3.7 30.3 - - + -
236B GLY 3.9 8.1 - - - +
237B THR 3.6 22.9 - - - +
238B PRO* 3.1 22.0 + - + +
239B ASP 4.7 0.3 - - - +
240B TYR* 1.3 80.2 - - + +
242B SER* 1.3 73.7 + - - +
245B VAL* 3.8 26.7 - - + -
246B LEU* 3.9 14.5 - - + +
262B TRP* 3.2 9.6 + - - -
263B SER* 4.7 1.6 - - - -
290B ILE* 3.8 11.6 - - - +
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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