Contacts of the strand formed by residues 235 - 239 (chain G) in PDB entry 2OX4
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 235 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G VAL* 3.8 28.5 - - + -
210G ILE* 3.6 15.9 - - + +
212G VAL* 4.0 24.2 - - + -
230G ILE* 3.6 35.2 - - + +
231G GLU* 4.6 2.0 + - - -
233G PHE* 4.0 7.4 - - + +
234G ASN* 1.3 77.3 + - - +
236G PHE* 1.3 66.7 + - - +
237G PHE 3.4 23.8 - - - +
238G TYR* 4.7 1.3 - - + +
259G ILE* 3.7 35.9 - - + +
260G PRO* 4.2 4.7 - - - +
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Residues in contact with PHE 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E PRO* 3.6 44.7 - - + +
185E LEU 4.3 9.6 - - - -
225E GLN* 6.0 0.9 - - - -
125G ARG* 3.4 24.7 - - - -
209G ASP* 3.3 43.1 - - + +
210G ILE 2.8 22.2 + - - +
211G ILE* 3.9 10.8 - - + -
234G ASN* 3.5 5.0 + - - +
235G ILE* 1.3 73.2 - - - +
237G PHE* 1.3 96.3 + + - +
260G PRO* 3.5 17.8 - - - +
337G CYS* 4.2 15.0 - - - -
338G ILE* 4.4 9.0 - - + -
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Residues in contact with PHE 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E PRO* 5.0 1.6 - - + -
127G TYR* 5.1 0.2 - - - -
210G ILE 4.3 0.2 + - - -
211G ILE* 3.4 37.5 - - + +
212G VAL 3.1 23.9 + - - -
235G ILE* 3.4 7.1 - - - +
236G PHE* 1.3 108.6 - + - +
238G TYR* 1.3 60.5 + - - +
239G GLU* 4.4 3.1 - - + -
259G ILE* 4.2 2.7 - - - -
260G PRO* 3.3 24.2 - - + +
262G ALA* 3.4 21.1 - - + -
284G VAL* 3.9 22.7 - - + -
286G GLN* 3.6 21.3 - - - -
313G GLN* 3.6 18.6 - - - -
337G CYS* 4.1 14.6 - - - -
338G ILE* 4.2 5.4 - - + -
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Residues in contact with TYR 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G VAL* 3.4 24.7 - - + -
214G ASN* 3.1 39.3 + - - -
223G ALA* 2.9 32.5 + - - -
226G PHE* 3.7 18.3 - + - +
227G ALA* 3.7 17.3 - - + -
230G ILE* 4.7 4.5 - - + -
235G ILE* 4.9 0.7 - - + -
237G PHE* 1.3 74.9 - - - +
239G GLU* 1.3 59.8 + - - +
241G ILE* 3.6 23.0 - - + +
257G ILE* 4.0 15.3 - - + -
259G ILE* 3.8 14.1 - - + -
260G PRO 2.9 14.7 + - - +
261G LEU* 3.5 17.5 - - + +
262G ALA* 2.9 22.4 + - - +
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Residues in contact with GLU 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G LYS* 2.8 28.0 + - - +
211G ILE* 4.8 0.9 - - + -
212G VAL 2.8 15.9 + - - +
213G GLU* 3.4 16.6 - - - +
214G ASN* 2.9 25.8 + - - +
237G PHE* 4.4 5.3 - - + -
238G TYR* 1.3 73.5 - - - +
240G GLU* 1.3 74.7 + - + +
241G ILE* 3.5 2.4 + - - +
262G ALA* 3.5 11.7 - - + -
265G GLU* 3.0 7.4 - - - +
286G GLN* 2.9 35.8 + - - +
315G HIS* 5.1 1.2 - - - -
502G MG 2.1 32.8 - - - -
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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