Contacts of the strand formed by residues 286 - 291 (chain B) in PDB entry 4JU5
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 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A CYS* 3.8 28.3 - - + +
346A PHE* 3.7 27.1 - - + -
236B LEU* 5.9 1.9 - - - +
253B ILE* 3.9 3.6 - - - -
255B THR* 3.5 27.4 - - + +
257B ILE* 3.6 35.2 - - + +
279B ALA 5.6 0.2 - - - +
282B PHE* 3.1 31.0 + - + +
283B LYS* 5.4 0.5 - - - -
284B GLY 5.1 1.7 + - - -
285B LYS* 1.3 83.3 + - - +
287B LEU* 1.3 64.0 + - - +
288B PHE* 3.6 16.0 + - + -
317B LEU* 4.4 4.3 - - + -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 4.2 28.5 - - + -
235B PRO 5.4 2.0 - - - +
236B LEU 5.3 4.9 - - - +
238B ILE* 4.7 7.9 - - + -
248B ILE* 3.8 36.8 - - + +
251B GLY* 5.5 3.8 - - - -
253B ILE* 3.6 19.7 - - + +
255B THR 2.9 7.9 + - - +
256B HIS* 3.3 29.3 - - + +
257B ILE 2.8 32.1 + - - +
286B ILE* 1.3 72.8 - - - +
288B PHE* 1.3 59.6 + - - +
289B ILE* 3.8 10.1 + - + +
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 4.0 11.2 - - + -
343A CYS* 3.8 20.4 - - - -
236B LEU* 3.7 18.8 + - + +
237B VAL* 3.7 3.9 - - + -
238B ILE* 3.1 28.4 + - - +
257B ILE* 3.6 18.6 - - + -
275B PHE* 3.4 57.9 - + + -
278B ALA 3.7 10.1 - - - -
279B ALA* 3.5 29.6 - - + -
282B PHE* 3.9 20.2 - + + -
286B ILE* 3.6 18.4 + - + -
287B LEU* 1.3 71.7 - - - +
289B ILE* 1.3 60.3 + - - +
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 5.9 4.0 - - + -
238B ILE* 3.4 23.6 - - + +
240B PHE* 4.0 15.0 - - + -
248B ILE* 3.8 22.9 - - + -
256B HIS* 3.5 35.2 - - + +
257B ILE 2.9 11.1 + - - +
258B LEU* 3.3 21.1 - - + -
259B LEU 2.7 32.1 + - - -
275B PHE* 3.6 5.6 - - - -
287B LEU* 4.3 6.7 - - + +
288B PHE* 1.3 77.4 - - - +
290B PHE* 1.3 56.5 + - - +
291B ILE* 3.9 23.5 + - + -
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Residues in contact with PHE 290 (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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237B VAL* 3.2 37.2 - - + -
238B ILE 3.0 12.4 + - - -
239B GLU* 3.3 51.0 - - + +
240B PHE 3.1 24.1 + - - -
259B LEU* 3.2 19.5 - - + +
261B LEU* 5.0 7.2 - - + -
263B LYS* 5.3 2.0 - - - -
268B TYR* 3.7 21.8 - - - -
272B LEU* 3.7 30.5 - - + -
275B PHE* 4.4 3.8 - - + -
289B ILE* 1.3 74.4 - - - +
291B ILE* 1.3 67.7 + - - +
292B ASP* 4.3 2.6 + - + -
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 4.7 7.2 - - + -
240B PHE* 3.7 33.0 - - + -
258B LEU* 4.3 17.9 - - + -
259B LEU 2.7 17.2 + - - +
260B PHE* 3.5 35.7 - - + -
261B LEU 2.7 32.6 + - - +
289B ILE* 3.9 14.1 - - + -
290B PHE* 1.3 76.5 - - - +
292B ASP* 1.3 58.1 + - - +
293B SER 3.2 2.9 + - - -
298B ASN* 3.5 36.6 - - + +
301B ILE* 4.9 7.4 - - + -
302B LEU* 5.2 0.4 - - + -
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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
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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