Contacts of the strand formed by residues 287 - 291 (chain A) 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 LEU 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 3.6 33.2 - - + -
235A PRO 4.9 0.4 - - - +
236A LEU 4.9 5.2 - - - +
238A ILE* 3.8 18.8 - - + -
247A LYS 5.3 0.2 - - - +
248A ILE* 4.0 17.3 - - + +
251A GLY* 5.3 4.5 - - - -
253A ILE* 3.6 27.2 - - + +
255A THR 3.0 13.1 + - - +
256A HIS* 3.5 31.3 - - + +
257A ILE 3.1 22.9 + - - +
286A ILE* 1.3 69.8 - - - +
288A PHE* 1.3 64.7 + - - +
289A ILE* 3.7 14.5 + - + +
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Residues in contact with PHE 288 (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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236A LEU* 3.7 19.5 + - + +
237A VAL* 4.4 2.2 - - + -
238A ILE* 3.2 29.1 + - - +
257A ILE* 3.5 22.4 - - + -
275A PHE* 3.4 57.0 - + + -
278A ALA* 3.6 25.1 - - + -
279A ALA* 3.6 22.2 - - + -
282A PHE* 4.0 16.8 - + + -
286A ILE* 3.2 28.9 + - + -
287A LEU* 1.3 73.5 - - - +
289A ILE* 1.3 59.5 + - - +
339B ILE* 4.2 3.6 - - + -
343B CYS* 4.1 16.4 - - - -
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ILE* 3.4 24.7 - - + +
240A PHE* 3.9 12.6 - - + -
248A ILE* 3.7 31.6 - - + -
256A HIS* 3.3 42.4 - - + +
257A ILE 2.9 12.4 + - - +
258A LEU* 3.3 14.1 - - + -
259A LEU 2.7 31.5 + - - -
275A PHE* 3.3 6.0 - - - -
287A LEU* 3.9 9.4 - - + +
288A PHE* 1.3 79.6 - - - +
290A PHE* 1.3 64.5 + - - +
291A ILE* 4.5 5.4 - - + -
304B PHE* 6.1 2.7 - - + -
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Residues in contact with PHE 290 (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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237A VAL* 3.2 34.3 - - + -
238A ILE 3.0 13.6 + - - -
239A GLU* 3.4 48.0 - - + +
240A PHE* 2.8 31.9 + - - +
259A LEU* 3.2 22.2 - - + +
261A LEU* 4.8 8.1 - - + -
268A TYR* 3.5 25.1 - - - -
272A LEU* 3.9 27.4 - - + -
275A PHE* 4.3 3.8 - - + -
289A ILE* 1.3 73.2 - - - +
291A ILE* 1.3 64.9 + - - +
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Residues in contact with ILE 291 (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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239A GLU* 5.8 0.9 - - - -
240A PHE* 3.9 28.9 - - + +
258A LEU* 3.4 36.6 - - + -
259A LEU 2.8 11.3 + - - +
260A PHE* 3.6 25.8 - - + -
261A LEU* 2.9 27.3 + - - +
289A ILE* 4.5 4.0 - - + -
290A PHE* 1.3 84.2 - - - +
292A ASP* 1.3 63.2 + - - +
293A SER 3.3 3.3 + - - -
298A ASN* 3.6 31.6 - - + +
301A ILE* 4.1 11.7 - - + -
302A LEU* 5.9 0.4 - - + -
304B PHE* 4.7 4.5 - - + -
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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