Contacts of the strand formed by residues 288 - 293 (chain F) in PDB entry 1P8J
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 288 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248F HIS 3.2 13.4 + - - +
249F ILE* 3.5 4.7 - - + +
250F TYR* 2.8 30.3 + - - +
282F ARG* 3.8 23.3 - - - +
286F GLY 4.0 0.4 - - - +
287F SER* 1.3 77.1 - - - +
289F PHE* 1.3 60.5 + - - +
290F VAL* 4.2 8.5 - - + -
315F LEU* 3.7 26.0 - - + -
378F ILE* 4.1 17.3 - - + -
382F LEU* 4.1 17.3 - - + -
389F THR 5.1 0.7 - - - +
390F TRP* 4.3 13.0 - - - -
393F MET* 3.8 35.2 - - + -
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Residues in contact with PHE 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F LEU* 3.5 44.6 - - + -
250F TYR* 3.7 30.5 - + + -
273F ALA 4.5 4.9 - - - -
274F PHE* 3.7 39.0 - + + -
277F GLY* 4.4 7.6 - - - -
278F VAL* 4.4 4.5 - - + -
287F SER* 3.6 28.5 + - - -
288F ILE* 1.3 72.0 - - - +
290F VAL* 1.3 61.8 + - - +
291F TRP* 4.6 5.4 - + + -
313F TYR* 3.6 23.8 + - + +
314F THR* 3.1 16.0 - - + -
315F LEU* 2.8 28.9 + - - +
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Residues in contact with VAL 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F ILE* 4.0 21.3 - - + -
250F TYR 2.8 11.6 + - - +
251F SER* 3.6 5.1 + - - +
252F ALA* 2.9 27.4 + - - -
288F ILE* 4.2 4.5 - - + -
289F PHE* 1.3 74.8 - - - +
291F TRP* 1.3 65.0 + - - +
315F LEU* 3.7 6.5 - - + +
317F ILE* 4.1 10.8 - - + -
371F ALA* 3.3 32.7 - - + +
374F ALA* 4.0 13.5 - - + -
375F ALA* 4.2 5.4 - - + -
378F ILE* 3.6 28.7 - - + -
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Residues in contact with TRP 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F LEU* 3.8 13.2 - - + -
250F TYR* 6.5 0.2 - - + -
252F ALA* 3.5 32.9 + - + -
254F TRP* 2.6 48.4 + + - -
274F PHE* 3.6 24.9 - + - -
289F PHE* 3.9 6.5 + + + -
290F VAL* 1.3 77.6 - - - +
292F ALA* 1.3 79.0 + - - +
308F TYR* 3.5 42.1 - + + +
309F THR* 3.6 20.2 - - + -
314F THR* 3.7 27.1 - - + +
315F LEU 2.9 11.3 + - - +
316F SER* 3.5 2.9 - - - -
317F ILE* 2.7 35.7 + - - +
371F ALA* 3.9 4.9 - - - -
805P AR7 4.3 0.6 + - - -
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Residues in contact with ALA 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F ALA 3.2 7.5 + - - -
253F SER* 3.8 24.7 - - - -
291F TRP* 1.3 72.3 - - - +
293F SER* 1.3 59.4 + - - +
294F GLY 3.3 0.2 - - - -
309F THR* 3.2 6.0 - - - +
317F ILE 3.9 4.9 - - - -
367F THR* 3.3 35.4 - - - +
368F SER 4.3 0.2 - - - +
371F ALA* 3.7 8.6 - - + +
805P AR7 2.8 32.2 + - - -
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Residues in contact with SER 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F TRP 3.6 1.2 + - - -
292F ALA* 1.3 71.9 - - - +
294F GLY* 1.3 58.6 + - - +
303F CYS* 3.3 29.2 - - - +
306F ASP* 4.5 1.4 - - - +
309F THR* 3.6 13.5 + - - +
316F SER* 3.5 15.3 - - - -
317F ILE 2.9 20.5 + - - -
318F SER* 2.8 29.6 + - - -
331F GLU* 3.8 10.0 + - - +
336F THR* 4.2 6.7 - - - -
367F THR* 3.8 7.4 - - - +
805P AR7 3.8 3.5 + - - -
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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