Contacts of the strand formed by residues 285 - 291 (chain B) in PDB entry 1OPL
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 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279B VAL* 3.3 1.5 - - - -
280B TRP* 2.6 42.8 + - + +
283B TYR* 2.7 32.9 - - + +
284B SER* 1.3 76.3 - - - +
286B THR* 1.3 74.3 + - - +
287B VAL* 4.1 5.2 - - + -
321B LEU* 4.1 25.1 - - + -
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Residues in contact with THR 286 (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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277B GLU* 3.8 22.2 + - + +
278B GLY 3.4 10.9 + - - +
279B VAL* 4.4 9.3 - - + +
284B SER 3.8 4.8 + - - -
285B LEU* 1.3 83.0 - - - +
287B VAL* 1.3 68.0 + - - +
335B GLU* 5.1 0.7 - - - -
336B PHE* 3.5 43.8 + - + +
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Residues in contact with VAL 287 (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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261B ILE* 4.7 5.2 - - + -
277B GLU* 3.5 4.9 - - - +
278B GLY 2.7 48.5 + - - +
279B VAL 4.2 2.7 - - - +
280B TRP* 4.3 13.0 - - + +
285B LEU* 3.9 16.4 - - + +
286B THR* 1.3 80.4 - - - +
288B ALA* 1.3 60.1 - - - +
289B VAL* 3.8 12.1 - - + -
321B LEU* 3.9 19.3 - - + -
333B ILE* 3.7 21.8 - - + -
334B THR 3.3 15.0 - - - +
336B PHE* 3.8 13.0 - - - -
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Residues in contact with ALA 288 (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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267B LEU* 4.4 10.5 - - + -
275B VAL* 4.6 0.9 - - + -
276B TYR 3.4 7.0 - - - +
277B GLU* 4.6 0.7 - - - +
287B VAL* 1.3 76.2 - - - +
289B VAL* 1.3 62.6 + - - +
332B ILE 3.8 0.7 - - - +
333B ILE* 3.4 3.8 - - - +
334B THR* 2.9 47.9 + - - +
335B GLU 3.9 2.0 + - - +
336B PHE* 4.5 2.0 - - + -
538B P16 3.8 36.0 - - + +
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Residues in contact with VAL 289 (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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261B ILE* 4.1 12.3 - - + -
263B MET* 3.8 33.2 - - + -
274B GLU 3.7 1.0 - - - +
275B VAL* 3.3 1.0 - - - -
276B TYR* 2.8 43.5 + - - +
278B GLY* 4.8 2.9 - - - -
287B VAL* 3.8 20.0 - - + -
288B ALA* 1.3 80.1 - - - +
290B LYS* 1.3 62.8 + - - +
291B THR 3.7 1.0 + - - -
331B TYR* 3.7 35.0 - - + -
332B ILE 3.4 7.9 - - - +
333B ILE* 4.1 9.2 - - + -
538B P16 4.2 2.9 - - - -
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Residues in contact with LYS 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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272B TYR 4.1 11.4 + - - -
274B GLU* 3.3 14.8 - - + +
275B VAL* 3.6 20.2 - - + +
289B VAL* 1.3 72.5 - - - +
291B THR* 1.3 65.0 + - - +
292B LEU* 5.6 0.2 - - - -
302B PHE* 3.3 29.5 - - + -
305B GLU* 2.9 36.0 + - - +
331B TYR* 3.4 1.7 - - - -
332B ILE* 2.9 38.5 + - + +
401B PHE* 4.3 13.9 - - - +
538B P16 3.9 25.3 + - + +
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Residues in contact with THR 291 (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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164B ILE* 3.4 37.3 - - + +
263B MET* 4.2 3.6 - - + -
274B GLU* 2.8 36.4 + - + +
276B TYR* 3.8 21.3 - - + -
289B VAL 3.7 1.2 + - - -
290B LYS* 1.3 78.2 - - - +
292B LEU* 1.3 61.3 + - - +
293B LYS 3.5 0.2 + - - -
302B PHE* 4.2 1.8 - - - -
329B PRO* 3.5 13.0 - - - +
330B PHE 3.5 4.5 - - - -
331B TYR* 3.4 23.6 - - - -
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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
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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