Contacts of the helix formed by residues 287 - 295 (chain F) in PDB entry 6OY5
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 THR 287 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814C GLU* 3.1 31.2 - - + +
285F GLU 4.0 0.2 + - - -
286F PRO* 1.3 77.2 - - - +
288F TYR* 1.3 66.1 + - - +
289F GLU* 3.2 15.4 - - - +
290F GLU* 2.3 41.3 + - - +
291F ILE* 3.2 23.9 + - - +
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Residues in contact with TYR 288 (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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808C ARG* 4.9 6.7 - - - -
814C GLU* 3.3 38.3 + - + +
815C LEU 3.2 21.6 + - - -
817C PRO* 3.5 23.7 - - + +
287F THR* 1.3 77.3 - - - +
289F GLU* 1.3 52.6 + - - +
291F ILE* 3.3 7.7 + - + +
292F ALA* 2.7 34.3 + - - +
301F ALA* 3.8 26.9 - - + +
304F VAL* 3.8 21.5 - - + +
305F GLU* 3.7 38.8 - - + -
308F LEU* 4.3 20.4 - - + -
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Residues in contact with GLU 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814C GLU* 3.3 20.8 - - - +
287F THR* 3.5 11.6 - - - +
288F TYR* 1.3 72.4 - - - +
290F GLU* 1.3 60.7 + - + +
292F ALA* 3.6 4.2 - - - +
293F GLU* 2.8 31.2 + - - +
301F ALA* 3.4 26.4 - - + +
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Residues in contact with GLU 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F LEU* 3.5 10.9 - - + +
282F LEU* 3.1 33.4 - - + +
284F ARG* 3.0 33.0 + - - -
286F PRO* 4.1 7.4 - - + -
287F THR* 2.3 38.8 + - - +
288F TYR 3.4 0.6 - - - -
289F GLU* 1.3 77.4 - - + +
291F ILE* 1.3 62.2 + - - +
293F GLU* 3.7 9.2 + - - +
294F ALA* 3.2 23.2 + - - +
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Residues in contact with ILE 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F LEU* 4.7 13.9 - - + +
274F THR* 4.8 9.2 - - + -
275F ALA* 4.1 19.3 - - + -
278F LEU* 3.6 21.1 - - + -
286F PRO* 3.9 12.8 - - + +
287F THR 3.2 18.1 + - - +
288F TYR* 3.3 9.6 + - + +
289F GLU 3.2 0.4 - - - -
290F GLU* 1.3 75.3 - - - +
292F ALA* 1.3 64.4 + - - +
294F ALA 3.2 1.0 + - - -
295F MET* 3.0 43.1 + - + +
304F VAL* 3.9 26.2 - - + -
308F LEU* 5.6 5.4 - - + -
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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
----------------------------------------------------------
288F TYR 2.7 21.8 + - - +
289F GLU* 3.1 6.3 + - - +
291F ILE* 1.3 74.0 - - - +
293F GLU* 1.3 62.6 + - - +
295F MET 3.5 5.0 + - - -
296F GLY 3.6 4.3 - - - +
299F TRP* 3.5 24.2 - - - +
300F ASP* 3.2 42.6 - - - +
301F ALA* 3.5 2.7 - - - +
304F VAL* 3.7 8.3 - - + +
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Residues in contact with GLU 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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289F GLU 2.8 16.8 + - - +
290F GLU* 3.9 7.9 - - - +
292F ALA* 1.3 76.5 - - - +
294F ALA* 1.3 65.0 + - + +
296F GLY* 3.0 17.6 + - - -
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Residues in contact with ALA 294 (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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274F THR* 3.9 14.8 - - + +
278F LEU* 3.7 27.8 - - + -
290F GLU 3.2 16.4 + - - +
291F ILE 3.2 2.9 + - - +
293F GLU* 1.3 81.1 - - - +
295F MET* 1.3 60.3 + - - +
296F GLY 3.3 0.6 + - - -
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Residues in contact with MET 295 (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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267F THR* 5.1 0.9 - - + -
270F LYS* 4.2 41.4 + - + +
271F LEU* 3.6 27.4 - - + -
274F THR* 3.7 24.7 - - + -
291F ILE* 3.0 31.1 + - + +
292F ALA* 4.0 2.0 - - - +
293F GLU 3.0 0.8 + - - -
294F ALA* 1.3 77.8 - - - +
296F GLY* 1.3 59.2 + - - +
297F PRO* 4.6 1.7 - - - +
299F TRP* 3.3 64.6 + - + +
304F VAL* 5.4 0.2 - - + -
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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