Contacts of the helix formed by residues 245 - 251 (chain F) in PDB entry 6V3O
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 MET 245 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174F PHE* 6.2 1.1 - - - -
184F ARG* 4.5 0.7 - - - +
241F MET* 3.2 37.0 - - + +
242F ARG 3.2 7.1 + - - +
244F GLY* 1.3 77.1 - - - +
246F SER* 1.3 62.9 + - - +
247F TYR 3.3 1.6 - - - -
248F ILE* 3.2 34.4 + - + +
249F HIS* 3.1 28.2 + - + +
287F SER* 5.4 1.8 - - - -
289F MET* 5.1 7.9 - - - -
311F ALA* 5.6 1.6 - - + -
314F MET* 3.7 28.3 - - - -
449F SER 5.2 0.2 - - - +
450F LEU* 3.6 26.5 - - + -
451F VAL* 3.8 24.0 - - + -
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Residues in contact with SER 246 (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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182F ALA 2.9 16.1 + - - -
184F ARG* 3.8 34.1 - - - +
187F LEU* 3.9 12.4 - - - +
242F ARG 3.8 1.4 + - - -
243F TYR* 2.3 29.7 + - - -
244F GLY 3.1 0.2 - - - -
245F MET* 1.3 77.4 - - - +
247F TYR* 1.3 69.2 + - - +
249F HIS* 3.3 2.6 + - - +
250F GLU* 2.9 32.9 + - - +
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Residues in contact with TYR 247 (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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174F PHE* 5.9 3.1 - - + -
182F ALA* 3.9 24.0 - - + +
187F LEU* 3.6 26.7 - - + +
243F TYR 5.0 1.3 - - - -
244F GLY* 4.0 10.7 + - - +
245F MET 3.3 0.6 - - - -
246F SER* 1.3 80.9 + - - +
248F ILE* 1.3 67.4 + - + +
250F GLU* 4.4 1.6 - - - +
251F THR* 3.1 24.6 + - + +
252F VAL* 3.3 9.4 + - + +
677F ILE* 3.8 45.8 - - + +
678F GLU* 2.7 47.8 + - - +
681F PHE* 4.3 21.3 - - + -
682F GLY* 4.1 7.0 - - - -
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Residues in contact with ILE 248 (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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174F PHE* 3.7 31.4 - - + -
244F GLY 5.0 2.2 - - - +
245F MET* 3.2 40.2 + - + +
247F TYR* 1.3 77.4 - - + +
249F HIS* 1.3 65.8 + - - +
252F VAL* 3.5 13.6 + - + -
253F TRP* 3.0 33.0 + - + +
285F PHE* 4.9 3.4 - - + -
318F LEU* 5.5 0.2 - - + -
446F PHE* 3.8 27.6 - - + -
450F LEU* 4.3 18.6 - - + -
451F VAL* 3.5 19.7 - - + -
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Residues in contact with HIS 249 (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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184F ARG* 3.5 42.0 + - - -
245F MET* 3.1 30.3 + - + -
246F SER 3.5 7.6 - - - +
248F ILE* 1.3 80.5 - - - +
250F GLU* 1.3 65.5 + - + +
253F TRP* 4.1 9.5 - - - +
254F LYS* 5.2 4.7 - - - +
314F MET* 3.6 40.9 - - + +
317F ASN* 6.1 2.2 - - + -
318F LEU* 4.0 38.2 - - + +
450F LEU* 4.2 5.1 - - + +
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Residues in contact with GLU 250 (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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184F ARG* 3.9 20.4 - - + +
187F LEU* 3.9 29.0 - - + +
188F GLN* 3.1 41.6 + - - +
246F SER 2.9 20.2 + - - +
247F TYR* 4.4 1.8 - - - +
249F HIS* 1.3 78.9 - - - +
251F THR* 1.3 63.5 + - - +
254F LYS* 3.5 20.1 + - - +
684F GLU* 5.7 0.7 - - - +
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Residues in contact with THR 251 (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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247F TYR* 3.1 15.1 + - + +
249F HIS 3.5 1.8 + - - -
250F GLU* 1.3 83.2 + - - +
252F VAL* 1.3 76.6 + - + +
253F TRP 3.4 1.6 - - - -
254F LYS* 3.6 11.1 + - - +
255F GLY* 2.9 24.9 + - - -
681F PHE* 2.9 31.3 + - + +
682F GLY 5.1 3.8 - - - -
684F GLU* 3.7 30.8 + - - +
687F CYS* 3.9 12.8 - - - +
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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