Contacts of the helix formed by residues 439 - 443 (chain F) in PDB entry 6O81
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 GLU 439 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F ASN* 3.5 19.4 + - - +
311F LYS* 4.3 3.1 - - + +
312F ILE* 4.6 10.7 - - - +
315F ALA* 3.7 27.4 - - + -
316F ALA* 4.8 2.3 - - - +
319F ILE* 4.2 7.0 - - + -
341F LEU* 3.6 27.4 - - - +
438F CYS* 1.3 82.2 - - - +
440F THR* 1.3 66.5 + - - +
441F TYR* 3.3 27.1 - - + -
442F LYS* 3.3 33.2 + - + +
443F PHE* 3.4 12.5 - - - -
503F GLU* 4.3 5.2 - - - -
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Residues in contact with THR 440 (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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311F LYS* 5.5 8.5 - - - +
439F GLU* 1.3 75.8 - - - +
441F TYR* 1.3 61.2 + - - +
442F LYS 3.1 1.6 + - - -
443F PHE* 3.2 41.5 + - + +
502F THR* 4.3 5.0 - - - -
503F GLU* 2.6 35.4 + - - -
504F LEU* 3.8 8.8 - - - +
515F VAL* 4.3 6.3 - - + +
516F LEU* 5.3 2.6 - - + +
519F LYS* 3.7 36.1 - - + -
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Residues in contact with TYR 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F ASN* 2.4 36.2 + - - -
226F CYS* 3.6 29.0 - - - +
272F SER* 3.7 18.5 - - - -
275F ASN* 2.8 26.6 + - + +
307F TYR* 3.6 29.2 - + + +
311F LYS* 3.6 46.4 - - + +
312F ILE* 3.4 14.9 - - + +
439F GLU* 3.6 14.6 - - + -
440F THR* 1.3 77.7 - - - +
442F LYS* 1.3 76.1 + - + +
443F PHE 3.4 2.2 - - - -
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Residues in contact with LYS 442 (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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222F SER* 3.5 20.1 + - - +
223F ASN* 3.6 20.4 + - - +
271F ALA* 5.5 0.9 - - - -
272F SER* 3.7 17.5 - - - +
275F ASN* 3.8 3.6 - - - +
339F SER* 6.3 0.8 - - - -
341F LEU* 5.6 1.6 - - - +
405F ALA 2.8 25.0 + - - -
406F HIS* 3.4 22.7 - - - +
407F ALA* 3.4 7.1 - - - +
408F LEU 3.2 20.1 + - - -
437F CYS 4.9 2.8 + - - -
438F CYS* 3.7 13.3 - - - -
439F GLU* 3.3 30.1 + - + +
440F THR 3.1 1.6 - - - -
441F TYR* 1.3 95.8 - - + +
443F PHE* 1.3 64.8 + - - +
444F CYS* 5.3 0.4 - - - -
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Residues in contact with PHE 443 (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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275F ASN* 2.6 32.1 + - - +
408F LEU* 3.4 38.8 - - + +
438F CYS* 3.9 5.2 - - + -
439F GLU 3.4 18.2 - - - -
440F THR* 3.2 34.8 - - + +
441F TYR 3.4 2.6 - - - -
442F LYS* 1.3 85.5 - - - +
444F CYS* 1.3 66.1 + - - +
445F GLU* 5.2 0.8 - - - +
500F VAL* 5.0 0.7 - - + -
502F THR* 4.0 21.8 - - + -
507F ILE* 5.4 0.2 - - + -
512F VAL* 4.2 11.9 - - + -
515F VAL* 3.6 25.6 - - + -
516F LEU* 3.9 34.3 - - + -
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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