Contacts of the strand formed by residues 363 - 368 (chain F) in PDB entry 3FZ7
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 TYR 363 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357F ILE* 3.4 33.2 - - + -
358F ALA* 4.4 1.1 - - - +
360F LEU* 4.1 1.3 - - + -
361F GLY* 3.3 36.7 + - - +
362F PRO* 1.3 81.0 - - - +
364F GLU* 1.3 61.3 + - - +
365F PHE* 3.6 23.4 - + + -
380F PHE* 3.6 22.7 - + + -
381F LYS 3.3 8.1 - - - +
382F LEU* 3.8 17.9 - - + -
383F LYS* 3.3 20.0 - - - +
390F TYR* 2.7 29.2 + - - -
392F LEU* 4.4 3.4 - - + -
395F LEU* 4.3 0.5 - - - +
441F TYR* 2.9 34.1 + - - -
445F LEU* 4.2 1.9 - - - +
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Residues in contact with GLU 364 (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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363F TYR* 1.3 75.9 - - - +
365F PHE* 1.3 70.3 + - - +
366F ILE* 3.9 3.6 + - + +
380F PHE* 3.2 2.5 - - - -
381F LYS* 2.9 71.7 + - + +
383F LYS* 4.1 15.8 - - + +
384F ASP* 4.9 3.8 + - - +
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Residues in contact with PHE 365 (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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354F ALA* 3.7 11.0 - - - -
357F ILE* 4.1 10.8 - - + -
358F ALA* 3.6 41.7 - - + -
363F TYR* 3.6 28.3 - - + -
364F GLU* 1.3 83.8 - - - +
366F ILE* 1.3 62.9 + - - +
367F CYS 4.1 0.4 - - - -
368F THR* 3.7 32.5 - - + -
378F VAL* 3.8 24.2 - - + -
379F CYS 3.4 6.5 - - - -
380F PHE* 3.7 17.7 - + + -
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Residues in contact with ILE 366 (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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187F LEU* 3.7 33.0 - - + -
188F PHE* 4.5 3.1 - - + -
214F THR* 3.9 14.4 - - + -
216F ASN* 3.1 34.3 + - - +
364F GLU* 4.6 8.7 - - + +
365F PHE* 1.3 79.6 - - - +
367F CYS* 1.3 58.2 + - - +
373F GLU* 5.2 1.6 - - - +
379F CYS* 2.7 15.1 + - - +
380F PHE 5.1 1.1 - - - -
381F LYS* 4.5 16.6 - - + -
411F LEU* 4.2 8.5 - - + -
418F ILE* 6.3 0.4 - - + -
420F VAL* 3.7 29.6 - - + -
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Residues in contact with CYS 367 (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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214F THR 3.2 26.9 - - - +
215F GLY* 3.8 22.7 - - - -
216F ASN* 3.6 13.0 - - - +
365F PHE* 3.6 0.5 - - - -
366F ILE* 1.3 81.3 - - - +
368F THR* 1.3 67.4 + - - +
369F GLY* 3.7 4.7 - - - -
370F ARG 5.5 0.9 - - - -
373F GLU* 5.2 5.2 - - - -
374F GLY* 5.0 4.0 - - - -
375F ILE 4.3 8.3 - - - -
377F ALA 3.5 14.8 - - - -
378F VAL* 3.4 5.5 - - - +
379F CYS* 2.8 31.4 + - + +
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Residues in contact with THR 368 (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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350F ALA 4.6 1.3 - - - -
351F ALA* 3.6 21.0 - - - +
354F ALA* 3.7 26.6 - - + +
355F ASP* 6.0 0.4 - - - -
365F PHE* 3.7 27.6 - - + -
367F CYS* 1.3 76.4 - - - +
369F GLY* 1.3 63.2 + - - +
370F ARG* 3.2 28.4 + - - +
373F GLU* 4.1 5.9 + - - -
377F ALA 3.8 2.2 - - - -
378F VAL* 4.9 0.7 - - - +
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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