Contacts of the strand formed by residues 377 - 382 (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 ALA 377 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F THR 4.3 5.4 - - - +
215F GLY* 4.1 15.0 - - - -
350F ALA* 3.9 2.3 - - - +
367F CYS* 3.5 7.6 - - - -
369F GLY* 3.0 24.2 + - - -
375F ILE* 2.7 25.3 + - + +
376F PRO* 1.3 75.3 - - - +
378F VAL* 1.3 65.3 + - - +
422F ARG* 4.8 6.3 - - + -
423F ILE 3.2 12.6 - - - +
424F MET* 4.0 10.1 - - - -
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Residues in contact with VAL 378 (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* 3.4 33.0 - - + +
353F LEU* 4.1 12.1 - - + +
354F ALA* 3.9 17.3 - - + +
357F ILE* 5.0 1.3 - - + -
365F PHE* 3.8 26.9 - - + -
367F CYS 3.4 6.7 - - - +
368F THR 5.2 0.4 - - - -
377F ALA* 1.3 77.5 - - - +
379F CYS* 1.3 62.5 + - - +
380F PHE* 4.2 10.9 - - + -
421F MET 3.8 0.5 - - - +
422F ARG* 3.3 4.5 - - - +
423F ILE* 2.8 52.0 + - + +
425F CYS* 5.0 0.4 - - - -
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Residues in contact with CYS 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F TYR 4.1 5.6 - - - -
214F THR* 3.3 43.3 - - - +
365F PHE* 3.4 2.8 - - - -
366F ILE* 2.7 40.3 + - + -
367F CYS* 2.8 20.5 + - + +
378F VAL* 1.3 74.2 - - - +
380F PHE* 1.3 61.4 + - - +
420F VAL* 3.9 25.4 - - - -
421F MET 3.3 11.9 - - - +
422F ARG* 4.3 4.3 - - + -
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Residues in contact with PHE 380 (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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357F ILE* 3.8 19.7 - - + -
363F TYR* 3.6 39.0 - + - -
364F GLU 3.2 15.0 - - - +
365F PHE* 3.7 27.1 - + + -
366F ILE* 4.4 2.2 - - - +
378F VAL* 4.2 6.7 - - + -
379F CYS* 1.3 79.1 - - - +
381F LYS* 1.3 63.1 + - - +
392F LEU* 3.7 12.2 - - + +
420F VAL* 3.1 9.2 - - - -
421F MET* 2.9 63.7 + - + -
423F ILE* 4.5 8.7 - - + -
441F TYR* 3.3 28.3 - + - -
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Residues in contact with LYS 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363F TYR* 3.3 9.1 - - - +
364F GLU* 2.9 65.3 + - + +
366F ILE* 4.5 13.2 - - + -
380F PHE* 1.3 76.1 - - - +
382F LEU* 1.3 78.7 + - - +
384F ASP* 2.8 31.3 + - - +
392F LEU* 3.9 6.7 - - - -
418F ILE* 4.0 41.3 - - + +
419F VAL 3.4 21.8 - - - +
420F VAL* 4.4 2.0 - - + -
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Residues in contact with LEU 382 (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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362F PRO* 3.5 7.0 - - + +
363F TYR* 3.8 26.7 - - + -
364F GLU 4.4 0.2 - - - -
381F LYS* 1.3 96.9 + - - +
383F LYS* 1.3 71.4 + - - +
384F ASP* 3.3 0.9 + - - -
386F GLU 4.2 11.7 - - - +
387F ASP* 5.6 0.2 - - - -
388F PRO* 3.8 36.1 - - + -
390F TYR* 4.1 13.7 - - + +
391F THR* 4.6 10.3 - - - -
392F LEU* 4.3 19.9 - - + +
419F VAL 4.6 0.8 + - - -
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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