Contacts of the strand formed by residues 363 - 368 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A ILE* 3.4 28.9 - - + -
358A ALA* 4.4 3.1 - - - +
360A LEU* 3.9 2.4 - - + -
361A GLY* 3.0 38.9 + - - +
362A PRO* 1.3 77.7 - - + +
364A GLU* 1.3 60.5 + - - +
365A PHE* 3.8 22.0 + + + -
380A PHE* 3.6 24.7 - + + -
381A LYS 3.4 8.7 - - - +
382A LEU* 3.9 17.9 - - + -
383A LYS* 3.3 22.9 - - - +
390A TYR* 2.9 29.7 + - - -
392A LEU* 4.2 4.7 - - + -
395A LEU* 4.3 0.2 - - - +
441A TYR* 2.8 34.1 + - - -
445A LEU* 4.3 1.2 - - - +
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Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A TYR* 1.3 74.8 - - - +
365A PHE* 1.3 71.2 + - - +
366A ILE* 3.7 6.4 + - - +
380A PHE* 3.3 2.8 - - - -
381A LYS* 2.9 71.5 + - + +
383A LYS* 4.0 15.4 - - + +
384A ASP* 5.1 3.5 + - - +
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Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ALA* 3.6 22.2 - - - -
357A ILE* 4.0 12.3 - - + -
358A ALA* 3.6 31.9 - - + -
363A TYR* 3.8 22.2 - - + -
364A GLU* 1.3 83.1 - - - +
366A ILE* 1.3 63.9 + - - +
368A THR* 3.5 29.4 - - + -
378A VAL* 3.7 30.1 - - + -
379A CYS 3.6 4.3 - - - +
380A PHE* 3.7 20.2 - + + -
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Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU* 3.7 35.2 - - + -
214A THR* 3.9 15.7 - - + -
216A ASN* 2.9 38.3 + - - +
364A GLU* 4.6 10.5 - - - +
365A PHE* 1.3 74.8 - - - +
367A CYS* 1.3 57.6 + - - +
368A THR* 5.6 0.4 - - - -
373A GLU* 5.2 2.6 - - - +
379A CYS* 2.8 17.5 + - - +
380A PHE 5.1 1.1 - - - -
381A LYS* 4.6 15.5 - - + -
411A LEU* 4.4 4.9 - - + -
420A VAL* 3.6 31.4 - - + -
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Residues in contact with CYS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A THR 3.0 28.9 - - - +
215A GLY* 3.8 17.0 - - - -
216A ASN* 3.6 17.0 - - - +
365A PHE* 3.5 1.3 - - - -
366A ILE* 1.3 80.0 - - - +
368A THR* 1.3 68.4 + - - +
369A GLY 3.7 4.7 - - - -
370A ARG 5.4 1.1 - - - -
373A GLU* 5.5 4.5 - - - -
374A GLY* 5.3 2.5 - - - -
375A ILE 4.3 6.1 - - - -
377A ALA* 3.8 17.7 - - - -
378A VAL* 3.4 6.5 - - - +
379A CYS* 2.9 32.2 + - + +
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Residues in contact with THR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ALA 4.7 0.7 - - - -
351A ALA* 3.6 19.1 - - - +
354A ALA* 3.8 19.7 - - + +
365A PHE* 3.5 33.2 - - + -
366A ILE 5.6 0.2 - - - -
367A CYS* 1.3 79.2 - - - +
369A GLY* 1.3 64.3 + - - +
370A ARG* 3.1 30.4 + - - +
373A GLU* 4.7 5.4 + - - -
377A ALA 3.5 2.9 - - - -
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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