Contacts of the strand formed by residues 353 - 357 (chain C) in PDB entry 1OEY
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 THR 353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352C TYR* 1.3 82.1 - - - +
354C LEU* 1.3 61.4 + - - +
363C VAL* 3.7 22.9 - - + +
364C MSE 3.3 12.3 - - - +
365C LYS* 4.5 4.3 - - + -
366C THR* 3.7 10.9 - - - +
414C TRP* 5.2 0.9 - - - -
420C TYR 2.9 6.4 + - - +
421C CYS* 3.4 24.6 - - - +
422C LEU* 3.0 24.3 + - - +
305L LEU* 4.4 19.7 - - + -
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Residues in contact with LEU 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C THR* 1.3 77.0 - - - +
355C LYS* 1.3 60.7 + - - +
356C VAL* 4.0 2.5 + - + -
362C VAL 3.8 0.5 - - - +
363C VAL* 3.3 4.1 - - - -
364C MSE 2.9 43.8 + - + +
366C THR* 3.7 22.0 - - + +
375C VAL* 3.9 24.7 - - + -
378C MSE 4.3 21.8 - - + -
379C VAL* 3.9 20.2 - - + -
414C TRP* 3.7 19.5 - - + -
422C LEU* 3.4 20.4 - - + +
424C LEU* 4.1 12.3 - - + -
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Residues in contact with LYS 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LEU* 1.3 71.2 - - - +
356C VAL* 1.3 58.3 + - - +
357C HIS* 4.3 8.5 - - + +
361C THR* 3.8 24.7 - - + -
362C VAL 3.4 4.9 - - - +
363C VAL* 4.1 13.2 - - + -
421C CYS* 3.6 20.9 - - - -
422C LEU 2.9 6.9 + - - -
423C THR* 3.3 17.2 - - + +
424C LEU* 2.7 33.3 + - - +
289L ASP* 2.6 32.9 + - - +
291L GLU* 2.8 27.3 + - - +
293L ASP* 2.7 32.1 + - + +
295L VAL* 4.8 0.4 - - + -
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Residues in contact with VAL 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LEU* 4.5 8.3 - - + +
355C LYS* 1.3 77.3 - - - +
357C HIS* 1.3 64.4 + - - +
358C TYR 3.5 2.8 + - - -
360C TYR 3.8 0.5 - - - +
361C THR* 3.3 2.6 - - - -
362C VAL* 2.8 45.7 + - + +
364C MSE 3.6 27.1 - - + -
379C VAL* 3.9 31.9 - - + -
383C LEU* 4.3 6.7 - - + -
392C LEU* 4.5 5.8 - - + -
424C LEU* 3.4 15.0 - - + +
426C CYS* 4.0 21.8 - - + +
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Residues in contact with HIS 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C LYS* 4.3 3.5 - - + +
356C VAL* 1.3 70.3 - - - +
358C TYR* 1.3 60.9 + - - +
360C TYR 4.0 3.4 - - - -
361C THR* 2.7 40.2 + - + +
423C THR* 3.8 20.8 - - + +
424C LEU 3.0 8.9 + - - -
425C TRP* 3.4 44.9 - + + +
426C CYS 2.9 27.7 + - - +
428C ASN* 4.4 2.3 + - - -
293L ASP* 3.7 24.1 + - + -
336L ASN* 3.1 25.5 + - - -
337L THR* 3.8 13.6 - - - +
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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