Contacts of the strand formed by residues 332 - 336 (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 VAL 332 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330F GLY 4.9 2.7 - - - +
331F ASP* 1.3 81.2 - - - +
333F ILE* 1.3 63.5 + - - +
357F ARG* 3.5 48.2 - - + +
359F VAL* 4.0 24.9 - - + -
394F VAL* 5.8 0.2 - - + -
397F GLU 4.1 16.8 - - - +
398F VAL* 3.9 16.7 - - + +
399F SER* 3.2 8.5 + - - +
400F LYS* 3.2 27.4 + - - +
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Residues in contact with ILE 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F ILE* 3.8 38.6 - - + -
331F ASP* 3.3 16.8 - - - +
332F VAL* 1.3 75.1 - - - +
334F LEU* 1.3 58.0 + - - +
335F VAL* 4.2 6.7 - - + -
346F LEU* 4.0 6.3 - - + -
356F PHE* 3.6 32.3 - - + -
357F ARG 3.2 7.3 + - - +
358F VAL* 3.3 10.1 - - + +
359F VAL* 2.8 33.1 + - - +
400F LYS* 3.3 13.5 - - + +
402F LEU* 3.7 32.5 - - + +
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Residues in contact with LEU 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333F ILE* 1.3 74.5 - - - +
335F VAL* 1.3 63.4 - - - +
359F VAL* 3.4 7.2 - - + +
361F VAL* 3.7 24.7 - - + -
391F ALA* 5.1 0.7 - - + +
394F VAL* 4.0 17.5 - - + -
395F LEU* 4.0 21.1 - - + -
398F VAL* 3.7 34.3 - - + -
400F LYS 2.9 6.7 + - - -
401F VAL* 3.5 16.9 - - + +
402F LEU* 2.6 33.6 + - - +
423F LEU* 3.7 34.5 - - + -
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Residues in contact with VAL 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333F ILE* 4.4 2.7 - - + -
334F LEU* 1.3 81.5 - - - +
336F TYR* 1.3 64.0 + - - +
337F GLY 5.7 1.3 - - - +
342F VAL* 3.7 26.7 - - + -
346F LEU* 3.8 10.1 - - + -
358F VAL* 3.8 19.1 - - + -
359F VAL 3.0 7.6 + - - +
360F VAL* 3.7 35.9 - - + -
361F VAL* 3.0 28.2 + - - +
372F THR* 5.4 4.9 - - - +
376F LEU* 5.4 0.4 - - + -
402F LEU* 3.3 23.6 - - + +
403F LEU* 5.0 0.4 - - - -
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Residues in contact with TYR 336 (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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220C ALA* 4.6 0.2 - - - +
335F VAL* 1.3 78.4 - - - +
337F GLY* 1.3 71.7 + - - +
339F SER* 5.0 4.7 + - - -
342F VAL* 5.6 3.5 - - - +
360F VAL* 5.8 0.7 - - - -
361F VAL* 3.2 33.4 - - + -
362F ASP* 4.1 3.4 - - - -
363F SER* 2.6 32.3 + - - -
388F ILE* 3.9 19.5 - - + -
402F LEU 4.2 4.0 + - - -
403F LEU* 3.9 8.9 - - + +
404F GLY* 4.7 11.4 + - - -
416F SER* 5.6 0.7 - - - -
417F ARG* 3.7 22.0 - - + +
418F VAL* 4.2 5.7 + - - +
419F GLY* 3.1 48.8 + - - -
420F THR* 4.1 7.9 - - - -
423F LEU* 3.7 17.3 - - + -
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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