Contacts of the strand formed by residues 574 - 578 (chain B) in PDB entry 2OBF
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 574 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B ARG* 1.3 116.7 - - + +
575B LEU* 1.3 61.3 + - - +
576B ILE* 6.0 0.9 - - - -
594B PHE* 3.5 3.9 - - - -
596B ASP* 3.3 12.8 - - + -
672B PRO* 3.7 28.9 + - + -
674B PRO 3.9 4.5 + - - -
675B ALA* 3.2 23.5 - - - -
676B ASP* 2.9 42.0 + - - +
677B ALA 3.4 1.7 + - - -
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Residues in contact with LEU 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B PHE* 4.9 2.0 - - + -
574B THR* 1.3 77.0 - - - +
576B ILE* 1.3 82.5 + - - +
577B ASP 3.9 0.4 - - - +
587B LEU* 3.8 25.1 - - + -
590B ALA* 4.1 14.4 - - + -
594B PHE* 3.6 44.0 - - + -
596B ASP* 2.8 8.4 + - - +
597B ILE* 3.4 13.5 - - + -
598B THR* 2.9 25.3 + - - -
677B ALA* 3.4 17.7 - - + +
679B VAL* 3.8 22.9 - - + -
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Residues in contact with ILE 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B THR* 6.0 1.1 - - - -
575B LEU* 1.3 82.4 - - - +
577B ASP* 1.3 67.5 + - - +
578B ILE* 3.7 21.0 + - + -
598B THR* 3.6 25.4 - - + +
600B THR* 4.3 6.5 - - + -
665B LEU* 4.3 15.5 - - + -
671B ALA* 4.4 4.0 - - + -
672B PRO* 4.3 5.4 - - + +
673B LEU* 3.6 31.0 - - + -
675B ALA* 3.6 17.3 - - + -
677B ALA 3.0 6.9 + - - -
678B LEU* 3.2 19.0 - - + +
679B VAL 2.9 23.0 + - - +
704B LEU* 4.5 5.4 - - + -
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Residues in contact with ASP 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU* 3.9 1.4 - - - +
576B ILE* 1.3 71.2 - - - +
578B ILE* 1.3 54.7 + - - +
580B SER* 2.5 26.6 + - - +
586B GLN* 2.8 33.5 + - - +
587B LEU* 4.1 22.4 - - + -
598B THR 2.9 16.3 + - - +
599B MET* 4.0 4.5 - - - +
600B THR* 2.7 36.2 + - - +
679B VAL* 3.0 30.3 - - + +
680B SER* 4.0 3.8 + - - -
681B ALA 4.7 1.0 + - - -
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Residues in contact with ILE 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B ILE* 3.9 26.0 - - + +
577B ASP* 1.3 68.9 + - - +
579B GLY* 1.3 68.2 + - - +
600B THR* 3.6 2.0 - - - -
657B ILE* 4.0 11.7 - - + -
659B VAL* 3.8 29.2 - - + -
678B LEU* 4.3 14.1 - - + -
679B VAL 2.6 14.5 + - - +
680B SER* 2.8 41.9 + - - +
681B ALA 4.2 1.4 + - - -
683B CYS* 3.9 4.9 - - - +
684B LEU* 4.9 1.6 - - + -
701B ILE* 3.8 24.0 - - + -
704B LEU* 3.9 23.1 - - + -
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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