Contacts of the strand formed by residues 676 - 680 (chain B) in PDB entry 5OF4
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 LEU 676 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B CYS* 3.3 31.0 - - + +
493B MET* 4.8 8.5 - - - -
527B MET* 3.6 31.6 - - + -
531B VAL* 4.4 6.5 - - + -
616B ARG 3.3 8.3 + - - +
617B ALA* 3.5 29.4 - - + -
618B VAL* 2.9 24.3 + - - +
667B ALA* 4.6 2.1 - - - +
675B GLY* 1.3 75.2 - - - +
677B MET* 1.3 68.9 + - - +
678B VAL* 3.6 19.1 - - + -
717B ALA* 4.9 9.9 - - + -
720B PHE* 4.1 17.9 - - + -
721B LEU* 5.7 7.9 - - + -
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Residues in contact with MET 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B LEU* 3.6 29.4 - - + -
491B CYS 3.0 12.6 + - - +
492B PRO* 2.9 42.9 - - + +
493B MET 3.1 1.0 + - - -
618B VAL* 3.3 5.8 - - + +
664B VAL* 3.5 44.4 - - + +
665B GLY* 4.8 4.0 - - - -
667B ALA* 4.0 18.2 - - + +
668B ILE* 4.4 4.7 - - + -
676B LEU* 1.3 76.9 - - - +
678B VAL* 1.3 61.3 + - - +
679B PHE* 4.1 8.0 - - + -
692B LYS* 3.2 29.8 - - - +
696B TRP* 5.1 4.7 - - + -
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Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B MET* 3.2 35.4 - - + +
495B ILE* 4.0 15.5 - - + -
527B MET* 4.7 9.2 - - + -
617B ALA 5.6 0.2 - - - +
618B VAL 3.0 8.1 + - - +
619B ILE* 3.3 36.8 - - + +
620B MET 3.0 21.8 + - - -
664B VAL* 5.5 0.2 - - - +
676B LEU* 3.6 31.6 - - + -
677B MET* 1.3 77.8 - - - +
679B PHE* 1.4 61.6 - - - +
680B ALA 3.7 0.2 - - - -
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Residues in contact with PHE 679 (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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492B PRO* 4.4 13.2 - - + -
493B MET 2.9 9.5 + - - -
494B ILE* 3.6 22.3 - - + +
495B ILE* 2.9 20.1 + - - -
620B MET* 3.6 15.5 - - + -
660B ALA* 5.0 10.3 - - + -
661B ALA* 6.3 0.9 - - - -
664B VAL* 3.6 39.9 - - + -
677B MET* 4.1 16.4 - - + -
678B VAL* 1.4 69.7 - - - +
680B ALA* 1.3 61.9 + - - +
681B ASP* 2.9 10.8 + - - +
684B PHE* 3.4 37.5 - + + -
688B ASP* 3.8 21.1 - - - +
692B LYS* 4.8 19.3 - - + -
701B LEU* 5.1 1.8 - - + -
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Residues in contact with ALA 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ILE* 4.0 16.8 - - + +
504B ILE* 3.4 11.2 - - + +
520B TYR* 4.0 3.1 - - + -
523B LEU* 3.7 21.8 - - + -
619B ILE* 4.3 4.5 - - + -
620B MET 2.8 18.3 + - - +
621B PHE* 3.7 23.1 - - + -
622B GLY 2.9 25.1 + - - -
678B VAL 3.6 1.6 + - - -
679B PHE* 1.3 67.5 - - - +
681B ASP* 1.3 59.4 + - - +
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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
------------------------------------------------------------
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