Contacts of the strand formed by residues 664 - 667 (chain A) in PDB entry 2O8F
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 PHE 664 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663A MET* 1.3 79.3 + - + +
665A HIS* 1.3 66.2 + - - +
666A ILE* 3.8 28.3 - - + -
747A ILE* 5.3 1.6 - - + -
767A SER* 3.6 43.3 - - - -
770A ILE* 4.0 14.6 - - + -
771A ALA* 4.0 24.7 - - + -
776A ALA 5.5 0.9 - - - +
778A CYS* 3.4 31.4 - - + -
780A PHE* 4.0 23.6 - + + -
796A THR 2.8 13.2 + - - +
797A VAL* 3.8 17.3 - - + -
798A ASN* 2.9 28.1 + - - +
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Residues in contact with HIS 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A TYR* 2.9 33.9 + - + -
657A PHE* 3.5 31.5 - + - -
662A GLN* 3.9 14.9 - - + +
664A PHE* 1.3 81.2 + - - +
666A ILE* 1.3 60.2 + - - +
667A ILE* 3.9 5.3 + - + +
678A TYR* 6.1 0.4 - - - -
778A CYS 3.0 10.7 + - - +
779A MET* 3.6 12.5 - - + -
780A PHE* 2.8 33.4 + - - +
798A ASN* 3.4 30.6 + - + +
800A LEU* 3.6 30.0 - - + +
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Residues in contact with ILE 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A PHE* 3.8 18.2 - - + -
665A HIS* 1.3 74.1 - - - +
667A ILE* 1.3 59.8 + - - +
668A THR* 4.1 1.1 + - - +
780A PHE* 3.5 5.2 - - + +
782A THR* 3.8 25.6 - - + -
787A LEU* 3.4 35.7 - - + +
788A THR* 4.0 21.3 - - + -
790A LEU* 4.1 10.8 - - + -
797A VAL* 3.7 24.5 - - + -
798A ASN 2.8 8.7 + - - -
799A ASN* 3.5 16.4 - - - +
800A LEU* 2.7 33.4 + - - +
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Residues in contact with ILE 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A HIS* 4.5 8.5 - - + +
666A ILE* 1.3 77.6 - - - +
668A THR* 1.3 71.9 + - - +
675A LYS* 4.0 28.7 - - + +
678A TYR* 3.7 28.9 - - + -
679A ILE* 3.6 29.6 - - + -
779A MET* 4.1 6.3 - - + -
780A PHE 3.1 8.4 + - - +
781A ALA* 3.6 9.7 - - + +
782A THR* 3.0 32.1 + - - +
800A LEU* 3.2 21.8 - - + +
801A HIS 5.3 0.2 - - - -
802A VAL* 4.5 7.6 - - + -
817A VAL* 5.2 2.7 - - + -
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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