Contacts of the strand formed by residues 708 - 711 (chain C) in PDB entry 2OX8
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 CYS 708 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628C PHE* 3.4 35.4 - - + -
665C TRP* 2.9 35.1 - - + -
668C LEU 3.8 5.2 - - - -
669C THR* 3.9 2.7 - - - -
671C SER* 6.0 0.7 - - - -
677C TRP* 4.0 1.6 - - - -
706C GLU 3.7 1.2 - - - -
707C ASP* 1.3 81.7 - - - +
709C ALA* 1.3 62.5 + - - +
720C PHE* 3.0 19.2 + - - +
722C CYS* 2.0 47.1 - - + -
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Residues in contact with ALA 709 (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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628C PHE* 5.3 0.2 - - - -
665C TRP* 3.2 13.3 - - - -
666C ILE* 3.6 32.7 + - + +
668C LEU* 2.9 25.2 + - + +
677C TRP* 3.5 14.2 - - + -
690C TRP* 3.9 14.1 - - + -
708C CYS* 1.3 77.9 - - - +
710C GLY* 1.3 59.4 + - - +
717C TRP* 4.9 1.8 - - + -
718C ASN 3.1 13.0 - - - +
719C ASP* 4.0 2.0 - - - +
720C PHE* 3.9 0.7 - - - -
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Residues in contact with GLY 710 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C SER 5.7 0.2 - - - -
664C HIS 3.4 11.9 - - - -
665C TRP* 4.1 5.4 - - - -
666C ILE* 4.1 4.6 - - - +
709C ALA* 1.3 79.0 - - - +
711C LEU* 1.3 64.4 + - - -
712C ILE 3.3 2.1 + - - -
717C TRP* 3.7 3.3 - - - -
718C ASN 2.8 24.0 + - - -
720C PHE* 3.1 25.0 - - - -
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Residues in contact with LEU 711 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C ILE* 4.8 7.6 - - + -
651C GLN* 3.7 22.4 - - - +
654C ILE* 3.9 23.8 - - + -
655C LYS* 5.3 3.1 - - - +
658C MET* 3.3 29.7 - - + +
663C SER* 3.1 23.5 - - - -
664C HIS* 2.8 18.7 + - + +
666C ILE* 3.9 13.5 - - + +
710C GLY* 1.3 71.6 - - - -
712C ILE* 1.3 86.0 + - - +
713C TYR* 4.5 0.4 - - - -
715C GLY* 3.6 20.2 - - - +
716C GLN 4.5 2.9 - - - -
717C TRP* 4.6 9.0 - - + +
729C ILE* 5.0 6.1 - - + -
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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
------------------------------------------------------------
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