Contacts of the strand formed by residues 727 - 733 (chain A) 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 ASN 727 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A SER* 3.3 19.0 + - - +
623A VAL* 3.1 27.3 + - - +
624A GLU 3.9 2.9 - - - -
625A LYS* 2.7 37.5 + - - +
662A GLU* 3.2 26.2 + - - +
663A SER 3.3 6.4 + - - +
664A HIS* 3.0 23.2 - - + +
665A TRP* 2.8 21.3 + - - -
726A ASN* 1.3 77.4 - - - +
728A PHE* 1.3 63.6 + - - +
698C TRP* 3.9 6.3 - - - +
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Residues in contact with PHE 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A TYR* 3.5 1.1 - + - +
622A SER* 2.7 54.5 + - - -
624A GLU* 3.5 23.6 - - + -
626A GLU* 4.8 14.4 - - + -
631A ALA* 3.6 26.0 - - + -
634A PHE* 3.4 52.7 - + + -
635A CYS* 4.1 5.8 - - - -
642A LEU* 3.6 16.6 - - + -
664A HIS* 3.9 2.8 + - - -
665A TRP* 3.7 10.5 - - + +
726A ASN 4.1 5.6 - - - -
727A ASN* 1.3 79.1 - - - +
729A ILE* 1.3 64.4 + - - +
730A CYS* 3.6 17.5 - - - -
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Residues in contact with ILE 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A TYR* 4.3 10.5 - - + -
620A TYR 3.1 9.2 - - - +
621A PHE* 3.2 43.3 - - + -
635A CYS* 4.4 0.4 - - - -
642A LEU* 3.3 10.6 - - - +
643A VAL* 2.9 55.4 + - + +
654A ILE* 4.0 18.6 - - + -
658A MET* 5.3 0.4 - - - -
664A HIS* 3.9 22.4 - - + +
665A TRP 3.5 6.5 + - - +
666A ILE* 5.4 0.9 - - + -
711A LEU* 4.4 8.1 - - + -
728A PHE* 1.3 78.5 - - - +
730A CYS* 1.3 69.3 + - - +
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Residues in contact with CYS 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A TRP* 4.0 5.8 - - + -
618A CYS 3.8 0.2 - - - +
619A TYR* 3.2 5.9 - - - -
620A TYR* 2.8 45.2 + - + -
634A PHE* 3.6 22.9 - - - -
635A CYS* 2.0 52.5 - - - -
640A SER* 3.5 11.0 - - - +
641A HIS 3.6 0.4 - - - -
728A PHE* 3.6 10.8 - - - -
729A ILE* 1.3 76.6 - - - +
731A GLU* 1.3 63.5 + - - +
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Residues in contact with GLU 731 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ZN 1.9 34.7 - - - -
8A CL 4.1 1.0 - - - +
611A TRP* 4.8 0.2 - - - -
617A LYS* 3.6 13.2 - - + +
618A CYS 3.4 7.2 - - - +
619A TYR* 3.2 20.0 + - + -
640A SER* 2.8 21.9 - - - -
641A HIS* 2.9 38.7 + - + +
643A VAL* 3.7 18.2 - - + -
644A PHE* 2.8 28.7 + - - +
650A GLU* 2.8 5.5 - - - +
730A CYS* 1.3 77.2 - - - +
732A LYS* 1.3 62.9 + - - +
733A ASP 5.2 0.2 - - - +
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Residues in contact with LYS 732 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A PRO* 4.5 15.9 - - - +
611A TRP* 3.6 38.5 - - + -
617A LYS* 3.4 5.0 - - - -
618A CYS* 3.0 40.4 + - + +
638A LYS* 3.2 21.4 + - - +
639A SER* 3.8 21.6 - - - +
640A SER* 3.6 7.2 - - - -
641A HIS* 4.9 5.6 - - - -
731A GLU* 1.3 81.9 - - - +
733A ASP* 1.3 63.7 + - - +
734A ARG* 3.8 1.9 + - + +
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Residues in contact with ASP 733 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ZN 1.8 40.4 - - - -
616A ASP* 2.4 13.6 - - - +
617A LYS* 3.8 16.7 + - + +
641A HIS* 5.7 1.0 + - - -
731A GLU* 5.2 0.4 - - - +
732A LYS* 1.3 74.6 - - - +
734A ARG* 1.3 90.3 + - - +
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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