Contacts of the strand formed by residues 687 - 691 (chain C) in PDB entry 1XSK
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 ALA 687 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568C ARG* 4.2 17.5 - - - +
671C LEU* 2.8 28.8 + - - +
672C GLY 5.4 0.2 - - - +
685C GLY 3.4 4.5 + - - +
686C THR* 1.3 73.8 - - - +
688C PHE* 1.3 59.9 + - - +
689C HIS* 2.9 28.5 - - - +
735C THR* 3.6 18.4 - - + -
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Residues in contact with PHE 688 (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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668C LEU* 4.2 4.0 - - + -
669C LEU 3.3 4.3 - - - -
670C ALA* 4.0 6.3 - - + +
686C THR* 3.5 22.9 - - + -
687C ALA* 1.3 74.3 - - - +
689C HIS* 1.3 62.5 + - - +
701C CYS* 3.9 24.7 - - + -
703C VAL* 3.8 20.0 - - + -
712C PHE* 3.9 22.2 - + - -
714C LEU* 4.4 16.2 - - + -
734C TRP* 3.5 46.7 - + + -
735C THR* 2.8 22.2 + - - +
736C LEU* 3.4 19.2 - - + -
737C CYS* 2.8 26.3 + - - +
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Residues in contact with HIS 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C ARG* 5.4 1.6 + - - -
668C LEU* 3.3 5.9 - - - +
669C LEU* 2.8 38.7 + - + +
671C LEU* 3.7 28.3 - - + +
687C ALA* 2.9 36.9 + - - +
688C PHE* 1.3 75.6 + - - +
690C LEU* 1.3 59.8 + - - +
691C PHE* 3.3 25.8 - + + -
737C CYS* 3.6 27.6 - - + +
739C ARG* 2.5 31.2 + - - +
757C GLN* 3.7 17.9 - - - -
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Residues in contact with LEU 690 (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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667C THR 3.4 13.5 - - - +
668C LEU* 3.9 12.0 - - + +
688C PHE 4.3 0.2 - - - -
689C HIS* 1.3 71.5 - - - +
691C PHE* 1.3 63.0 + - - +
692C ASN 4.2 0.9 + - - -
693C LEU* 3.9 36.8 - - + +
699C ALA* 3.9 15.5 - - + -
716C ALA* 3.8 25.8 - - + -
723C ILE* 4.3 13.5 - - + -
736C LEU* 4.3 9.8 - - + +
737C CYS 3.1 12.3 + - - +
738C LEU* 4.2 20.4 - - + -
739C ARG* 3.0 28.1 + - - +
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Residues in contact with PHE 691 (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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636C THR* 3.6 32.3 - - + +
637C HIS 4.8 0.4 - - - -
638C LEU* 4.5 2.7 - - + -
663C VAL* 3.9 35.9 - - + -
664C ARG 4.1 15.0 - - - +
665C ASP* 4.9 1.1 - - - -
666C ASN 2.9 19.4 + - - -
667C THR* 2.7 21.8 + - + +
669C LEU* 3.9 21.1 - - + -
689C HIS* 3.3 30.7 - - + -
690C LEU* 1.3 73.1 - - - +
692C ASN* 1.3 70.5 + - - +
693C LEU* 3.2 2.7 + - - +
739C ARG* 3.5 49.1 - - + -
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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