Contacts of the strand formed by residues 687 - 691 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A ARG* 4.3 13.2 - - - +
671A LEU 2.9 37.9 + - - +
672A GLY 5.3 0.9 - - - +
685A GLY 4.4 3.8 - - - +
686A THR* 1.3 75.8 - - - +
688A PHE* 1.3 61.8 + - - +
689A HIS* 3.0 22.1 - - - +
735A THR* 4.0 13.7 - - + +
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Residues in contact with PHE 688 (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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668A LEU* 4.5 4.3 - - + -
669A LEU 3.2 8.1 - - - +
670A ALA* 3.8 13.7 - - + -
686A THR* 3.6 22.0 - - + -
687A ALA* 1.3 68.9 - - - +
689A HIS* 1.3 70.9 + - - +
701A CYS* 3.5 35.9 - - + -
703A VAL* 3.8 14.6 - - + -
712A PHE* 3.9 19.1 - + - -
714A LEU* 4.2 15.0 - - + -
731A ALA* 5.8 0.4 - - + -
734A TRP* 3.8 35.4 - + + -
735A THR* 2.9 28.4 + - - +
736A LEU* 3.4 17.9 - - + -
737A CYS* 2.9 25.2 + - - +
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Residues in contact with HIS 689 (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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568A ARG* 5.1 3.1 + - - -
668A LEU* 3.5 4.9 - - - -
669A LEU* 2.8 38.4 + - + +
671A LEU* 3.7 23.4 - - + +
687A ALA* 3.0 39.5 + - - +
688A PHE* 1.3 80.9 + - - +
690A LEU* 1.3 60.3 + - - +
691A PHE* 3.6 24.8 - - + -
737A CYS* 3.4 19.9 - - + +
739A ARG* 2.6 39.0 + - - +
757A GLN* 3.4 15.9 - - - -
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Residues in contact with LEU 690 (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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667A THR 3.5 10.5 - - - +
668A LEU* 3.6 23.3 - - + +
688A PHE 4.3 0.2 - - - -
689A HIS* 1.3 73.4 - - - +
691A PHE* 1.3 62.4 + - - +
692A ASN 4.2 0.5 + - - -
693A LEU* 3.8 46.4 - - + +
699A ALA* 3.9 12.1 - - + -
716A ALA* 4.0 7.0 - - + -
723A ILE* 3.9 12.1 - - + -
736A LEU* 4.6 4.7 - - + +
737A CYS 2.9 11.9 + - - +
738A LEU* 3.8 27.8 - - + -
739A ARG* 3.1 28.1 + - - +
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Residues in contact with PHE 691 (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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636A THR* 3.6 36.3 - - + +
637A HIS 4.6 1.3 - - - -
638A LEU* 4.6 2.2 - - + -
663A VAL* 3.7 39.7 - - + -
664A ARG 4.0 15.7 - - - +
665A ASP* 4.8 2.0 - - - -
666A ASN* 3.1 16.2 + - - -
667A THR* 3.0 17.3 + - - +
669A LEU* 4.0 17.7 - - + -
689A HIS* 3.6 28.9 - - + -
690A LEU* 1.3 74.2 - - - +
692A ASN* 1.3 70.9 + - - +
693A LEU* 3.0 5.1 + - - +
739A ARG* 3.5 49.4 - - + -
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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
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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