Contacts of the strand formed by residues 685 - 689 (chain A) in PDB entry 1WXR
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 ARG 685 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A ARG* 3.5 27.7 - - - +
604A THR* 3.9 16.5 + - - +
659A ASP* 2.6 43.9 + - - -
661A GLY* 5.1 0.4 - - - -
680A THR* 4.6 7.9 + - - +
683A ASP* 2.6 56.4 + - - +
684A SER* 1.3 80.1 + - - +
686A VAL* 1.3 65.0 + - - +
687A PHE* 4.2 4.3 - - - -
702A GLU* 3.3 21.7 + - - +
703A GLY 3.6 7.4 - - - +
704A THR* 5.0 1.3 - - - +
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Residues in contact with VAL 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A THR* 5.0 0.7 - - + -
606A GLN* 3.3 23.1 - - + +
638A PHE* 3.3 14.0 - - + -
643A TRP* 4.2 10.5 - - + -
663A GLY* 3.9 18.2 - - - -
664A ARG* 4.3 11.2 - - + +
683A ASP 3.8 15.7 - - - +
684A SER 4.3 1.3 - - - +
685A ARG* 1.3 79.3 - - - +
687A PHE* 1.3 68.0 + - - +
702A GLU* 3.6 4.0 - - - +
703A GLY 2.9 29.3 + - - +
705A SER* 3.8 33.9 - - - +
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Residues in contact with PHE 687 (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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558A ALA 5.8 1.6 - - - -
561A LEU* 6.0 0.2 - - + -
583A ALA* 3.9 15.9 - - + -
585A VAL* 3.7 24.0 - - + -
587A ASP* 5.2 2.3 - - - +
602A ARG* 3.7 22.4 - - - -
604A THR* 3.5 25.1 - - + -
606A GLN* 2.8 37.1 + - - +
609A PRO* 4.9 3.1 - - - +
638A PHE* 3.8 1.3 - - - -
643A TRP* 5.2 1.0 - - - -
685A ARG 4.2 2.7 - - - -
686A VAL* 1.3 81.7 - - - +
688A ILE* 1.3 67.9 + - - +
700A LEU* 3.7 32.8 - - + -
701A GLU 3.2 6.3 - - - +
702A GLU* 3.5 37.9 - - + -
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Residues in contact with ILE 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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561A LEU* 5.6 0.4 - - - -
587A ASP* 5.9 2.5 - - - -
609A PRO* 4.2 12.8 - - + -
634A GLN* 3.4 15.9 - - - +
636A THR* 3.4 35.9 - - - +
637A SER* 4.0 18.8 - - - +
638A PHE* 3.5 37.0 - - + -
643A TRP* 5.5 1.6 - - + -
687A PHE* 1.3 80.6 - - - +
689A ASP* 1.3 60.5 + - - +
690A LYS* 3.9 18.6 - - + +
699A THR 3.7 0.2 - - - +
700A LEU* 3.6 8.9 - - - +
701A GLU* 3.0 42.1 + - + +
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Residues in contact with ASP 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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561A LEU* 3.7 8.7 - - + -
563A HIS* 2.7 40.2 + - + +
587A ASP* 5.6 1.0 + - - -
635A PRO* 4.0 2.6 - - - +
636A THR* 3.8 9.8 + - - -
688A ILE* 1.3 75.0 - - - +
690A LYS* 1.3 57.2 + - - +
691A ASN 2.9 14.8 + - - +
692A ASP* 3.1 41.9 + - + +
695A GLY 5.6 0.7 - - - +
697A ALA 4.4 1.2 - - - +
698A PHE* 3.3 20.9 - - - +
699A THR 2.9 27.9 + - - -
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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