Contacts of the strand formed by residues 678 - 681 (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 SER 678 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A THR 3.1 5.6 + - - +
659A ASP* 3.5 25.6 + - - +
660A PHE* 2.8 28.6 + - - +
677A SER* 1.3 77.0 - - - +
679A VAL* 1.3 61.9 + - - +
680A THR* 4.8 3.8 + - - -
727A VAL* 3.2 20.6 - - - +
729A ASN* 5.0 7.0 - - - -
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Residues in contact with VAL 679 (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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655A LEU* 4.0 9.2 - - + -
660A PHE* 3.5 15.3 - - + -
672A ILE* 4.1 17.5 - - + -
674A ALA* 3.9 27.6 - - + -
677A SER 4.4 0.4 - - - +
678A SER* 1.3 77.2 - - - +
680A THR* 1.3 57.4 + - - +
681A LEU* 3.6 19.5 - - + -
720A VAL* 5.2 0.2 - - + -
722A LEU* 4.2 10.8 - - + -
727A VAL 2.6 17.9 + - - +
728A LEU* 3.3 23.2 - - + +
729A ASN* 2.7 32.2 + - - -
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Residues in contact with THR 680 (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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659A ASP* 5.1 0.3 + - - -
660A PHE 2.9 15.0 + - - -
661A GLY* 3.5 0.7 - - - -
662A LEU 2.8 32.2 + - - +
678A SER* 4.8 5.4 + - - -
679A VAL* 1.3 74.1 + - - +
681A LEU* 1.3 57.7 + - - +
682A GLY 3.6 8.4 + - - +
683A ASP* 3.7 21.8 - - + +
685A ARG* 4.6 6.5 + - - +
729A ASN* 3.3 24.6 + - + +
731A ASN* 3.6 26.0 - - - +
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Residues in contact with LEU 681 (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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660A PHE* 4.0 17.3 - - + -
662A LEU* 4.1 12.3 - - + -
668A LEU* 4.8 0.2 - - + -
672A ILE* 4.5 8.3 - - + -
679A VAL* 3.6 20.0 - - + -
680A THR* 1.3 74.3 - - - +
682A GLY* 1.3 58.5 + - - +
716A PHE* 4.2 20.6 - - + -
720A VAL* 5.0 0.4 - - + -
728A LEU* 3.4 31.2 - - + -
729A ASN 2.9 11.8 + - - +
730A ILE* 4.6 3.6 - - + -
731A ASN* 2.8 30.1 + - - +
732A ASP* 3.2 26.5 + - - +
734A PHE* 4.0 24.7 - - + -
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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