Contacts of the strand formed by residues 1818 - 1821 (chain A) in PDB entry 4W8F
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 VAL1818 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539A PHE* 3.7 35.7 - - + -
1816A VAL* 4.4 7.0 - - + +
1817A VAL* 1.3 74.7 - - - +
1819A VAL* 1.3 59.4 + - - +
1820A PHE* 3.9 22.4 + - + -
1834A LEU* 6.4 0.4 - - + -
1838A ILE* 3.3 29.8 - - + -
1843A ALA* 4.3 14.8 - - + -
1844A TRP 3.0 5.5 + - - +
1845A GLY* 3.4 0.5 - - - -
1846A CYS 3.0 21.5 + - - -
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Residues in contact with VAL1819 (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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1803A THR* 5.5 6.3 - - + +
1807A LYS* 4.1 22.7 - - + -
1817A VAL* 3.8 21.7 + - + +
1818A VAL* 1.3 82.1 - - - +
1820A PHE* 1.3 74.3 + - - +
1821A ASN* 3.8 22.8 + - - +
1834A LEU* 5.5 0.9 - - - +
1846A CYS* 3.4 15.7 - - + +
1848A ASP* 4.3 13.7 - - + -
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Residues in contact with PHE1820 (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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1818A VAL* 3.9 28.3 - - + -
1819A VAL* 1.3 76.4 - - - +
1821A ASN* 1.3 65.8 + - - +
1822A CYS* 3.6 5.4 + - - -
1826A PHE* 6.1 0.7 - - + -
1831A LEU* 3.5 20.6 - - + -
1834A LEU* 3.3 59.2 - - + -
1835A LEU* 4.3 11.4 - - + -
1838A ILE* 4.6 3.6 - - + -
1845A GLY* 4.8 7.0 - - - -
1846A CYS 2.9 13.5 + - - +
1847A PHE* 3.3 52.2 - + + -
1848A ASP 2.9 25.9 + - - -
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Residues in contact with ASN1821 (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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1819A VAL* 3.8 17.8 + - - +
1820A PHE* 1.3 72.8 - - - +
1822A CYS* 1.3 61.6 + - - +
1823A ASP 4.2 0.3 + - - -
1824A ASP* 2.9 38.9 + - - +
1826A PHE* 4.6 10.9 - - - +
1848A ASP* 3.5 28.2 + - - +
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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