Contacts of the strand formed by residues 1747 - 1751 (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 VAL1747 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1623A PHE* 3.7 30.3 - - + -
1650A LEU* 3.9 22.7 - - + -
1654A VAL* 4.7 6.3 - - + -
1734A PHE* 5.8 0.4 - - + -
1735A TYR 3.7 9.9 - - - +
1736A GLN* 4.4 6.1 - - + -
1743A ASP 4.4 0.4 + - - -
1744A LEU 4.9 1.6 + - - -
1745A ASN 3.4 2.0 - - - +
1746A SER* 1.3 90.7 - - - +
1748A PHE* 1.3 67.4 + - - +
1749A ILE* 4.8 2.0 - - + -
1757A GLN* 3.7 4.3 - - - +
1758A TYR* 2.8 46.5 + - + +
1760A PHE* 3.8 17.3 - - + -
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Residues in contact with PHE1748 (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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1734A PHE* 3.9 0.3 - - - -
1735A TYR* 3.0 73.6 + + + +
1736A GLN 4.6 0.7 - - - -
1737A LYS* 3.5 45.8 - - + -
1747A VAL* 1.3 75.3 - - - +
1749A ILE* 1.3 71.4 + - - +
1755A LEU* 3.7 42.2 - - + -
1756A LEU 3.3 13.7 - - - +
1757A GLN* 4.0 14.6 - - + +
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Residues in contact with ILE1749 (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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1732A GLN* 4.1 27.8 - - + +
1733A LYS 3.4 7.2 - - - +
1734A PHE* 3.6 37.7 - - + -
1747A VAL* 4.8 2.2 - - + -
1748A PHE* 1.3 86.8 - - - +
1750A SER* 1.3 66.9 + - - +
1751A GLN* 4.6 2.7 - - + +
1754A TYR 3.6 1.0 - - - +
1755A LEU* 3.3 6.1 - - - +
1756A LEU* 2.6 45.9 + - + +
1758A TYR* 4.1 18.8 - - + -
1783A THR* 6.0 0.7 - - - +
1813A LEU* 3.4 33.0 - - + -
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Residues in contact with SER1750 (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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1733A LYS* 2.9 50.8 + - - -
1735A TYR* 3.6 27.8 - - - -
1748A PHE* 4.9 0.2 - - - -
1749A ILE* 1.3 72.6 - - - +
1751A GLN* 1.3 62.9 + - - +
1753A GLY* 4.5 10.9 + - - -
1754A TYR 3.5 5.4 + - - -
1755A LEU* 3.4 20.3 - - - +
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Residues in contact with GLN1751 (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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1730A LYS 2.9 25.6 + - - +
1731A VAL* 4.0 11.6 - - - +
1732A GLN* 3.4 31.3 + - + +
1733A LYS* 3.9 3.6 - - - +
1749A ILE* 4.2 3.7 - - + +
1750A SER* 1.3 76.0 + - - +
1752A SER* 1.3 73.6 + - - +
1753A GLY 3.0 4.0 - - - -
1754A TYR* 2.8 33.8 + - - +
1776A LEU* 3.3 23.6 + - - +
1779A PHE* 3.4 24.5 - - - +
1780A ALA* 4.0 12.0 - - - +
1783A THR* 3.8 12.8 - - + +
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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