Contacts of the strand formed by residues 1782 - 1785 (chain A) in PDB entry 5V7W
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 LEU1782 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1714A TYR* 4.0 12.8 - - + -
1715A PHE 3.2 13.2 - - - +
1717A VAL* 4.1 0.2 - - - +
1721A TYR* 5.9 4.0 - - + -
1774A THR* 2.7 35.4 + - - -
1775A ASP* 3.2 33.0 + - + +
1780A PRO 3.8 0.4 - - - -
1781A SER* 1.3 84.1 - - - +
1783A PHE* 1.3 65.7 + - - +
1784A VAL* 3.8 24.5 - - + -
1901A 91J 4.2 31.4 - - + -
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Residues in contact with PHE1783 (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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1678A LYS* 3.9 30.7 - - + -
1680A LEU* 3.8 27.1 - - + -
1714A TYR* 3.6 1.7 - - - +
1715A PHE* 2.8 36.9 + - + -
1717A VAL* 4.0 16.2 - - + -
1743A VAL* 5.6 0.7 - - + -
1745A THR* 3.6 21.5 - - + -
1748A TYR* 3.6 34.8 - + - -
1772A THR* 3.9 15.7 - - + +
1773A VAL 3.3 3.8 - - - -
1774A THR* 3.8 13.9 - - - -
1780A PRO* 3.6 30.1 - - + -
1782A LEU* 1.3 74.1 - - - +
1784A VAL* 1.3 63.0 + - - +
1785A ALA 4.2 0.4 - - - -
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Residues in contact with VAL1784 (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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1712A GLY* 4.1 4.7 - - - +
1713A THR 3.3 25.4 - - - +
1714A TYR* 3.5 40.6 - - + -
1772A THR* 3.4 9.0 - - - -
1773A VAL* 2.9 47.1 + - + +
1782A LEU* 3.8 10.5 - - + -
1783A PHE* 1.3 77.5 - - - +
1785A ALA* 1.3 58.9 + - - +
1786A PHE* 3.7 25.1 - - + -
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Residues in contact with ALA1785 (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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1712A GLY* 3.4 3.8 - - - -
1713A THR* 2.9 33.7 + - - -
1715A PHE* 4.1 20.1 - - + -
1743A VAL* 4.5 6.7 - - + -
1771A ASP 5.0 0.2 - - - -
1772A THR* 3.9 11.9 - - + -
1783A PHE 4.2 1.0 - - - -
1784A VAL* 1.3 72.6 - - - +
1786A PHE* 1.3 62.7 + - - +
1787A TYR 5.0 1.3 - - - +
1790A GLN* 3.6 27.8 - - + +
1791A ALA* 5.4 2.2 - - + -
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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