Contacts of the strand formed by residues 1813 - 1817 (chain B) in PDB entry 2V5P
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 TYR1813 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1806B LEU 4.1 4.5 - - - +
1807B THR* 4.4 8.3 - - - -
1808B ASP 4.7 0.3 + - - -
1811B LEU* 3.3 63.4 + - + +
1812B LEU* 1.3 78.4 - - - +
1814B SER* 1.3 67.2 + - - +
1815B PHE* 3.6 34.0 - + - -
1987B CYS 4.4 2.8 + - - -
1988B PRO 4.2 15.5 - - - -
1989B PRO* 4.1 21.3 - - + +
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Residues in contact with SER1814 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805B THR* 5.0 8.7 - - - -
1806B LEU 3.2 12.6 - - - -
1807B THR* 4.6 9.2 - - - -
1813B TYR* 1.3 80.8 - - - +
1815B PHE* 1.3 67.9 + - - +
1816B ASN 4.0 1.0 + - - -
2993B NAG 4.5 16.2 - - - +
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Residues in contact with PHE1815 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805B THR* 3.4 9.1 - - - -
1806B LEU* 3.1 44.1 + - + +
1811B LEU* 3.5 27.1 - - + -
1813B TYR* 3.6 26.2 - + - -
1814B SER* 1.3 75.8 - - - +
1816B ASN* 1.3 62.5 + - - +
1817B LEU* 3.4 7.1 + - + +
1876B TYR* 4.3 16.4 - + - -
1883B VAL* 4.3 15.3 - - + -
1985B VAL 3.3 19.1 - - - +
1986B VAL* 3.6 24.7 - - + -
1987B CYS 3.5 30.7 - - - -
1988B PRO* 4.5 2.7 - - + -
2993B NAG 5.7 0.2 - - - -
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Residues in contact with ASN1816 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805B THR* 3.6 6.8 - - - +
1814B SER 4.0 2.6 + - - -
1815B PHE* 1.3 70.0 - - - +
1817B LEU* 1.3 60.2 + - - +
1818B SER* 3.2 21.1 + - - -
1819B SER* 3.6 13.1 + - - +
1985B VAL* 3.2 34.8 - - + +
2993B NAG 1.4 76.8 + - + +
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Residues in contact with LEU1817 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804B CYS* 3.3 27.1 + - - +
1805B THR* 5.0 0.7 - - - -
1806B LEU* 5.0 2.5 - - + +
1815B PHE* 3.4 10.5 + - + +
1816B ASN* 1.3 76.3 + - - +
1818B SER* 1.3 60.0 - - - +
1819B SER* 3.1 7.2 - - - -
1820B LEU* 3.2 26.1 + - + +
1821B SER 3.6 6.6 + - - -
1838B VAL* 4.1 9.2 - - + +
1872B MET* 5.9 0.4 - - + -
1874B LEU* 3.8 39.3 - - + -
1883B VAL* 4.4 10.8 - - + -
1885B LEU* 6.1 0.4 - - + -
1955B PHE* 4.0 30.1 - - + -
1983B THR* 5.9 0.2 - - - +
1985B VAL* 5.7 1.1 - - + -
1986B VAL* 3.8 28.3 - - + -
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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