Contacts of the strand formed by residues 1824 - 1829 (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 THR1824 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1823B SER* 1.3 86.1 + - - +
1825B PHE* 1.3 69.5 + - - +
1826B LYS* 3.8 25.0 - - - +
1835B SER* 3.3 26.5 - - - +
1836B VAL 4.7 2.2 - - - +
1837B GLY* 5.2 2.5 - - - -
1841B PHE 5.2 2.5 + - - -
1842B ALA 3.4 13.8 + - - +
1843B VAL* 5.4 3.3 - - - -
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Residues in contact with PHE1825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1820B LEU* 4.0 12.3 - - - -
1822B THR* 4.2 17.3 - - + -
1823B SER* 3.4 24.2 - - - -
1824B THR* 1.3 77.9 - - - +
1826B LYS* 1.3 65.9 + - - +
1827B VAL* 3.8 2.0 - - + -
1835B SER* 3.3 9.9 - - - -
1836B VAL* 3.2 44.8 + - + +
1837B GLY* 5.0 0.9 - - - -
1838B VAL 5.5 0.7 - - - -
1963B ILE* 5.2 9.4 - - + -
1964B GLY 4.4 8.7 - - - -
1965B ARG* 5.3 13.7 - - - +
1966B PRO* 4.0 26.7 - - + -
1981B TRP* 3.5 34.8 - + - -
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Residues in contact with LYS1826 (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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1824B THR* 3.8 28.3 - - + +
1825B PHE* 1.3 78.1 - - - +
1827B VAL* 1.3 63.8 + - - +
1828B THR* 3.4 9.7 + - - +
1833B THR* 4.5 12.6 - - + -
1834B TYR 4.0 12.8 - - - +
1835B SER* 5.0 1.6 - - - +
1858B LEU* 4.7 13.4 - - + +
1965B ARG* 4.5 18.6 + - - +
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Residues in contact with VAL1827 (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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1825B PHE* 3.8 2.0 + - + -
1826B LYS* 1.3 73.7 - - - +
1828B THR* 1.3 63.1 + - - +
1829B ARG* 6.1 0.2 - - + -
1832B ARG 3.8 1.0 - - - +
1834B TYR* 2.8 36.7 + - + +
1836B VAL* 3.9 20.2 - - + -
1965B ARG* 5.9 1.3 - - + +
1966B PRO* 3.4 50.9 - - + +
1967B GLN* 3.7 7.9 - - - +
1968B VAL* 3.5 35.7 - - + +
1979B PHE* 3.8 11.4 - - + -
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Residues in contact with THR1828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1826B LYS* 3.4 9.9 + - - +
1827B VAL* 1.3 79.8 - - - +
1829B ARG* 1.3 73.1 + - - +
1831B SER* 4.4 10.3 - - - +
1832B ARG 3.3 12.6 - - - +
1833B THR* 3.4 37.1 - - - +
1968B VAL* 5.0 1.8 - - - -
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Residues in contact with ARG1829 (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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1827B VAL* 6.1 0.2 - - + -
1828B THR* 1.3 81.2 - - - +
1830B ASP* 1.3 82.9 + - - +
1831B SER 3.5 1.1 - - - -
1832B ARG* 3.0 29.7 + - - +
1834B TYR* 5.6 0.6 - - + -
1968B VAL* 3.0 62.6 + - + +
1969B PHE 3.9 11.1 + - - -
1970B SER* 5.1 2.0 - - - +
1971B GLU* 4.6 15.0 + - - +
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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