Contacts of the strand formed by residues 1832 - 1837 (chain A) 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 ARG1832 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1827A VAL 3.8 0.5 - - - +
1828A THR* 3.3 5.2 - - - -
1829A ARG* 3.1 27.2 + - - +
1830A ASP* 2.7 47.4 + - - +
1831A SER* 1.3 69.9 - - - +
1833A THR* 1.3 60.1 + - - +
1834A TYR* 3.5 16.1 + - + -
1857A LEU* 3.8 26.7 - - + -
1858A LEU 5.6 0.9 - - - -
1971A GLU* 2.8 43.4 + - - +
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Residues in contact with THR1833 (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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1826A LYS* 4.4 17.9 - - + -
1828A THR* 3.3 27.0 - - - +
1831A SER 3.2 11.9 + - - -
1832A ARG* 1.3 68.7 - - - +
1834A TYR* 1.3 68.0 + - - +
1857A LEU* 4.6 2.7 - - - +
1858A LEU* 3.2 46.2 + - + +
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Residues in contact with TYR1834 (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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1826A LYS* 3.5 13.0 - - - +
1827A VAL* 2.8 37.9 + - + +
1829A ARG 5.6 0.7 - - - -
1832A ARG* 3.5 18.2 + - + -
1833A THR* 1.3 75.6 - - - +
1835A SER* 1.3 62.3 + - - +
1836A VAL* 4.2 1.3 - - + -
1855A VAL* 4.2 10.1 - - + -
1856A CYS 3.7 1.8 - - - -
1857A LEU* 3.6 41.2 - - + +
1866A PHE* 3.9 16.0 - + - -
1968A VAL* 4.2 10.3 - - + -
1971A GLU* 2.6 32.4 + - - +
1974A GLY* 5.8 1.2 - - - -
1977A VAL* 3.4 30.3 - - + +
1979A PHE* 3.7 30.1 - + + -
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Residues in contact with SER1835 (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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1824A THR* 3.2 14.0 - - - +
1825A PHE 3.3 5.4 - - - -
1826A LYS* 4.2 10.1 - - - -
1834A TYR* 1.3 76.1 - - - +
1836A VAL* 1.3 61.2 + - - +
1842A ALA* 2.7 42.5 + - - +
1843A VAL* 4.2 10.9 - - - +
1855A VAL* 3.3 5.7 - - - +
1856A CYS 3.1 33.1 + - - -
1858A LEU* 4.4 4.3 - - - -
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Residues in contact with VAL1836 (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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1824A THR* 4.0 1.0 - - - -
1825A PHE* 3.1 42.1 + - + +
1827A VAL* 4.2 20.4 - - + -
1834A TYR* 4.7 0.4 - - + -
1835A SER* 1.3 80.3 + - - +
1837A GLY* 1.3 63.9 + - - +
1838A VAL 4.2 0.2 - - - -
1842A ALA* 4.9 2.0 - - - -
1854A GLY 4.1 2.2 - - - +
1855A VAL* 4.2 10.3 - - + -
1887A TYR* 5.6 0.4 - - + -
1953A ILE* 3.6 31.4 - - + -
1966A PRO* 5.0 3.1 - - + -
1979A PHE* 3.8 36.1 - - + -
1981A TRP* 4.5 14.6 - - + -
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Residues in contact with GLY1837 (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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1823A SER 4.4 11.7 - - - -
1824A THR* 5.3 1.6 - - - -
1825A PHE* 5.1 0.4 - - - -
1836A VAL* 1.3 77.4 - - - +
1838A VAL* 1.3 64.5 + - - -
1839A CYS 3.2 0.5 + - - -
1840A THR* 2.7 31.1 + - - +
1841A PHE 4.9 4.5 - - - -
1842A ALA* 4.5 1.6 - - - +
1854A GLY 3.5 10.1 + - - +
1887A TYR* 2.9 17.8 + - - -
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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