Contacts of the strand formed by residues 1939 - 1943 (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 TRP1939 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1544A GLU* 3.2 22.4 + - + -
1897A THR* 4.8 3.1 - - - -
1899A ASP* 5.5 1.9 - - - +
1901A VAL* 6.2 0.2 - - - +
1922A ARG* 3.1 52.4 - - + +
1926A TRP* 3.8 17.5 - - + -
1927A CYS 3.3 15.3 - - - +
1928A SER* 4.5 0.9 - - - +
1929A THR* 3.7 10.1 + - - +
1933A TYR* 3.9 14.8 - + + -
1937A HIS* 4.2 8.3 - - + -
1938A GLU* 1.3 76.7 + - - +
1940A GLY* 1.3 83.9 + - - +
1941A PHE* 3.6 41.5 - + - -
23D ASP* 6.0 0.2 - - - -
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Residues in contact with GLY1940 (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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1897A THR* 3.7 24.0 - - - +
1899A ASP* 5.3 4.9 - - - -
1926A TRP* 3.6 1.6 - - - -
1927A CYS* 3.3 24.9 + - - +
1939A TRP* 1.3 89.5 - - - +
1941A PHE* 1.3 65.3 + - - -
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Residues in contact with PHE1941 (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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1543A SER 5.7 1.1 - - - -
1897A THR* 3.1 5.1 - - - -
1898A ASP* 3.1 47.2 + - - +
1922A ARG* 4.7 7.4 - - + -
1923A ALA* 5.2 5.2 - - + -
1924A LYS* 3.6 53.6 - - + -
1925A LEU 3.7 4.7 - - - +
1926A TRP* 4.2 2.9 - - + -
1939A TRP* 3.6 31.1 - + - -
1940A GLY* 1.3 71.0 - - - -
1942A CYS* 1.3 63.4 + - - +
23D ASP* 4.0 22.7 - - - -
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Residues in contact with CYS1942 (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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1895A PRO* 4.6 2.0 - - + -
1896A GLU 3.4 7.0 - - - +
1897A THR* 4.6 0.2 - - - +
1898A ASP* 4.5 2.3 - - - +
1903A CYS* 4.2 1.3 - - - -
1917A CYS* 2.0 50.9 - - + -
1924A LYS* 5.1 11.6 - - - +
1925A LEU* 2.8 23.4 + - + +
1926A TRP 3.6 14.6 - - - -
1927A CYS* 3.6 13.0 - - - -
1941A PHE* 1.3 73.6 - - - +
1943A ARG* 1.3 59.8 + - - +
1944A HIS* 3.8 16.7 + - + -
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Residues in contact with ARG1943 (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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1895A PRO* 4.4 0.2 - - - +
1896A GLU* 2.7 62.2 + - - +
1897A THR 3.4 17.4 + - - +
1898A ASP* 3.3 35.3 + - - +
1900A GLY* 4.2 10.7 - - - -
1942A CYS* 1.3 71.6 - - - +
1944A HIS* 1.3 66.0 + - - +
1945A SER* 3.8 3.8 + - - +
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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