Contacts of the helix formed by residues 1801 - 1805 (chain A) in PDB entry 2FR1
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 PHE1801 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A NDP 5.0 9.2 - + - -
1650A TRP* 5.6 0.7 - - + -
1800A SER* 1.3 84.0 + - - +
1802A ALA* 1.3 62.5 + - - +
1804A ALA* 3.8 11.4 - - + -
1805A PHE* 3.0 62.0 + + + -
1806A GLY 3.1 4.9 + - - -
1807A ALA* 4.5 6.3 - - + -
1810A LEU* 3.7 31.0 - - + -
1813A TYR* 6.2 0.4 - + - -
1838A ALA* 4.7 2.2 - - - +
1839A TRP 3.0 29.3 + - - +
1840A GLY* 3.9 10.8 - - - -
1841A THR* 4.4 19.7 - - + -
1856A PHE* 4.3 22.9 - + + -
1861A VAL* 5.3 4.9 - - + -
1885A ILE* 5.9 1.6 - - + -
1887A ILE* 4.0 15.7 - - + -
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Residues in contact with ALA1802 (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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1594A GLY 4.6 1.0 - - - +
1597A ARG* 5.4 0.2 + - - -
1598A VAL* 4.7 0.2 - - - +
1800A SER* 2.8 16.1 + - - +
1801A PHE* 1.3 85.0 - - - +
1803A SER* 1.3 56.7 + - - +
1806A GLY* 3.0 25.1 - - - -
1810A LEU* 3.8 21.3 - - + -
1813A TYR* 3.6 24.2 - - + -
1814A ALA* 3.3 25.8 - - - +
1817A ASN* 4.4 0.7 - - - +
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Residues in contact with SER1803 (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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1594A GLY* 5.0 1.3 - - - -
1597A ARG* 2.8 33.6 + - - +
1648A ARG* 3.7 1.7 + - - -
1799A SER* 3.0 19.9 + - - -
1800A SER 2.8 13.7 + - - -
1802A ALA* 1.3 78.5 - - - +
1804A ALA* 1.3 63.6 + - - +
1805A PHE 3.4 0.7 - - - -
1814A ALA* 3.8 8.1 - - - -
1817A ASN* 3.2 8.0 - - - +
1818A ALA* 3.7 28.9 - - - -
1821A ASP* 3.5 11.6 + - - +
1838A ALA* 5.1 0.7 - - - +
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Residues in contact with ALA1804 (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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1457A ILE* 5.8 0.2 - - - -
1648A ARG* 2.9 34.0 + - - +
1650A TRP* 3.2 30.6 + - + -
1800A SER 3.2 6.2 + - - +
1801A PHE* 3.1 17.2 + - - +
1803A SER* 1.3 79.9 + - - +
1805A PHE* 1.3 59.5 + - - +
1821A ASP* 5.8 0.4 - - - -
1838A ALA* 4.2 10.3 - - + +
1885A ILE* 4.1 16.4 - - + -
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Residues in contact with PHE1805 (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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1597A ARG* 3.8 21.6 - - - +
1601A LEU* 4.6 1.2 - - - +
1650A TRP* 3.2 35.7 - + + +
1801A PHE* 3.0 46.4 + + + -
1804A ALA* 1.3 75.2 - - - +
1806A GLY* 1.3 96.7 + - - +
1807A ALA* 4.4 6.5 - - + -
1859A HIS* 5.6 2.5 - + - -
1861A VAL* 4.4 10.5 - - + -
1887A ILE* 4.2 8.7 - - + -
1889A VAL* 5.6 2.0 - - + -
1894A PHE* 3.5 41.1 - + - -
1898A TYR* 2.9 31.9 + + + +
1906A LEU* 4.5 2.2 - - + -
1907A PHE* 4.1 11.9 - - + -
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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