Contacts of the strand formed by residues 1794 - 1800 (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 ALA1794 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1662A TRP* 3.4 31.0 - - + +
1747A SER 3.7 1.1 + - - +
1748A ALA* 3.2 7.2 - - + -
1749A VAL 3.0 23.0 + - - -
1750A PHE* 5.0 1.1 - - + -
1792A LEU* 3.5 7.6 - - - +
1793A THR* 1.3 83.9 + - - +
1795A PHE* 1.3 61.6 + - - +
1796A VAL* 4.0 15.7 - - + -
1833A PRO* 4.3 5.8 - - - +
1834A ALA 5.5 0.2 - - - +
1835A THR* 5.9 0.7 - - - -
1877A LEU* 4.4 11.9 - - + -
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Residues in contact with PHE1795 (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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1749A VAL* 3.5 17.9 - - + -
1780A ALA 4.1 4.0 - - - -
1783A LEU* 3.9 21.3 - - + -
1784A HIS* 3.6 26.7 - - + -
1787A THR* 3.8 14.4 - - - -
1792A LEU* 4.0 19.7 - - + -
1794A ALA* 1.3 74.0 - - - +
1796A VAL* 1.3 60.5 + - - +
1797A LEU* 3.8 32.5 + - + +
1823A LEU* 4.9 1.6 - - + -
1827A ARG* 3.3 36.8 - - - +
1833A PRO* 3.4 19.9 + - + +
1834A ALA* 3.2 6.9 - - + +
1835A THR* 2.9 25.2 + - - +
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Residues in contact with VAL1796 (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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1749A VAL* 2.7 12.0 + - - +
1750A PHE* 3.5 34.7 - - + -
1751A HIS* 2.9 29.1 + - - +
1794A ALA* 4.4 1.8 - - + -
1795A PHE* 1.3 79.3 - - - +
1797A LEU* 1.3 65.6 + - - +
1798A PHE* 3.9 17.9 - - + -
1835A THR* 3.3 12.3 - - - +
1837A VAL* 3.8 24.0 - - + -
1873A LEU* 4.2 7.6 - - + -
1877A LEU* 4.0 24.2 - - + -
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Residues in contact with LEU1797 (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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1751A HIS* 3.8 20.9 - - + -
1780A ALA* 3.7 22.4 - - + -
1795A PHE* 3.8 29.4 - - + +
1796A VAL* 1.3 76.6 - - - +
1798A PHE* 1.3 64.7 + - - +
1799A SER 3.3 1.2 + - - -
1820A LEU* 3.6 45.5 - - + +
1823A LEU* 4.0 25.1 - - + -
1824A ALA* 4.4 9.0 - - + +
1835A THR 2.8 11.8 + - - +
1836A ALA* 3.6 2.6 - - - -
1837A VAL* 3.1 25.6 + - - -
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Residues in contact with PHE1798 (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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301A NDP 3.5 10.4 + - - +
1677A VAL* 3.5 23.6 - - + -
1681A ILE* 3.3 46.7 - - + -
1750A PHE* 4.1 17.0 - + + -
1751A HIS 3.2 23.6 + - - +
1752A ALA* 4.1 16.2 - - + -
1776A LYS* 2.9 29.0 + - - +
1796A VAL* 3.9 24.2 - - + -
1797A LEU* 1.3 77.2 - - - +
1799A SER* 1.3 60.5 + - - +
1820A LEU* 3.2 6.5 - - - +
1837A VAL* 4.0 3.6 - - + -
1839A TRP* 3.1 33.2 - + + +
1873A LEU* 4.8 0.9 - - + -
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Residues in contact with SER1799 (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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301A NDP 3.3 11.1 + - - -
1797A LEU 3.3 2.6 + - - -
1798A PHE* 1.3 76.1 - - - +
1800A SER* 1.3 68.6 + - - -
1803A SER* 3.0 14.7 + - - -
1817A ASN* 3.2 17.4 + - - +
1820A LEU* 4.1 5.4 - - - -
1821A ASP* 3.0 27.6 + - - -
1836A ALA* 4.4 6.5 - - - -
1837A VAL 2.7 30.1 + - - +
1838A ALA* 3.7 3.7 - - - +
1839A TRP* 3.3 10.4 + - - +
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Residues in contact with SER1800 (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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301A NDP 4.4 8.3 + - - -
1799A SER* 1.3 86.0 + - - +
1801A PHE* 1.3 82.0 + - - +
1802A ALA* 2.8 19.2 + - - +
1803A SER* 2.8 23.2 + - - -
1804A ALA 3.2 4.2 + - - -
1813A TYR* 3.6 13.2 - - - -
1817A ASN* 3.4 25.1 + - - -
1838A ALA* 3.6 10.8 - - - +
1839A TRP 3.7 8.4 + - - +
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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