Contacts of the strand formed by residues 1805 - 1810 (chain A) in PDB entry 4IFI
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 HIS1805 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1763A GLY* 3.2 27.2 + - - +
1764A LEU* 3.6 17.8 - - + +
1765A GLU 3.0 22.7 + - - +
1802A THR 4.3 10.3 + - - -
1803A GLY* 3.9 15.4 + - - -
1804A VAL* 1.3 83.1 + - - +
1806A PRO* 1.3 67.4 - - - +
1807A ILE* 4.0 5.5 - - + +
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Residues in contact with PRO1806 (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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1765A GLU* 3.6 7.9 - - + +
1798A PHE* 3.6 31.9 - - + -
1799A THR 5.5 1.8 - - - +
1804A VAL* 3.6 16.3 - - + +
1805A HIS* 1.3 85.5 - - - +
1807A ILE* 1.3 66.9 + - - +
1829A GLU* 4.9 4.9 - - + +
1830A ALA* 3.6 27.4 - - + +
1831A PRO* 3.4 16.5 - - + +
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Residues in contact with ILE1807 (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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1764A LEU* 3.7 43.5 - - + -
1765A GLU 3.0 9.1 + - - +
1766A ILE* 3.5 6.8 - - + +
1767A CYS 3.0 24.4 + - - -
1798A PHE* 3.4 3.2 - - - -
1805A HIS* 4.0 4.9 - - + +
1806A PRO* 1.3 80.3 - - - +
1808A VAL* 1.3 65.9 + - - +
1809A VAL* 3.9 12.6 - - + -
1830A ALA* 4.1 0.2 - - - -
1831A PRO* 3.7 19.5 - - + +
1833A VAL* 3.8 28.0 - - + -
1837A TRP* 4.0 15.9 - - + -
1850A LEU* 4.6 13.0 - - + -
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Residues in contact with VAL1808 (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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1767A CYS* 3.5 3.6 - - + +
1769A TYR* 3.8 25.8 - - + -
1795A LEU* 4.1 6.3 - - + -
1798A PHE* 3.5 30.3 - - + -
1807A ILE* 1.3 73.8 - - - +
1809A VAL* 1.3 60.4 + - - +
1810A VAL* 4.1 10.9 + - + -
1824A ILE* 4.2 15.7 - - + -
1828A CYS* 3.8 19.3 - - - -
1830A ALA* 4.0 6.5 - - + -
1831A PRO 2.9 11.6 + - - +
1832A VAL* 3.4 11.4 - - + +
1833A VAL* 2.7 34.7 + - - +
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Residues in contact with VAL1809 (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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1766A ILE* 3.7 25.1 - - + -
1767A CYS 2.8 12.4 + - - +
1768A CYS* 4.6 4.9 - - - -
1769A TYR 3.0 24.4 + - - -
1772A PHE* 3.4 4.6 - - + -
1780A LEU* 4.6 9.6 - - + -
1807A ILE* 3.9 13.7 - - + -
1808A VAL* 1.3 76.7 - - - +
1810A VAL* 1.3 65.7 + - - +
1833A VAL* 3.3 9.2 - - + -
1834A THR 4.0 1.8 - - - +
1835A ARG* 3.6 35.4 - - + +
1837A TRP* 4.2 1.3 - - + -
1838A VAL* 4.0 23.1 - - + -
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Residues in contact with VAL1810 (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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1769A TYR* 3.6 19.1 - - + +
1772A PHE* 4.0 4.3 - - - -
1808A VAL* 4.1 11.4 - - + -
1809A VAL* 1.3 81.6 - - - +
1811A GLN* 1.3 61.3 + - - +
1812A PRO* 3.2 10.8 - - + +
1815A TRP* 4.3 8.1 - - - +
1821A PHE* 4.6 14.1 - - + -
1824A ILE* 3.8 26.5 - - + -
1832A VAL* 4.5 6.5 - - + -
1833A VAL 2.9 7.6 + - - +
1834A THR* 3.2 8.8 - - - -
1835A ARG 2.9 23.3 + - - -
1855A ILE* 3.6 27.4 - - + -
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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