Contacts of the helix formed by residues 1835 - 1844 (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 ARG1835 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1772A PHE* 3.8 19.0 - - + +
1773A THR* 3.1 20.2 + - - +
1774A ASN* 5.6 0.4 - - - +
1775A MET* 3.8 22.7 - - - +
1780A LEU* 3.9 33.0 - - + -
1809A VAL* 3.6 13.5 - - + -
1810A VAL 2.9 14.6 + - - +
1811A GLN* 3.0 42.8 + - + +
1834A THR* 1.3 68.5 - - - +
1836A GLU* 1.3 70.7 + - + +
1837A TRP 3.1 2.2 - - - -
1838A VAL* 3.0 13.7 + - - +
1839A LEU* 3.1 26.8 + - + +
9B PHE* 3.8 26.4 - - - -
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Residues in contact with GLU1836 (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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1699A ARG* 3.7 20.9 + - - -
1741A VAL* 5.5 1.4 - - - +
1834A THR* 3.2 13.2 - - - +
1835A ARG* 1.3 80.9 + - + +
1837A TRP* 1.3 65.8 + - - +
1839A LEU* 3.5 21.9 - - - +
1840A ASP* 3.0 40.7 + - - +
1853A TYR* 3.7 11.4 - - + -
9B PHE* 5.3 2.3 - - - +
10B SER 4.7 14.0 - - - +
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Residues in contact with TRP1837 (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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1761A PHE* 3.5 27.1 - + - -
1764A LEU* 3.8 18.6 - - + -
1766A ILE* 4.1 11.4 - - + -
1807A ILE* 4.0 20.6 - - + -
1809A VAL* 4.2 1.6 - - + -
1833A VAL* 3.7 23.3 - - + -
1834A THR 3.1 15.8 + - - +
1835A ARG 3.1 1.0 - - - -
1836A GLU* 1.3 78.6 - - - +
1838A VAL* 1.3 90.1 + - + +
1840A ASP* 4.0 1.0 - - - +
1841A SER* 2.9 39.3 + - - -
1847A CYS* 3.8 14.6 - - - -
1848A GLN* 2.8 23.7 + - - +
1849A GLU 3.7 2.2 - - - -
1850A LEU* 3.5 19.0 - - + +
1853A TYR* 3.3 46.0 - + + -
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Residues in contact with VAL1838 (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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1761A PHE* 4.4 6.7 - - + -
1766A ILE* 5.4 0.2 - - + -
1768A CYS* 6.0 0.2 - - - -
1780A LEU* 3.9 18.6 - - + -
1783A MET* 3.9 25.6 - - - -
1784A VAL* 4.0 24.5 - - + -
1809A VAL* 4.0 23.1 - - + -
1835A ARG* 3.0 9.2 + - - +
1837A TRP* 1.3 102.7 - - + +
1839A LEU* 1.3 60.0 + - + +
1841A SER* 3.4 1.7 + - - -
1842A VAL* 2.8 33.9 + - + +
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Residues in contact with LEU1839 (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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1699A ARG* 3.8 9.6 - - - +
1704A PHE* 3.3 41.2 - - + -
1775A MET* 4.0 18.6 - - + -
1780A LEU* 4.6 0.4 - - + -
1783A MET* 4.1 16.2 - - + -
1835A ARG* 3.1 35.8 + - + +
1836A GLU* 3.5 29.4 - - - +
1837A TRP 3.3 0.4 - - - -
1838A VAL* 1.3 80.1 - - + +
1840A ASP* 1.3 57.9 + - - +
1842A VAL 3.3 0.5 + - - -
1843A ALA* 2.9 31.2 + - - +
9B PHE* 4.5 16.8 - - + -
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Residues in contact with ASP1840 (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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1699A ARG* 2.8 29.1 + - - +
1741A VAL* 4.6 3.1 - - - +
1742A ASN* 3.0 20.1 - - - +
1836A GLU* 3.0 25.9 + - - +
1837A TRP 4.0 0.7 - - - +
1839A LEU* 1.3 73.2 - - - +
1841A SER* 1.3 68.1 + - - +
1843A ALA* 3.2 1.2 + - - +
1844A LEU* 3.0 30.3 + - + +
1848A GLN* 4.2 5.8 - - + -
1853A TYR* 2.6 36.7 + - - +
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Residues in contact with SER1841 (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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1760A ILE* 3.7 2.8 - - - +
1761A PHE* 3.8 22.2 - - - -
1837A TRP* 2.9 26.2 + - - -
1838A VAL 3.7 3.4 - - - -
1840A ASP* 1.3 78.9 - - - +
1842A VAL* 1.3 63.7 + - - +
1845A TYR* 3.0 4.0 + - - -
1846A GLN 2.9 42.7 + - - -
1847A CYS* 3.8 1.9 - - - -
1848A GLN* 2.9 27.8 + - - +
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Residues in contact with VAL1842 (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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1704A PHE* 3.5 44.4 - - + +
1707A ILE* 3.3 16.2 - - + +
1708A ALA* 4.3 10.1 - - + +
1760A ILE* 4.1 5.2 - - + -
1761A PHE* 4.3 7.9 - - + -
1783A MET* 3.8 19.3 - - + -
1787A CYS* 3.8 22.7 - - - -
1838A VAL* 2.8 29.8 + - + +
1839A LEU 3.8 3.6 - - - +
1841A SER* 1.3 73.1 - - - +
1843A ALA* 1.3 63.8 + - - +
1845A TYR* 3.0 11.9 + - + +
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Residues in contact with ALA1843 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1703A TYR* 4.3 4.5 - - + -
1704A PHE* 4.3 9.6 - - + -
1707A ILE* 3.8 15.0 - - - +
1739A ASP* 3.7 12.1 - - - +
1742A ASN* 3.2 32.3 - - - +
1746A HIS* 3.1 22.5 - - - -
1748A GLY* 3.4 7.6 - - - -
1839A LEU 2.9 15.3 + - - +
1840A ASP 3.2 1.5 + - - +
1842A VAL* 1.3 79.0 - - - +
1844A LEU* 1.3 58.2 + - - +
1845A TYR 3.1 0.4 - - - -
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Residues in contact with LEU1844 (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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1742A ASN* 3.8 27.1 - - + +
1746A HIS* 3.5 34.8 - - + -
1748A GLY* 3.9 6.5 - - - -
1751A ARG* 2.9 25.4 + - - +
1840A ASP* 3.0 20.9 + - + +
1841A SER 4.0 2.5 - - - +
1843A ALA* 1.3 77.8 - - - +
1845A TYR* 1.3 65.1 + - - +
1846A GLN* 3.1 16.9 + - + +
1848A GLN* 3.6 32.5 - - + +
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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