Contacts of the helix formed by residues 1819 - 1827 (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 ASN1819 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1817A GLU 3.8 3.7 + - - +
1818A ASP* 1.3 67.7 - - - +
1820A GLY* 1.3 57.9 + - - +
1821A PHE* 3.1 20.6 + - + -
1822A HIS* 3.3 34.8 + - + +
1823A ALA* 4.6 1.2 + - - +
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Residues in contact with GLY1820 (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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1815A TRP* 3.5 22.4 - - - -
1818A ASP* 3.0 11.7 + - - +
1819A ASN* 1.3 72.0 - - - +
1821A PHE* 1.3 57.2 + - - +
1822A HIS 3.0 5.8 - - - -
1823A ALA* 3.1 27.2 + - - +
1824A ILE* 4.0 4.7 + - - +
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Residues in contact with PHE1821 (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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1810A VAL* 4.6 7.9 - - + -
1812A PRO* 4.0 41.3 - - + -
1815A TRP* 3.6 45.7 - + + +
1818A ASP 4.4 1.6 - - - -
1819A ASN* 4.0 17.5 - - + -
1820A GLY* 1.3 79.7 - - - +
1822A HIS* 1.3 84.9 + + - +
1823A ALA 3.4 0.7 - - - -
1824A ILE* 3.9 20.8 - - + +
1832A VAL* 4.5 1.4 - - - +
1855A ILE* 3.8 15.6 - - + +
1857A GLN* 3.1 20.5 + - - +
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Residues in contact with HIS1822 (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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1819A ASN* 3.3 28.0 + - + +
1820A GLY 3.0 1.0 - - - -
1821A PHE* 1.3 100.4 - + - +
1823A ALA* 1.3 56.6 + - - +
1855A ILE* 3.6 17.7 - - + +
1856A PRO* 2.5 43.3 - - + +
1857A GLN* 3.0 15.9 - - - +
1858A ILE* 2.8 51.3 + - + +
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Residues in contact with ALA1823 (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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1819A ASN 5.5 0.7 - - - +
1820A GLY* 3.1 16.8 + - - +
1822A HIS* 1.3 79.7 - - - +
1824A ILE* 1.3 63.2 + - - +
1825A GLY 3.2 2.0 - - - -
1826A GLN* 3.3 39.9 + - - +
1827A MET* 4.2 10.2 + - - +
1858A ILE* 5.2 4.5 - - + -
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Residues in contact with ILE1824 (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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1769A TYR* 3.6 32.8 - - + +
1795A LEU* 3.9 20.6 - - + -
1808A VAL* 4.2 16.6 - - + -
1810A VAL* 3.8 20.2 - - + -
1815A TRP* 4.4 2.0 - - + -
1820A GLY 4.0 2.9 - - - +
1821A PHE* 3.9 31.9 - - + +
1823A ALA* 1.3 81.9 - - - +
1825A GLY* 1.3 57.6 + - - +
1827A MET* 3.1 26.1 + - - +
1828A CYS* 3.5 12.4 + - - -
1832A VAL* 4.2 13.0 - - + -
1857A GLN* 3.0 8.6 + - - +
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Residues in contact with GLY1825 (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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1823A ALA 3.2 0.8 - - - -
1824A ILE* 1.3 77.8 - - - +
1826A GLN* 1.3 56.1 + - - +
1827A MET 3.2 1.6 - - - -
1828A CYS* 2.8 21.7 - - - +
1830A ALA 5.4 3.1 - - - -
1832A VAL* 5.0 3.6 - - - -
1857A GLN* 2.9 33.1 + - - +
1858A ILE 5.0 2.7 - - - -
1859A PRO* 5.5 0.4 - - - -
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Residues in contact with GLN1826 (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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1823A ALA* 3.3 37.4 + - - +
1825A GLY* 1.3 76.3 - - - +
1827A MET* 1.3 61.6 + - + +
1828A CYS 3.5 0.4 - - - -
1858A ILE* 4.0 15.0 + - - +
1859A PRO* 2.8 40.2 - - - +
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Residues in contact with MET1827 (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* 4.1 13.0 - - + +
1795A LEU* 3.8 35.9 - - + +
1796A SER* 5.6 2.2 - - - -
1823A ALA 4.3 11.9 - - - +
1824A ILE* 3.1 13.5 + - - +
1826A GLN* 1.3 83.6 - - + +
1828A CYS* 1.3 61.7 + - - +
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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