Contacts of the helix formed by residues 1776 - 1787 (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 PRO1776 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1701A LEU* 4.7 7.0 - - + -
1774A ASN 4.5 1.6 - - - +
1775A MET* 1.3 86.8 - - + +
1777A THR* 1.3 69.2 + - - +
1778A ASP* 3.9 16.4 - - - +
1779A GLN* 2.9 30.8 + - + +
1780A LEU 3.2 7.8 + - - -
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Residues in contact with THR1777 (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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1768A CYS* 3.9 26.9 - - + +
1770A GLY 5.0 1.7 + - - +
1772A PHE* 3.7 25.1 + - + +
1775A MET 3.3 4.4 + - - -
1776A PRO* 1.3 70.3 - - - +
1778A ASP* 1.3 58.3 + - - +
1780A LEU* 3.1 10.1 + - - +
1781A GLU* 2.8 48.2 + - - +
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Residues in contact with ASP1778 (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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1776A PRO* 3.0 9.4 + - - +
1777A THR* 1.3 79.3 - - - +
1779A GLN* 1.3 73.0 + - - +
1781A GLU* 3.4 20.4 - - - +
1782A TRP* 2.9 25.8 + - - +
1793A LYS* 5.7 3.8 - - - +
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Residues in contact with GLN1779 (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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1680A ILE* 5.4 3.8 - - - +
1701A LEU* 3.6 37.0 - - + +
1705A LEU* 3.7 18.2 - - + +
1775A MET* 4.6 0.7 - - + -
1776A PRO* 2.9 27.0 + - + +
1778A ASP* 1.3 88.4 + - - +
1780A LEU* 1.3 59.9 + - - +
1781A GLU 3.2 0.2 - - - -
1782A TRP* 3.5 26.4 - - - +
1783A MET* 2.8 30.2 + - - +
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Residues in contact with LEU1780 (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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1768A CYS* 3.6 25.6 - - + -
1772A PHE* 3.8 34.3 - - + -
1775A MET* 3.9 28.8 - - + +
1776A PRO 3.2 5.9 + - - +
1777A THR* 3.1 11.1 + - - +
1779A GLN* 1.3 77.2 - - - +
1781A GLU* 1.3 56.8 - - - +
1783A MET* 3.1 11.9 + - + +
1784A VAL* 2.9 32.3 + - + +
1809A VAL* 4.6 4.0 - - + -
1835A ARG* 3.9 20.6 - - + -
1838A VAL* 3.9 29.8 - - + -
1839A LEU* 4.6 1.1 - - + -
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Residues in contact with GLU1781 (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 6.0 0.2 - - - +
1768A CYS* 3.9 23.8 - - + +
1777A THR* 2.8 35.3 + - - +
1778A ASP* 3.4 23.1 - - - +
1780A LEU* 1.3 68.0 - - - +
1782A TRP* 1.3 67.2 + - - +
1784A VAL* 3.2 11.7 - - - +
1785A GLN* 2.9 24.8 + - - +
1791A VAL* 3.4 27.9 - - + +
1792A VAL 4.8 3.5 - - - +
1793A LYS* 4.1 31.6 + - - +
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Residues in contact with TRP1782 (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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1680A ILE* 3.8 16.6 - - + -
1681A THR* 3.8 27.1 - - - -
1682A GLU* 4.0 35.5 + - + +
1705A LEU* 3.8 26.5 - - + -
1711A LYS* 5.9 2.2 - - - -
1778A ASP 2.9 19.6 + - - +
1779A GLN* 3.3 28.2 + - - +
1781A GLU* 1.3 74.4 - - - +
1783A MET* 1.3 58.2 + - - +
1785A GLN* 3.1 22.7 + - - +
1786A LEU* 2.8 57.9 + - + +
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Residues in contact with MET1783 (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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1701A LEU* 3.8 23.6 - - + -
1704A PHE* 3.4 38.6 - - + -
1705A LEU* 3.8 13.9 - - + +
1708A ALA* 3.8 15.2 - - + +
1775A MET* 3.9 19.5 - - + -
1779A GLN 2.8 10.8 + - - +
1780A LEU* 3.1 10.7 + - + +
1782A TRP* 1.3 78.3 - - - +
1784A VAL* 1.3 62.3 + - - +
1786A LEU* 3.6 5.7 + - - +
1787A CYS* 3.4 22.9 + - - -
1838A VAL* 3.9 17.5 - - - -
1839A LEU* 4.1 5.2 - - + -
1842A VAL* 3.8 21.5 - - + -
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Residues in contact with VAL1784 (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* 3.9 13.0 - - + -
1766A ILE* 4.0 32.8 - - + +
1768A CYS* 4.8 4.3 - - - -
1780A LEU* 2.9 22.5 + - + +
1781A GLU* 3.2 18.2 - - - +
1783A MET* 1.3 72.7 - - - +
1785A GLN* 1.3 65.6 + - - +
1787A CYS* 3.1 10.6 + - - +
1788A GLY 3.2 0.5 + - - -
1789A ALA* 3.0 27.2 + - + +
1791A VAL* 3.8 16.4 - - + -
1838A VAL* 4.0 35.4 - - + -
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Residues in contact with GLN1785 (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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1759A LYS* 5.1 0.2 - - - +
1781A GLU 2.9 17.7 + - - +
1782A TRP* 3.6 23.8 + - - +
1784A VAL* 1.3 77.8 - - - +
1786A LEU* 1.3 67.0 + - - +
1788A GLY* 2.8 24.9 + - - -
1789A ALA 3.4 16.0 + - - +
1790A SER* 5.9 0.2 - - - -
1791A VAL* 3.9 13.9 - - + +
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Residues in contact with LEU1786 (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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1682A GLU* 5.4 6.7 - - + -
1705A LEU* 4.1 21.5 - - + +
1708A ALA* 3.5 33.2 - - + +
1709A GLY* 4.3 14.6 - - - +
1711A LYS* 6.2 1.3 - - - -
1759A LYS* 3.1 28.1 - - - +
1782A TRP* 2.8 59.4 + - + +
1783A MET 3.6 6.1 - - - +
1785A GLN* 1.3 84.2 - - - +
1787A CYS* 1.3 55.5 + - - +
1788A GLY 3.1 0.2 - - - -
1845A TYR* 4.9 0.2 + - - -
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Residues in contact with CYS1787 (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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1708A ALA* 3.7 19.1 - - - -
1759A LYS* 3.4 12.4 - - - +
1760A ILE* 3.6 7.1 + - + -
1761A PHE* 2.7 48.5 + - + +
1783A MET 3.4 13.4 + - - +
1784A VAL 3.1 11.9 + - - +
1786A LEU* 1.3 78.1 - - - +
1788A GLY* 1.3 54.7 - - - +
1842A VAL* 3.8 22.9 - - - -
1845A TYR* 3.9 26.2 - - - -
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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