Contacts of the helix formed by residues 1700 - 1709 (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 THR1700 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1655A SER* 2.7 28.6 + - - +
1656A GLY* 5.0 8.3 - - - +
1689A MET* 3.8 3.7 - - + +
1698A GLU* 3.5 13.1 + - + +
1699A ARG* 1.3 77.4 - - - +
1701A LEU* 1.3 66.5 + - - +
1702A LYS 3.5 1.1 + - - -
1703A TYR* 3.0 29.1 + - - +
1704A PHE* 3.3 11.7 + - - -
6B SEP 4.0 15.3 - - - +
7B PRO 3.6 18.8 - - - +
8B VAL* 4.7 10.8 - - + -
9B PHE* 4.3 0.7 - - - -
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Residues in contact with LEU1701 (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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1700A THR* 1.3 71.2 - - - +
1702A LYS* 1.3 66.7 + - + +
1704A PHE* 2.9 20.9 + - - +
1705A LEU* 2.9 27.3 + - + +
1774A ASN 5.7 2.0 - - - +
1775A MET* 3.7 34.8 - - + -
1776A PRO* 4.7 7.9 - - + -
1779A GLN* 3.6 39.5 - - + +
1783A MET* 3.8 16.2 - - + -
7B PRO* 4.3 3.0 + - + -
9B PHE* 3.9 17.7 - - + -
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Residues in contact with LYS1702 (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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1653A VAL* 3.7 17.2 - - + +
1654A VAL* 2.9 32.6 + - - +
1655A SER* 4.0 13.7 - - - +
1678A ASN* 3.2 28.3 + - - +
1679A LEU* 5.4 2.2 - - - +
1680A ILE* 4.0 19.5 - - + +
1687A VAL* 3.9 15.0 - - + +
1700A THR* 3.3 1.6 + - - -
1701A LEU* 1.3 78.4 - - + +
1703A TYR* 1.3 52.7 + - - +
1705A LEU* 3.7 6.9 - - + +
1706A GLY* 2.8 32.9 + - - -
6B SEP 2.9 30.8 + - - +
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Residues in contact with TYR1703 (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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1687A VAL* 4.9 1.6 - - - -
1689A MET* 3.9 15.1 - - + -
1697A CYS* 3.4 23.6 - - - -
1698A GLU 4.3 0.9 - - - -
1699A ARG* 3.6 31.0 - - + -
1700A THR* 3.0 27.6 + - - +
1702A LYS* 1.3 75.4 - - - +
1704A PHE* 1.3 68.5 + + - +
1706A GLY* 3.3 1.3 + - - -
1707A ILE* 3.0 53.8 + - + +
1713A VAL* 4.2 15.9 - - + +
1736A VAL* 4.3 9.1 - - + +
1738A GLY 4.2 1.6 - - - -
1739A ASP* 2.7 39.2 + - + +
1746A HIS* 3.6 16.5 - - - -
1749A PRO* 4.7 2.7 - - + +
1843A ALA* 4.2 8.5 + - + -
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Residues in contact with PHE1704 (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 37.2 - - + -
1700A THR 3.4 22.7 - - - -
1701A LEU* 2.9 9.0 + - - +
1703A TYR* 1.3 85.8 - + - +
1705A LEU* 1.3 52.2 + - - +
1707A ILE* 3.4 1.5 + - - -
1708A ALA* 2.7 36.4 + - - +
1775A MET* 4.3 2.0 - - + -
1783A MET* 3.4 31.2 - - + -
1839A LEU* 3.3 55.2 - - + -
1842A VAL* 3.5 20.9 - - + +
1843A ALA* 4.3 7.9 - - + -
9B PHE* 3.9 22.4 - + + -
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Residues in contact with LEU1705 (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* 3.9 32.1 - - + -
1701A LEU* 2.9 41.5 + - + +
1702A LYS* 4.1 0.4 - - + +
1704A PHE* 1.3 75.1 - - - +
1706A GLY* 1.3 61.2 + - - +
1708A ALA* 3.8 3.6 - - - +
1709A GLY* 3.0 24.8 + - - -
1711A LYS* 4.3 5.0 - - - -
1779A GLN* 3.7 40.8 - - - +
1782A TRP* 3.8 22.7 - - + -
1783A MET* 3.8 23.1 - - + -
1786A LEU* 4.1 10.6 - - + +
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Residues in contact with GLY1706 (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* 3.9 0.8 - - - +
1687A VAL* 3.8 21.8 - - - -
1702A LYS 2.8 16.7 + - - -
1703A TYR 3.8 1.3 - - - -
1705A LEU* 1.3 74.3 - - - +
1707A ILE* 1.3 62.3 + - - +
1709A GLY 3.3 1.7 + - - -
1710A GLY 3.1 3.1 + - - -
1711A LYS* 2.8 36.4 + - - +
1713A VAL* 3.8 10.1 - - - -
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Residues in contact with ILE1707 (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* 3.0 54.4 + - + +
1704A PHE* 3.7 4.0 - - - +
1706A GLY* 1.3 75.7 - - - +
1708A ALA* 1.3 62.2 + - - +
1710A GLY* 2.9 12.5 + - - -
1711A LYS 5.5 0.2 - - - -
1713A VAL* 3.8 15.2 - - + +
1748A GLY 4.2 9.2 - - - +
1749A PRO* 4.1 16.6 - - + -
1752A ALA* 3.2 36.4 - - + +
1842A VAL* 3.3 22.0 - - + +
1843A ALA* 3.8 18.4 - - - +
1845A TYR* 4.2 4.6 - - + -
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Residues in contact with ALA1708 (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 2.7 21.4 + - - +
1705A LEU* 3.9 4.5 - - - +
1707A ILE* 1.3 73.9 - - - +
1709A GLY* 1.3 58.7 + - - +
1710A GLY 3.2 1.1 + - - -
1756A GLN* 4.6 7.3 + - - +
1783A MET* 3.8 14.6 - - + +
1786A LEU* 3.5 40.4 - - + +
1787A CYS* 3.7 27.7 - - - -
1842A VAL* 4.3 2.4 - - + +
1845A TYR* 4.8 4.8 + - - -
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Residues in contact with GLY1709 (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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1705A LEU 3.0 17.2 + - - -
1706A GLY 3.8 0.4 - - - -
1707A ILE 3.2 0.4 - - - -
1708A ALA* 1.3 75.0 - - - +
1710A GLY* 1.3 64.6 + - - +
1711A LYS* 3.2 20.3 + - - +
1756A GLN* 4.5 10.3 + - - -
1786A LEU* 4.3 17.2 - - - +
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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