Contacts of the helix formed by residues 1747 - 1754 (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 GLN1747 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1735A GLU* 4.9 2.9 - - - +
1736A VAL 5.1 2.6 - - - +
1737A ARG* 2.8 42.2 + - - +
1745A ASN* 2.9 36.5 + - - +
1746A HIS* 1.3 75.7 + - - +
1748A GLY* 1.3 64.1 + - - +
1749A PRO* 3.3 6.3 - - - -
1750A LYS* 3.3 34.0 + - + +
1751A ARG* 3.1 26.4 + - - +
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Residues in contact with GLY1748 (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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1707A ILE* 4.3 4.9 - - - -
1746A HIS* 3.0 12.3 + - - -
1747A GLN* 1.3 74.8 - - - +
1749A PRO* 1.3 61.7 - - - +
1751A ARG* 2.9 14.4 + - - +
1752A ALA* 2.8 31.5 + - - +
1843A ALA 3.4 20.4 - - - -
1844A LEU 3.9 7.2 - - - -
1845A TYR* 3.8 1.3 - - - +
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Residues in contact with PRO1749 (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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1703A TYR* 4.7 1.3 - - + +
1707A ILE* 4.1 31.1 - - + -
1710A GLY* 5.5 0.2 - - - -
1711A LYS 4.7 1.2 - - - +
1713A VAL* 4.0 24.0 - - + +
1735A GLU* 3.5 11.4 - - + +
1736A VAL* 3.3 39.9 - - + +
1737A ARG 5.0 0.9 - - - -
1738A GLY 5.3 0.2 - - - +
1746A HIS* 4.2 10.1 - - + -
1747A GLN* 3.5 4.0 - - - -
1748A GLY* 1.3 88.9 - - - +
1750A LYS* 1.3 56.4 + - - +
1752A ALA* 3.5 2.8 + - + +
1753A ARG* 3.0 31.9 + - - +
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Residues in contact with LYS1750 (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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1732A HIS* 6.5 0.7 - - - -
1735A GLU* 3.2 22.3 + - - +
1736A VAL 5.2 0.2 + - - -
1747A GLN* 3.3 33.0 + - + +
1748A GLY 3.2 0.2 - - - -
1749A PRO* 1.3 78.0 - - - +
1751A ARG* 1.3 65.8 + - - +
1753A ARG* 3.2 19.5 + - - +
1754A GLU* 3.0 64.8 + - - +
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Residues in contact with ARG1751 (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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1746A HIS* 2.7 32.9 + - - +
1747A GLN* 3.1 10.7 + - - +
1748A GLY 2.9 16.9 + - - +
1750A LYS* 1.3 77.3 - - - +
1752A ALA* 1.3 58.5 + - - +
1754A GLU* 2.9 18.4 + - - -
1755A SER* 2.5 35.0 + - - +
1844A LEU* 2.9 30.3 + - - +
1845A TYR* 3.4 19.7 + - + +
1846A GLN* 4.7 6.5 - - - +
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Residues in contact with ALA1752 (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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1707A ILE* 3.2 41.5 - - + +
1710A GLY* 4.2 3.8 - - - -
1748A GLY 2.8 11.4 + - - +
1749A PRO 3.8 3.4 - - - +
1751A ARG* 1.3 74.5 - - - +
1753A ARG* 1.3 61.8 + - - +
1754A GLU 3.2 0.5 + - - -
1755A SER* 3.4 5.2 + - - -
1756A GLN* 2.8 24.2 + - - +
1845A TYR* 3.4 30.9 - - + -
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Residues in contact with ARG1753 (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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1710A GLY* 3.7 24.2 - - - +
1711A LYS 3.8 11.0 - - - +
1712A TRP* 3.5 40.2 - - - +
1732A HIS* 4.1 16.4 + - - -
1735A GLU* 2.6 41.6 + - - +
1749A PRO 3.0 16.5 + - - +
1750A LYS* 3.5 24.2 - - - +
1751A ARG 3.2 0.2 - - - -
1752A ALA* 1.3 76.3 - - - +
1754A GLU* 1.3 74.1 + - - +
1755A SER 3.4 1.0 + - - -
1756A GLN* 4.3 10.3 + - - +
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Residues in contact with GLU1754 (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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1750A LYS* 3.0 57.5 + - - +
1751A ARG* 2.9 7.8 + - - +
1753A ARG* 1.3 95.9 + - - +
1755A SER* 1.3 60.1 + - - +
1756A GLN 3.7 1.6 - - - -
1758A ARG* 5.3 2.1 - - - +
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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