Contacts of the helix formed by residues 1683 - 1687 (chain B) in PDB entry 2IUK
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 HIS1683 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238B TYR 5.4 1.1 - - - -
1239B PRO* 4.1 4.8 - - + +
1532B VAL* 3.1 37.5 + - - +
1535B PRO* 3.5 21.2 - - + +
1536B PHE* 3.5 25.9 - + - -
1597B TYR* 2.9 29.4 - + - +
1600B TRP* 3.5 27.3 - + - -
1602B PHE* 4.7 12.7 - + + -
1678B ALA 2.9 12.6 + - - +
1679B VAL* 3.1 19.4 + - - +
1681B LYS 3.3 0.4 - - - -
1682B GLY* 1.3 72.5 - - - +
1684B GLY* 1.3 63.3 + - - +
1685B ASP 3.4 2.0 - - - -
1686B LEU* 3.0 17.8 + - + +
1687B LYS 3.5 3.3 + - - -
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Residues in contact with GLY1684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238B TYR 5.4 0.2 + - - -
1240B LEU* 4.9 6.5 - - - +
1679B VAL 3.5 1.3 + - - -
1680B GLU 3.1 23.3 - - - -
1681B LYS 3.1 9.7 + - - -
1682B GLY 3.5 0.4 + - - -
1683B HIS* 1.3 74.5 - - - +
1685B ASP* 1.3 62.7 + - - +
1686B LEU 3.0 5.7 + - - -
1687B LYS* 3.1 25.0 + - - +
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Residues in contact with ASP1685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231B GLY* 3.7 0.9 - - - -
1232B GLY* 3.3 35.0 + - - +
1233B CYS 3.4 15.7 - - - +
1234B SER* 5.3 5.9 - - - -
1237B PRO* 3.3 23.5 - - + +
1238B TYR 3.2 33.0 + - - +
1240B LEU* 4.5 4.8 - - - +
1597B TYR* 4.7 2.2 + - + -
1683B HIS 3.1 1.4 + - - -
1684B GLY* 1.3 75.6 - - - +
1686B LEU* 1.3 67.8 + - - +
1687B LYS 3.8 0.2 - - - -
1689B LYS* 5.6 0.5 - - - -
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Residues in contact with LEU1686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237B PRO* 5.3 2.9 - - + -
1597B TYR* 3.6 52.0 - - + +
1598B LYS* 4.3 10.1 - - - +
1600B TRP* 3.6 31.2 - - + +
1602B PHE* 4.5 15.3 - - + -
1683B HIS* 3.0 10.0 + - + +
1685B ASP* 1.3 89.4 - - - +
1687B LYS* 1.3 53.7 + - - +
1688B GLU* 2.8 12.7 + - - -
1689B LYS* 3.0 49.6 + - + +
1691B TRP* 4.2 4.0 - - + -
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Residues in contact with LYS1687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1679B VAL* 3.6 29.2 - - - +
1680B GLU* 3.9 43.7 + - + +
1683B HIS 3.5 1.2 + - - -
1684B GLY* 3.1 20.0 + - - +
1685B ASP 3.8 0.2 - - - -
1686B LEU* 1.3 74.1 - - - +
1688B GLU* 1.3 75.8 + - + +
1689B LYS 3.5 0.4 - - - -
1692B TRP* 3.4 30.3 + - - -
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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