Contacts of the helix formed by residues 1831 - 1835 (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 LEU1831 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1632B GLU 5.9 0.9 - - - +
1633B ASP* 3.4 27.6 - - + +
1825B ARG* 3.7 42.2 - - + +
1826B ASN 6.1 0.2 - - - -
1828B ASP* 3.2 34.6 + - - +
1830B SER* 1.3 90.3 - - - +
1832B ARG* 1.3 65.6 + - - +
1833B ASN 3.3 2.9 - - - -
1834B ARG* 3.4 30.0 + - - +
1835B THR* 4.1 7.4 + - - +
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Residues in contact with ARG1832 (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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1466B ASP* 5.0 17.0 - - + +
1467B GLY 5.7 0.2 - - - +
1468B THR* 4.3 11.7 - - - +
1633B ASP* 3.3 2.7 + - - +
1828B ASP 4.8 2.2 + - - -
1829B PRO* 3.2 44.1 + - - +
1830B SER* 3.3 8.5 + - - +
1831B LEU* 1.3 76.0 + - - +
1833B ASN* 1.3 63.4 + - - +
1834B ARG 3.2 0.7 - - - -
1835B THR* 3.6 21.8 + - - +
1836B GLY* 3.1 29.6 + - - -
1839B GLN* 5.4 5.6 - - - +
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Residues in contact with ASN1833 (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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1372B ARG* 3.2 34.2 + - + +
1375B ILE* 3.1 30.3 - - + +
1376B ALA* 3.3 15.9 - - - +
1467B GLY 2.5 26.5 + - - -
1468B THR* 3.3 24.7 + - - +
1469B LEU 4.6 3.5 + - - +
1631B ILE* 4.7 2.0 - - - +
1633B ASP* 3.2 26.9 + - - +
1635B PRO* 3.4 3.4 - - + +
1832B ARG* 1.3 76.0 - - - +
1834B ARG* 1.3 58.4 + - - +
1835B THR 3.6 0.4 - - - -
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Residues in contact with ARG1834 (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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1372B ARG* 3.8 4.8 + - - -
1633B ASP* 3.6 17.3 + - - +
1635B PRO* 3.7 25.8 - - + +
1638B VAL* 4.4 4.9 - - - +
1639B ASP* 2.9 41.8 + - - -
1822B ILE* 3.9 13.3 + - - +
1825B ARG* 3.7 39.0 - - - +
1826B ASN* 3.2 28.6 + - - +
1831B LEU* 3.6 24.1 - - - +
1832B ARG 3.2 1.4 - - - -
1833B ASN* 1.3 77.3 - - - +
1835B THR* 1.3 64.1 + - + +
1840B LEU 3.2 2.3 - - - +
1841B PRO* 3.1 5.7 - - - +
1842B TYR* 2.9 37.8 + - + +
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Residues in contact with THR1835 (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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1372B ARG* 3.5 12.4 + - - -
1826B ASN 3.6 23.8 - - - +
1828B ASP 5.8 1.3 - - - +
1831B LEU 4.1 5.2 + - - +
1832B ARG* 3.6 27.3 + - - +
1833B ASN 3.6 0.2 - - - -
1834B ARG* 1.3 86.1 - - + +
1836B GLY* 1.3 71.3 + - - +
1839B GLN* 3.2 16.7 + - - -
1840B LEU 2.7 28.0 + - - +
1841B PRO* 4.4 13.2 - - + -
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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