Contacts of the helix formed by residues 1831 - 1838 (chain A) in PDB entry 2KBI
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 ASN1831 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1815A SER* 2.9 48.7 + - - -
1818A ALA* 3.5 13.7 - - + +
1819A ASP* 3.6 8.9 - - - +
1827A ILE* 2.8 45.5 + - + +
1828A ALA 3.8 1.1 - - - +
1829A LYS* 4.0 7.0 - - - +
1830A PRO* 1.3 73.7 - - - +
1832A GLN* 1.3 65.9 + - - +
1833A ILE 3.3 3.1 - - - -
1834A SER* 3.1 12.0 + - - +
1835A LEU* 3.0 24.6 + - + +
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Residues in contact with GLN1832 (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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1811A TYR* 6.2 2.9 - - + -
1815A SER* 5.2 7.2 - - - -
1830A PRO* 5.3 10.7 - - + +
1831A ASN* 1.3 82.7 + - - +
1833A ILE* 1.3 69.1 + - + +
1835A LEU* 3.4 10.7 + - - +
1836A ILE* 2.9 46.9 + - + +
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Residues in contact with ILE1833 (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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1830A PRO* 5.6 4.9 - - + +
1831A ASN* 3.3 0.6 - - - -
1832A GLN* 1.3 82.8 - - + +
1834A SER* 1.3 64.7 + - - +
1836A ILE* 3.4 9.6 + - + +
1837A ASN* 2.8 43.8 + - - +
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Residues in contact with SER1834 (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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1827A ILE* 3.8 25.6 - - - +
1831A ASN* 3.1 13.7 + - - -
1833A ILE* 1.3 78.1 - - - +
1835A LEU* 1.3 60.6 + - - +
1837A ASN* 3.1 10.0 + - - +
1838A MET* 3.1 35.6 + - - +
1860A ARG* 5.3 3.6 - - - -
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Residues in contact with LEU1835 (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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1811A TYR* 3.3 25.7 + - + +
1814A LEU* 4.0 21.5 - - + +
1815A SER* 3.7 38.1 - - - +
1818A ALA* 4.5 4.3 - - + -
1827A ILE* 5.1 2.7 - - + -
1831A ASN* 3.0 24.4 + - + +
1832A GLN* 3.6 9.4 - - - +
1834A SER* 1.3 74.2 - - - +
1836A ILE* 1.3 62.0 + - - +
1838A MET* 3.3 28.9 + - + +
1840A LEU* 3.8 12.3 - - + +
1857A PHE* 3.8 31.6 - - + -
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Residues in contact with ILE1836 (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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1811A TYR* 3.7 19.7 - - + +
1832A GLN* 2.9 38.5 + - + +
1833A ILE* 3.7 10.3 - - + +
1834A SER 3.3 0.2 - - - -
1835A LEU* 1.3 75.2 - - - +
1837A ASN* 1.3 65.2 + - - +
1838A MET 3.6 6.8 - - - +
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Residues in contact with ASN1837 (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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1833A ILE* 2.8 43.8 + - - +
1834A SER* 3.1 7.4 + - - +
1836A ILE* 1.3 80.1 - - - +
1838A MET* 1.3 61.5 + - - +
1839A ASP 4.0 0.2 + - - -
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Residues in contact with MET1838 (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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1827A ILE* 4.2 15.0 - - + -
1834A SER* 3.1 32.7 + - - +
1835A LEU* 3.3 20.2 + - + +
1836A ILE 3.6 9.0 - - - +
1837A ASN* 1.3 79.0 - - - +
1839A ASP* 1.3 60.5 + - - +
1840A LEU* 3.2 33.9 + - + +
1856A ALA* 4.0 30.5 - - + +
1857A PHE* 4.0 24.7 - - + -
1860A ARG* 4.2 14.1 - - + -
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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