Contacts of the strand formed by residues 1804 - 1811 (chain B) in PDB entry 4ASI
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 VAL1804 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1767B ILE* 3.3 38.6 - - + -
1790B LEU* 4.0 12.8 - - + -
1795B TYR* 4.2 15.2 + - + -
1798B VAL* 4.3 10.2 + - + -
1799B SER* 5.5 4.0 - - - +
1802B ASN* 5.2 2.1 - - - -
1803B SER* 1.3 87.5 + - - +
1805B HIS* 1.3 76.6 + - - +
1806B CYS* 3.8 23.1 - - - -
1819B ILE* 4.8 2.9 - - + -
1821B ASP 3.5 11.0 - - - +
1822B ILE* 4.6 7.2 - - + -
1823B ILE* 4.3 3.1 - - - +
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Residues in contact with HIS1805 (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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1802B ASN* 5.7 3.2 + - - -
1804B VAL* 1.3 84.0 - - - +
1806B CYS* 1.3 65.7 + - - +
1819B ILE* 3.8 0.9 - - - +
1820B THR* 3.0 40.1 + - - +
1821B ASP* 2.8 33.4 + - + +
1823B ILE* 4.0 22.2 - - + +
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Residues in contact with CYS1806 (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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1790B LEU* 4.1 11.4 - - - -
1795B TYR* 4.1 14.8 + - + -
1804B VAL* 3.8 20.5 - - - +
1805B HIS* 1.3 81.4 - - - +
1807B GLU* 1.3 61.5 + - - +
1817B TYR* 3.5 48.7 - - + -
1818B LYS 3.0 11.7 - - - +
1819B ILE* 4.0 7.9 - - - -
1820B THR* 4.3 4.9 - - - -
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Residues in contact with GLU1807 (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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1806B CYS* 1.3 77.4 - - - +
1808B HIS* 1.3 65.9 + - - +
1809B VAL* 4.0 14.7 - - + +
1817B TYR* 4.5 0.7 - - - -
1818B LYS* 2.9 58.9 + - + +
1820B THR* 4.1 16.3 - - + +
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Residues in contact with HIS1808 (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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1806B CYS 4.3 0.2 - - - -
1807B GLU* 1.3 78.6 - - - +
1809B VAL* 1.3 93.0 + - - +
1810B GLU* 4.5 6.0 + - + -
1815B SER* 2.9 29.9 + - - -
1816B ARG 3.5 5.4 - - - -
1817B TYR* 3.6 41.7 - + + +
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Residues in contact with VAL1809 (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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1787B TYR* 4.6 11.7 - - + +
1807B GLU* 4.0 24.2 - - + +
1808B HIS* 1.3 91.5 + - - +
1810B GLU* 1.3 64.7 + - - +
1811B ASP* 3.9 3.1 + - + -
1815B SER* 3.7 2.6 - - - -
1816B ARG* 2.9 47.6 + - + +
1818B LYS* 4.1 26.9 - - + +
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Residues in contact with GLU1810 (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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1808B HIS* 4.5 6.7 + - + -
1809B VAL* 1.3 73.2 - - - +
1811B ASP* 1.3 62.6 + - - +
1813B GLY 5.4 4.5 - - - +
1814B GLU 3.8 7.6 - - - +
1815B SER* 4.8 2.9 - - - +
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Residues in contact with ASP1811 (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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1774B ALA* 5.3 0.2 - - - +
1786B ARG* 4.8 8.1 - - - -
1787B TYR* 2.7 38.5 + - - +
1809B VAL* 3.9 5.6 - - + -
1810B GLU* 1.3 75.9 - - - +
1812B GLU* 1.3 103.7 + - - +
1813B GLY 2.8 4.7 + - - +
1814B GLU 2.9 20.5 + - - +
1816B ARG* 3.1 17.0 + - - -
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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