Contacts of the strand formed by residues 1877 - 1882 (chain B) in PDB entry 4ILG
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 GLY1877 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1856B ASN 3.0 15.3 - - - -
1857B VAL 3.7 11.4 + - - -
1859B ARG* 4.0 4.9 - - - -
1875B ILE 3.5 2.0 + - - -
1876B ASN* 1.3 75.0 - - - +
1878B CYS* 1.3 61.1 + - - +
1893B ILE* 3.5 8.5 - - - +
1894B ILE* 2.7 37.0 + - - +
1899B TRP* 6.1 0.2 - - - +
1978B VAL* 3.9 4.1 - - - +
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Residues in contact with CYS1878 (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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1853B ASP 4.4 1.4 - - - +
1856B ASN* 2.8 42.8 + - - +
1857B VAL* 3.4 11.1 - - - +
1877B GLY* 1.3 76.4 - - - +
1879B ILE* 1.3 60.4 + - - +
1880B PHE* 3.9 5.3 + - - +
1891B LEU* 4.0 23.6 - - + -
1892B LYS 3.2 13.7 - - - +
1893B ILE* 4.3 0.4 - - - -
1894B ILE* 4.1 2.0 - - - -
1968B ALA* 6.1 0.9 - - - -
1969B MET* 3.6 37.0 - - - -
1978B VAL* 4.0 9.6 - - + -
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Residues in contact with ILE1879 (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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1852B VAL* 4.2 4.7 - - + -
1853B ASP 3.9 9.2 - - - +
1857B VAL* 3.6 19.5 - - + -
1878B CYS* 1.3 71.4 - - - +
1880B PHE* 1.3 60.4 + - - +
1881B THR* 3.5 19.1 - - - +
1890B PHE 3.5 6.1 - - - +
1891B LEU* 3.5 6.3 - - - +
1892B LYS* 2.9 37.7 + - + +
1894B ILE* 4.0 15.3 - - + -
1913B THR* 3.9 32.1 - - + +
1916B GLU* 3.4 39.0 - - + -
1917B VAL* 4.1 8.7 - - + -
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Residues in contact with PHE1880 (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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1851B PHE 3.6 0.8 - - - +
1852B VAL* 3.5 3.1 - - - -
1853B ASP* 2.9 49.7 + - + +
1856B ASN* 6.4 0.2 - - - +
1878B CYS* 3.9 5.0 + - - +
1879B ILE* 1.3 70.3 - - - +
1881B THR* 1.3 59.0 + - - +
1882B LEU* 3.7 28.5 - - + -
1889B LEU* 3.7 20.9 - - + -
1891B LEU* 4.3 14.4 - - + -
1965B PHE* 3.7 47.1 - + + +
1968B ALA* 3.6 32.8 - - + -
1974B LEU* 4.9 0.7 - - + -
1991B ILE* 3.9 27.1 - - + -
2012B LEU* 5.2 2.5 - - + -
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Residues in contact with THR1881 (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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1850B LEU* 3.9 29.4 - - + -
1851B PHE 3.2 9.6 - - - +
1852B VAL* 3.9 15.2 - - + +
1879B ILE* 3.5 19.4 - - - +
1880B PHE* 1.3 73.0 + - - +
1882B LEU* 1.3 61.5 + - - +
1889B LEU* 3.4 4.3 - - - +
1890B PHE* 2.8 56.4 + - + -
1917B VAL* 4.2 7.6 - - + +
1920B LEU* 4.1 15.9 - - + +
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Residues in contact with LEU1882 (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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1850B LEU* 3.2 7.5 - - - -
1851B PHE* 2.8 43.9 + - + +
1880B PHE* 3.7 28.9 - - + -
1881B THR* 1.3 75.1 - - - +
1883B ASN* 1.3 73.4 + - - +
1884B PRO* 3.3 17.3 - - + +
1887B GLY* 3.6 17.9 - - - +
1888B HIS 3.6 11.9 - - - +
1889B LEU* 4.4 6.1 - - + -
1965B PHE* 4.1 18.4 - - + -
1991B ILE* 3.7 16.2 - - + -
1992B TYR* 5.1 0.9 - - - +
2005B PHE* 4.5 5.4 - - + -
2008B LEU* 4.2 17.7 - - + -
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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