Contacts of the helix formed by residues 1971 - 1981 (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 ILE1971 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1967B ALA 4.6 0.4 - - - +
1968B ALA* 3.1 14.2 + - - +
1969B MET 4.5 0.9 - - - -
1970B SER* 1.3 79.7 - - - +
1972B ASP* 1.3 65.2 + - - +
1973B LYS* 4.2 3.4 - - + +
1974B LEU* 3.0 33.2 + - + +
1975B SER* 3.0 20.4 + - - -
1991B ILE* 4.3 13.0 - - + -
2012B LEU* 4.2 16.6 - - + -
2015B LEU* 4.6 3.6 - - + -
2039B LEU* 4.2 31.4 - - + +
2040B TRP* 3.7 37.2 - - + -
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Residues in contact with ASP1972 (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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1970B SER 3.6 1.7 + - - -
1971B ILE* 1.3 71.8 - - - +
1973B LYS* 1.3 61.4 + - + +
1975B SER* 3.3 6.6 + - - -
1976B ASP* 2.9 41.7 + - - +
2023B LYS* 2.9 27.9 + - - +
2163C TYR* 3.8 16.5 + - - -
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Residues in contact with LYS1973 (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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1971B ILE* 3.2 2.8 + - + +
1972B ASP* 1.3 83.3 - - + +
1974B LEU* 1.3 61.4 + - - +
1976B ASP* 3.7 8.0 + - - +
1977B VAL* 3.3 23.2 + - - +
1989B PHE* 4.5 8.9 - - + -
2034B ILE* 3.8 15.8 + - - +
2035B LYS 3.0 19.0 + - - -
2036B SER* 3.1 21.7 + - - +
2038B HIS 2.7 28.2 + - - +
2039B LEU* 3.8 23.8 - - + +
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Residues in contact with LEU1974 (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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1880B PHE* 4.9 0.2 - - + -
1889B LEU* 4.1 18.8 - - + -
1891B LEU* 4.5 5.6 - - + -
1968B ALA* 3.7 24.9 - - + +
1969B MET* 3.8 15.9 - - + -
1971B ILE* 3.0 33.9 + - + +
1973B LYS* 1.3 72.1 - - - +
1975B SER* 1.3 66.5 + - - +
1976B ASP 3.1 1.3 - - - -
1977B VAL* 3.3 5.6 - - - +
1978B VAL* 3.2 28.9 + - - +
1989B PHE* 3.4 47.1 - - + -
1991B ILE* 4.7 4.7 - - + -
2039B LEU* 4.0 10.5 - - + -
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Residues in contact with SER1975 (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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1859B ARG* 5.6 2.3 + - - -
1969B MET* 3.2 40.8 + - - +
1971B ILE 3.0 7.5 + - - -
1972B ASP* 3.7 10.5 - - - -
1974B LEU* 1.3 75.8 - - - +
1976B ASP* 1.3 60.3 + - - +
1978B VAL* 3.4 1.2 + - - +
1979B MET* 2.9 43.6 + - - +
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Residues in contact with ASP1976 (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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1972B ASP* 2.9 28.0 + - - +
1973B LYS* 3.9 8.2 - - - +
1974B LEU 3.1 0.2 - - - -
1975B SER* 1.3 82.0 - - - +
1977B VAL* 1.3 62.8 + - - +
1979B MET* 3.4 4.0 + - - +
1980B LYS* 3.0 42.8 + - - +
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Residues in contact with VAL1977 (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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1891B LEU* 4.3 7.6 - - + -
1893B ILE* 3.7 16.7 - - + +
1973B LYS 3.3 13.2 + - - +
1974B LEU* 3.3 13.0 - - - +
1976B ASP* 1.3 79.0 - - - +
1978B VAL* 1.3 64.6 + - - +
1980B LYS* 3.5 14.0 + - + +
1981B ALA 3.3 16.8 + - - -
1985B GLN* 3.8 8.3 + - - +
1987B VAL* 3.7 27.8 - - + -
1989B PHE* 4.0 20.0 - - + -
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Residues in contact with VAL1978 (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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1859B ARG* 4.0 11.2 - - - +
1876B ASN* 3.0 52.7 + - + +
1877B GLY* 3.9 10.8 - - - +
1878B CYS* 4.0 7.9 - - + -
1891B LEU* 4.0 14.6 - - + -
1893B ILE* 3.9 23.7 - - + +
1969B MET* 3.9 17.9 - - + -
1974B LEU 3.2 17.4 + - - +
1975B SER 3.7 4.0 - - - +
1977B VAL* 1.3 79.8 - - - +
1979B MET* 1.3 59.3 + - - +
1981B ALA* 3.5 6.1 - - - +
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Residues in contact with MET1979 (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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1859B ARG* 3.5 28.7 - - - +
1875B ILE* 4.3 26.2 - - + -
1876B ASN* 3.9 19.7 + - - +
1975B SER* 2.9 29.0 + - - +
1976B ASP* 4.2 3.8 - - - +
1978B VAL* 1.3 76.7 - - - +
1980B LYS* 1.3 60.5 + - - +
1981B ALA 3.3 1.3 + - - +
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Residues in contact with LYS1980 (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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1976B ASP* 3.0 37.9 + - - +
1977B VAL* 3.6 17.9 - - + +
1978B VAL 3.3 0.2 - - - -
1979B MET* 1.3 77.2 - - - +
1981B ALA* 1.3 66.0 + - - +
1982B THR* 3.5 11.6 + - - +
1985B GLN* 5.5 1.3 - - - +
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Residues in contact with ALA1981 (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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1876B ASN* 3.2 18.0 + - - +
1893B ILE* 3.6 19.5 - - + -
1895B HIS* 3.5 6.8 + - + -
1977B VAL 3.3 4.4 + - - +
1978B VAL 3.5 15.0 - - - +
1979B MET 3.3 2.6 - - - +
1980B LYS* 1.3 79.3 - - - +
1982B THR* 1.3 61.4 + - - +
1983B GLU 4.0 8.7 - - - +
1985B GLN* 3.5 27.6 - - - +
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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