Contacts of the helix formed by residues 1940 - 1948 (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 MET1940 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1852B VAL* 5.2 7.2 - - + +
1854B ASP* 3.5 39.0 - - + +
1910B LYS* 3.4 47.1 - - - +
1913B THR* 3.6 21.3 - - + -
1914B ALA* 3.8 14.8 - - + +
1917B VAL* 6.0 0.2 - - + -
1935B VAL* 3.8 18.4 - - + -
1937B ARG* 2.8 15.7 + - + +
1939B ALA* 1.3 79.5 - - + +
1941B LEU* 1.3 63.4 + - - +
1942B ASP 3.6 0.4 - - - -
1943B PRO* 3.6 4.2 - - + +
1944B LEU* 3.2 31.9 + - + +
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Residues in contact with LEU1941 (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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184A LYS* 3.6 4.0 - - - +
1935B VAL* 4.1 8.8 - - + +
1938B LYS* 2.8 19.3 + - + +
1939B ALA 3.3 0.6 - - - -
1940B MET* 1.3 78.1 - - - +
1942B ASP* 1.3 71.8 + - - +
1944B LEU* 3.9 1.0 - - - +
1945B GLU* 2.9 56.1 + - - +
1956B ILE* 3.6 41.0 - - + +
1957B ARG* 4.0 15.7 - - - -
1958B PRO* 4.0 12.6 - - + -
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Residues in contact with ASP1942 (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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184A LYS* 3.0 34.5 + - + -
198A PHE* 3.9 30.0 - - + -
1911B TRP* 4.7 0.4 - - - -
1938B LYS 4.7 0.2 + - - -
1939B ALA 4.6 0.6 + - - -
1941B LEU* 1.3 79.1 - - - +
1943B PRO* 1.3 74.6 - - + +
1944B LEU 3.2 0.2 + - - -
1945B GLU* 3.2 1.0 + - - +
1946B VAL* 2.8 29.8 + - - +
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Residues in contact with PRO1943 (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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1910B LYS* 3.9 20.4 - - + +
1911B TRP* 3.7 44.4 - - + +
1914B ALA* 3.4 20.1 - - + +
1939B ALA 3.4 24.5 - - - +
1940B MET* 3.6 7.9 - - + +
1942B ASP* 1.3 93.5 - - + +
1944B LEU* 1.3 56.1 + - - +
1946B VAL* 3.4 1.9 + - - +
1947B HIS* 3.1 26.5 + - - -
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Residues in contact with LEU1944 (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* 4.8 3.4 - - + -
1914B ALA* 3.7 18.2 - - - +
1917B VAL* 3.9 28.9 - - + -
1933B ILE* 3.6 32.8 - - + -
1935B VAL* 3.7 19.1 - - + -
1940B MET* 3.2 25.8 + - + +
1941B LEU 4.0 1.3 - - - +
1942B ASP 3.2 0.6 - - - -
1943B PRO* 1.3 76.3 - - - +
1945B GLU* 1.3 66.8 + - - +
1947B HIS* 3.2 1.8 + - + -
1948B MET* 3.0 46.8 + - + +
1956B ILE* 4.0 13.2 - - + -
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Residues in contact with GLU1945 (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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184A LYS* 2.7 52.9 + - + +
1941B LEU* 2.9 30.8 + - - +
1942B ASP 3.9 2.5 - - - +
1944B LEU* 1.3 77.2 - - - +
1946B VAL* 1.3 61.3 + - - +
1948B MET* 3.3 10.9 + - - +
1949B LEU* 3.4 18.9 + - + +
1956B ILE* 4.0 26.3 - - + +
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Residues in contact with VAL1946 (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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184A LYS* 3.9 18.4 - - + -
186A ARG* 5.1 1.4 + - - -
189A ILE* 4.0 20.8 - - + +
194A GLU* 3.7 43.3 - - + +
198A PHE* 3.8 30.5 - - + -
1911B TRP* 4.0 6.1 - - + -
1942B ASP 2.8 21.9 + - - +
1943B PRO 3.8 3.8 - - - +
1945B GLU* 1.3 77.1 - - - +
1947B HIS* 1.3 60.8 + - - +
1949B LEU* 3.4 24.4 + - - +
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Residues in contact with HIS1947 (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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186A ARG* 5.6 1.2 + - - -
194A GLU* 3.6 40.4 - - + +
195A MET* 5.1 0.8 + - - +
1911B TRP* 3.9 17.5 + + - +
1914B ALA* 3.5 36.3 - - + +
1915B GLU* 3.3 40.4 + - + +
1918B SER* 3.4 11.4 + - - -
1922B ARG* 3.1 23.6 + - - -
1943B PRO 3.1 17.5 + - - +
1944B LEU* 3.2 4.2 + - - +
1946B VAL* 1.3 75.5 - - - +
1948B MET* 1.3 59.5 + - + +
1949B LEU 3.3 1.8 + - - -
1950B ASP 4.7 0.2 + - - -
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Residues in contact with MET1948 (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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1918B SER* 3.8 31.2 - - - -
1921B VAL* 4.0 14.4 - - + -
1922B ARG* 4.6 1.6 - - - +
1933B ILE* 4.1 14.6 - - + -
1944B LEU* 3.0 37.2 + - + +
1945B GLU* 3.3 6.2 + - - +
1946B VAL 3.2 0.8 - - - -
1947B HIS* 1.3 75.8 - - - +
1949B LEU* 1.3 58.8 + - - +
1950B ASP* 3.0 3.8 - - - -
1951B PHE* 2.8 48.9 + - + +
1954B ILE* 3.7 35.2 - - + +
1956B ILE* 4.2 14.8 - - + -
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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