Contacts of the helix formed by residues 2081 - 2089 (chain B) in PDB entry 4D0N
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 ILE2081 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1999B ARG* 4.4 0.2 - - - +
2003B ILE* 4.5 24.2 - - + -
2006B LEU* 4.8 5.8 - - + -
2060B ILE* 4.9 17.7 - - + -
2063B ARG* 4.2 17.9 - - + +
2078B ILE* 4.3 13.7 - - + -
2079B LYS 4.3 0.2 - - - -
2080B ARG* 1.3 73.1 - - - +
2082B GLY* 1.3 70.3 + - - +
2083B ASP* 3.3 5.2 - - - -
2084B VAL* 3.0 35.2 + - + +
2085B LEU* 3.3 26.8 + - + +
2164B ILE* 4.4 15.3 - - + -
2174B GLU* 2.9 13.4 + - - +
2178B LEU* 4.0 15.7 - - + -
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Residues in contact with GLY2082 (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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2080B ARG 3.9 0.2 - - - -
2081B ILE* 1.3 77.7 - - - +
2083B ASP* 1.3 56.7 + - - +
2085B LEU* 3.1 6.3 + - - +
2086B VAL* 3.0 31.4 + - - +
2174B GLU* 2.9 20.6 + - - -
2177B ASP* 3.8 15.3 - - - +
2178B LEU* 3.8 21.3 - - - -
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Residues in contact with ASP2083 (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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2063B ARG* 2.7 46.0 + - - -
2080B ARG* 3.8 23.1 + - - +
2081B ILE 3.8 3.8 - - - -
2082B GLY* 1.3 69.6 - - - +
2084B VAL* 1.3 67.3 + - - +
2086B VAL* 3.5 5.5 + - - +
2087B ASN* 3.2 23.7 + - - +
2177B ASP* 3.5 20.3 + - - +
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Residues in contact with VAL2084 (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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2056B PHE* 4.3 17.0 - - + -
2059B ARG* 4.1 33.0 - - + +
2060B ILE* 4.5 6.3 - - + +
2063B ARG* 4.0 37.0 - - + +
2081B ILE* 3.0 28.0 + - + +
2083B ASP* 1.3 77.0 + - - +
2085B LEU* 1.3 62.4 + - + +
2087B ASN* 3.6 6.7 + - - +
2088B GLN* 3.2 21.7 + - - +
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Residues in contact with LEU2085 (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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2006B LEU* 3.9 18.4 - - + -
2056B PHE* 3.8 31.0 - - + -
2060B ILE* 5.6 0.2 - - + -
2081B ILE* 3.5 26.5 - - + +
2082B GLY 3.1 6.2 + - - +
2084B VAL* 1.3 77.2 - - + +
2086B VAL* 1.3 65.5 + - - +
2087B ASN 3.2 0.4 + - - -
2088B GLN* 3.3 1.5 + - - -
2089B PHE* 3.1 31.6 + - - +
2161B PHE* 3.8 33.7 - - + -
2164B ILE* 4.8 2.5 - - + -
2178B LEU* 4.0 25.8 - - + -
2181B SER* 3.6 17.5 - - - +
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Residues in contact with VAL2086 (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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2082B GLY 3.0 16.9 + - - +
2083B ASP* 3.9 6.5 - - - +
2085B LEU* 1.3 75.1 - - - +
2087B ASN* 1.3 55.1 + - - +
2089B PHE* 3.4 1.1 + - - -
2090B SER* 2.3 41.5 + - - +
2177B ASP* 3.2 39.5 - - + +
2180B GLN* 4.2 18.6 - - + +
2181B SER* 3.9 14.1 - - - +
2184B LEU* 4.3 13.6 - - + +
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Residues in contact with ASN2087 (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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2059B ARG* 5.4 2.0 - - - +
2083B ASP 3.2 17.5 + - - +
2084B VAL* 3.7 6.8 + - - +
2085B LEU 3.2 0.6 - - - -
2086B VAL* 1.3 79.9 - - - +
2088B GLN* 1.3 63.3 + - - +
2089B PHE 3.3 0.5 + - - -
2090B SER* 3.5 14.9 + - - +
2093B ASN* 3.0 18.7 + - - +
3341B SO4 2.9 41.6 + - - -
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Residues in contact with GLN2088 (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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2052B ILE* 3.8 22.2 + - - +
2055B GLN* 5.4 0.7 - - - +
2056B PHE* 3.6 47.6 + - + +
2059B ARG* 5.9 0.5 - - - +
2084B VAL 3.2 14.6 + - - +
2085B LEU 3.3 0.4 + - - +
2087B ASN* 1.3 81.4 + - - +
2089B PHE* 1.3 83.5 + - + +
2090B SER 3.5 0.2 - - - -
2093B ASN* 3.2 31.2 + - - +
2097B LEU* 3.6 23.5 - - - +
3341B SO4 4.5 8.0 + - - -
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Residues in contact with PHE2089 (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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2056B PHE* 4.1 12.1 - + - -
2085B LEU* 3.1 27.1 + - - +
2086B VAL* 3.6 2.9 - - - +
2087B ASN 3.2 0.4 - - - -
2088B GLN* 1.3 97.6 - - + +
2090B SER* 1.3 55.7 + - - +
2094B ALA* 3.6 16.5 - - - +
2097B LEU* 3.6 25.6 - - + -
2154B ILE* 5.6 1.6 - - + -
2157B TYR* 3.9 29.4 - + - -
2161B PHE* 3.5 30.5 - + - -
2181B SER 4.8 2.2 - - - +
2184B LEU* 3.4 36.7 - - + +
2185B VAL* 3.6 35.0 - - + +
2188B VAL* 4.4 7.7 - - + +
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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