Contacts of the helix formed by residues 2081 - 2089 (chain A) in PDB entry 4D0O
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1980A TRP* 6.2 0.7 - - + -
1999A ARG* 4.3 1.1 - - - +
2003A ILE* 4.0 33.9 - - + -
2006A LEU* 5.1 5.8 - - + -
2060A ILE* 4.6 18.4 - - + +
2063A ARG* 4.0 18.8 - - + +
2078A ILE* 3.9 11.4 - - + -
2080A ARG* 1.3 73.2 - - - +
2082A GLY* 1.3 62.4 + - - +
2083A ASP* 3.4 6.1 - - - -
2084A VAL* 3.3 35.8 + - + -
2085A LEU* 3.4 23.9 + - + +
2164A ILE* 4.4 15.7 - - + -
2174A GLU* 2.7 19.4 + - - +
2178A LEU* 4.7 3.6 - - + -
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Residues in contact with GLY2082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2081A ILE* 1.3 76.0 - - - +
2083A ASP* 1.3 59.6 + - - +
2085A LEU* 3.2 4.5 + - - +
2086A VAL* 2.9 33.1 + - - +
2174A GLU* 3.0 21.1 + - - -
2177A ASP* 3.7 19.0 - - - +
2178A LEU* 4.2 16.2 - - - -
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Residues in contact with ASP2083 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2063A ARG* 2.7 47.0 + - - -
2080A ARG* 3.5 35.5 - - - +
2081A ILE 3.7 0.2 - - - -
2082A GLY* 1.3 75.3 + - - +
2084A VAL* 1.3 59.4 + - - +
2086A VAL* 4.0 4.6 - - - +
2087A ASN* 3.1 28.8 + - - +
2177A ASP* 3.5 12.2 + - - +
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Residues in contact with VAL2084 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2056A PHE* 4.3 14.6 - - + -
2059A ARG* 3.8 44.4 - - + +
2060A ILE* 4.4 3.1 - - + -
2063A ARG* 3.9 28.7 - - + +
2081A ILE* 3.5 31.2 - - + +
2082A GLY 3.2 0.8 - - - -
2083A ASP* 1.3 78.2 - - - +
2085A LEU* 1.3 62.1 + - + +
2087A ASN* 3.6 7.1 + - - +
2088A GLN* 3.2 22.2 + - - +
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Residues in contact with LEU2085 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006A LEU* 3.9 15.7 - - + -
2056A PHE* 3.7 20.4 - - + -
2060A ILE* 5.5 0.9 - - + -
2081A ILE* 3.4 24.2 - - + +
2082A GLY* 3.2 4.7 + - - +
2084A VAL* 1.3 77.2 - - + +
2086A VAL* 1.3 65.8 + - - +
2088A GLN* 3.2 5.0 + - - -
2089A PHE* 3.1 30.1 + - - +
2161A PHE* 3.7 45.8 - - + -
2164A ILE* 4.8 2.5 - - + -
2178A LEU* 3.8 29.4 - - + -
2181A SER* 3.8 15.8 - - - +
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Residues in contact with VAL2086 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2082A GLY 2.9 17.0 + - - +
2083A ASP* 4.0 6.3 - - - +
2085A LEU* 1.3 75.2 - - - +
2087A ASN* 1.3 58.8 + - - +
2089A PHE 3.2 2.6 + - - -
2090A SER* 2.5 40.4 + - - +
2177A ASP* 3.2 39.3 - - + +
2180A GLN* 4.0 21.3 - - + +
2181A SER* 3.8 11.7 - - - +
2184A LEU* 4.0 17.3 - - + -
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Residues in contact with ASN2087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2059A ARG* 4.0 34.4 - - - +
2083A ASP 3.1 18.6 + - - +
2084A VAL* 3.6 8.5 + - - +
2086A VAL* 1.3 79.3 - - - +
2088A GLN* 1.3 62.1 + - - +
2089A PHE 3.4 0.2 + - - -
2090A SER* 3.6 15.1 + - - +
2093A ASN* 2.9 21.3 + - - +
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Residues in contact with GLN2088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2052A ILE* 3.9 18.4 - - - +
2056A PHE* 3.4 51.9 + - + +
2059A ARG* 4.6 12.1 + - - -
2084A VAL 3.2 14.0 + - - +
2085A LEU 3.2 6.5 + - - +
2087A ASN* 1.3 81.1 - - - +
2089A PHE* 1.3 76.3 + - + +
2090A SER 3.5 0.4 - - - -
2093A ASN* 3.1 31.7 + - - +
2097A LEU* 3.8 17.4 - - - +
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Residues in contact with PHE2089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2056A PHE* 4.3 7.9 - + - -
2085A LEU 3.1 26.1 + - - +
2086A VAL 3.2 2.6 + - - +
2088A GLN* 1.3 93.6 - - + +
2090A SER* 1.3 58.1 + - - +
2094A ALA* 3.5 16.4 - - - +
2097A LEU* 3.5 26.9 - - + -
2154A ILE* 5.2 4.7 - - + -
2157A TYR* 3.8 35.2 - + - -
2161A PHE* 3.6 28.7 - + - -
2181A SER 4.9 1.3 - - - +
2184A LEU* 3.4 37.2 - - + +
2185A VAL* 3.7 31.6 - - + +
2188A VAL* 4.4 7.8 - - + +
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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