Contacts of the helix formed by residues 2063 - 2071 (chain B) in PDB entry 1OBO
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 GLN2063 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2009B GLY* 3.5 9.3 - - - -
2010B THR* 3.4 40.7 + - - +
2011B GLN* 4.7 4.2 + - - +
2054B CYS* 3.6 12.5 - - - -
2055B PRO* 3.8 25.8 + - + -
2057B LEU* 3.9 26.2 - - + -
2061B GLU 3.7 2.0 + - - -
2062B LEU* 1.3 69.9 - - - +
2064B SER* 1.3 76.4 + - - +
2065B ASP* 2.9 48.4 + - - +
2066B TRP* 2.9 19.9 + - - +
2067B GLU 2.9 9.7 + - - -
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Residues in contact with SER2064 (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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2011B GLN* 5.0 7.8 + - - -
2057B LEU* 5.1 1.4 - - - +
2062B LEU 3.2 3.5 + - - -
2063B GLN* 1.3 82.1 + - - +
2065B ASP* 1.3 67.3 + - - +
2067B GLU* 3.3 10.4 + - - +
2068B GLY* 3.1 18.2 + - - -
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Residues in contact with ASP2065 (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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2010B THR 4.6 2.9 + - - +
2035B ASP* 4.5 2.5 - - - +
2036B VAL* 3.8 13.9 - - + +
2037B SER* 3.5 42.7 - - - +
2063B GLN* 2.9 30.0 + - - +
2064B SER* 1.3 75.0 + - - +
2066B TRP* 1.3 65.9 + - - +
2068B GLY* 3.2 10.7 + - - +
2069B LEU* 3.3 17.7 + - - +
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Residues in contact with TRP2066 (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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2007B PHE* 3.6 24.5 + - + -
2008B TYR 3.9 0.8 - - - -
2009B GLY* 3.7 19.0 - - - +
2036B VAL* 3.6 24.7 - - + +
2044B LEU* 4.4 11.7 - - + -
2052B ILE* 3.6 32.8 - - + -
2053B GLY 2.9 27.9 + - - -
2054B CYS* 3.5 27.1 - - + +
2062B LEU* 4.3 6.7 - - + +
2063B GLN* 2.9 11.8 + - - +
2065B ASP* 1.3 75.8 - - - +
2067B GLU* 1.3 60.3 + - - +
2069B LEU* 3.2 23.0 + - + -
2070B TYR* 2.8 32.5 + - - +
2073B LEU* 4.8 15.0 - - + -
2105B LEU* 3.9 21.3 - - + -
2109B ILE* 5.3 3.4 - - + -
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Residues in contact with GLU2067 (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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2062B LEU* 3.1 35.4 + - + +
2063B GLN 2.9 10.8 + - - +
2064B SER* 3.3 15.5 - - - +
2066B TRP* 1.3 78.7 - - - +
2068B GLY* 1.3 62.9 + - - +
2070B TYR* 3.4 21.9 + - - +
2071B SER* 3.7 12.1 + - - -
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Residues in contact with GLY2068 (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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2064B SER 3.1 14.0 + - - -
2065B ASP* 3.2 4.9 + - - -
2066B TRP 3.1 0.6 - - - -
2067B GLU* 1.3 79.9 - - - +
2069B LEU* 1.3 61.2 + - - +
2071B SER* 3.9 13.0 + - - -
2072B GLU* 3.7 13.3 - - - +
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Residues in contact with LEU2069 (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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2007B PHE* 5.9 0.4 - - + -
2036B VAL* 3.7 36.3 - - + +
2039B ALA* 3.8 26.7 - - + +
2040B GLU* 4.4 6.5 - - - +
2041B VAL* 3.8 33.8 - - + +
2044B LEU* 5.5 4.3 - - + -
2065B ASP 3.3 10.6 + - - +
2066B TRP* 3.2 22.9 + - + +
2068B GLY* 1.3 74.0 - - - +
2070B TYR* 1.3 55.8 + - - +
2071B SER 3.1 2.9 - - - -
2072B GLU* 2.7 39.0 + - - +
2073B LEU* 3.3 13.0 + - + +
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Residues in contact with TYR2070 (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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2062B LEU* 3.7 23.3 - - + -
2066B TRP* 2.8 17.0 + - - +
2067B GLU* 3.4 16.6 - - - +
2069B LEU* 1.3 76.0 - - - +
2071B SER* 1.3 68.5 + - - +
2073B LEU* 3.2 36.2 + - + +
2074B ASP* 4.9 2.6 + - - +
2104B ILE* 3.8 29.1 + - + +
2105B LEU* 4.1 8.1 - - + -
2107B GLU* 5.0 5.7 + - - -
2108B LYS* 3.6 45.3 - - + +
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Residues in contact with SER2071 (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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2067B GLU* 3.7 13.7 + - - -
2068B GLY* 4.1 9.2 + - - -
2069B LEU 3.0 1.0 + - - -
2070B TYR* 1.3 84.1 - - - +
2072B GLU* 1.3 61.2 + - - +
2073B LEU 3.3 1.1 + - - -
2074B ASP* 4.0 14.4 + - - +
2075B ASP* 4.8 1.9 - - - +
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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