Contacts of the strand formed by residues 2082 - 2088 (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 LEU2082 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2048B GLN 3.0 7.4 + - - +
2049B TYR* 3.4 28.7 - - + -
2050B LEU* 2.9 24.3 + - - +
2080B GLY 4.6 7.2 - - - +
2081B LYS* 1.3 75.1 - - - +
2083B VAL* 1.3 61.7 + - - +
2115B LYS* 3.4 38.6 - - + +
2117B VAL* 4.4 8.5 - - + -
2166B GLU 3.9 21.3 - - - +
2167B PHE* 3.7 24.4 - - + +
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Residues in contact with VAL2083 (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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2050B LEU* 3.4 19.3 - - + +
2052B ILE* 3.6 23.3 - - + -
2078B PHE* 4.9 0.9 - - + -
2081B LYS* 4.2 18.2 - - + +
2082B LEU* 1.3 80.7 - - - +
2084B ALA* 1.3 61.7 + - - +
2085B TYR* 3.5 33.8 - - + +
2109B ILE* 4.1 19.1 - - + -
2114B GLY* 4.2 9.4 - - - -
2115B LYS 2.8 11.9 + - - +
2116B THR* 3.2 6.4 - - - -
2117B VAL* 3.0 25.2 + - - +
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Residues in contact with ALA2084 (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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2050B LEU 2.8 11.5 + - - +
2051B ILE* 3.3 4.3 - - + -
2052B ILE* 2.7 32.8 + - - +
2083B VAL* 1.3 74.4 - - - +
2085B TYR* 1.3 62.2 + - - +
2117B VAL* 3.5 16.4 - - + +
2159B TRP* 3.7 13.2 - - + -
2163B LEU* 3.6 29.4 - - + -
2167B PHE* 4.1 6.5 - - + -
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Residues in contact with TYR2085 (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* 3.2 36.6 - - + +
2083B VAL* 3.5 27.2 - - + +
2084B ALA* 1.3 78.0 - - - +
2086B PHE* 1.3 60.1 + - - +
2102B ILE* 4.0 28.3 - - + -
2105B LEU* 4.1 5.2 - - + -
2106B GLU* 3.4 46.3 + - + +
2109B ILE* 3.2 35.8 - - + +
2110B SER* 4.6 1.0 + - - -
2116B THR* 3.7 14.4 + - + -
2117B VAL 4.6 1.0 + - - -
2139B VAL* 4.2 6.1 - - + -
2140B GLY* 3.1 13.8 - - - -
2141B LEU 2.9 23.7 + - - -
2159B TRP* 3.1 8.1 - - - -
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Residues in contact with PHE2086 (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* 3.8 20.4 - - + -
2008B TYR* 4.4 0.7 - - + -
2015B THR* 3.7 26.5 - - + -
2018B VAL* 3.6 29.6 - - + -
2019B ALA* 4.0 11.2 - - + -
2022B ILE* 3.6 18.8 - - + -
2051B ILE* 3.5 30.5 - - + -
2052B ILE 2.8 7.4 + - - +
2053B GLY* 3.1 23.9 - - - -
2054B CYS 3.1 22.3 + - - -
2085B TYR* 1.3 75.8 - - - +
2087B GLY* 1.3 63.0 + - - +
2088B THR* 5.2 0.9 - - + -
2102B ILE* 3.4 5.9 - - - +
2141B LEU* 3.3 17.3 - - + +
2143B LEU* 4.7 4.0 - - + -
2159B TRP* 3.8 13.7 - - + -
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Residues in contact with GLY2087 (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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2054B CYS 3.3 12.3 - - - -
2086B PHE* 1.3 78.0 - - - +
2088B THR* 1.3 62.7 + - - -
2099B GLN* 3.0 19.6 + - - +
2102B ILE* 3.7 10.4 - - - +
2141B LEU 2.9 8.3 + - - +
2143B LEU* 2.8 31.0 + - - +
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Residues in contact with THR2088 (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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2014B LYS 4.5 1.1 - - - +
2015B THR* 2.6 46.1 + - + +
2018B VAL* 4.2 19.5 - - + -
2054B CYS 3.5 2.6 + - - -
2055B PRO* 3.0 29.8 - - - +
2056B THR 3.3 6.9 + - - -
2086B PHE* 5.2 1.3 - - + -
2087B GLY* 1.3 79.1 - - - +
2089B GLY* 1.3 58.9 + - - +
2099B GLN* 3.6 5.9 - - - +
2143B LEU* 3.3 13.7 - - + +
2145B GLU* 4.9 7.4 - - + -
2170B FMN 3.2 19.4 + - - +
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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