Contacts of the strand formed by residues 2049 - 2057 (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 TYR2049 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2003B LYS* 3.4 30.7 + - + +
2004B ILE* 3.5 17.0 - - + -
2005B GLY 3.1 22.5 + - - -
2047B TYR* 3.5 7.1 - - - +
2048B GLN* 1.3 108.1 + - + +
2050B LEU* 1.3 61.7 + - - +
2082B LEU* 3.4 19.5 - - + -
2167B PHE* 3.4 55.1 + + + -
2168B GLY 5.4 1.4 + - - -
2169B LEU* 4.8 11.8 - - + +
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Residues in contact with LEU2050 (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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2005B GLY 3.4 13.5 - - - +
2007B PHE* 3.6 24.9 - - + -
2044B LEU* 3.7 26.2 - - + +
2047B TYR* 3.8 14.1 - - + +
2049B TYR* 1.3 75.4 - - - +
2051B ILE* 1.3 67.0 + - - +
2052B ILE* 4.5 6.5 - - + -
2078B PHE* 3.9 22.4 - - + -
2081B LYS* 3.8 27.4 - - + -
2082B LEU 2.9 8.7 + - - +
2083B VAL* 3.4 21.0 - - + -
2084B ALA 2.8 26.3 + - - -
2167B PHE* 3.7 3.7 - - - -
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Residues in contact with ILE2051 (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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2004B ILE* 3.7 21.5 - - + -
2005B GLY 3.0 6.6 + - - +
2006B LEU* 3.2 16.9 - - + +
2007B PHE 2.8 27.2 + - - +
2022B ILE* 4.2 9.2 - - + -
2026B PHE* 3.7 30.7 - - + -
2031B VAL* 5.2 0.4 - - + -
2050B LEU* 1.3 77.3 - - - +
2052B ILE* 1.3 65.5 + - - +
2084B ALA* 3.3 7.9 - - + +
2086B PHE* 3.5 31.2 - - + -
2159B TRP* 4.1 14.4 - - + -
2163B LEU* 4.0 11.9 - - + -
2167B PHE* 4.2 9.6 - - + -
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Residues in contact with ILE2052 (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* 3.5 9.0 - - + -
2044B LEU* 4.4 10.8 - - + -
2050B LEU* 4.5 11.7 - - + -
2051B ILE* 1.3 79.3 - - - +
2053B GLY* 1.3 60.2 + - - +
2054B CYS* 4.3 0.4 + - + -
2066B TRP* 3.6 36.1 - - + -
2078B PHE* 6.1 0.2 - - + -
2083B VAL* 3.6 24.7 - - + -
2084B ALA 2.7 7.5 + - - -
2085B TYR* 3.2 26.1 - - + +
2086B PHE* 2.8 28.2 + - - +
2102B ILE* 4.5 1.5 - - + +
2105B LEU* 3.7 24.7 - - + -
2109B ILE* 4.2 11.0 - - + -
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Residues in contact with GLY2053 (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 2.9 12.7 + - - -
2008B TYR* 3.2 2.2 - - - -
2009B GLY 3.1 12.3 + - - -
2015B THR* 4.0 6.5 - - - -
2052B ILE* 1.3 73.0 - - - +
2054B CYS* 1.3 61.4 + - - -
2066B TRP* 2.9 20.4 + - - -
2086B PHE* 3.1 34.2 - - - -
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Residues in contact with CYS2054 (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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2015B THR* 4.0 3.3 - - - +
2052B ILE 4.3 0.2 + - - -
2053B GLY* 1.3 75.7 - - - +
2055B PRO* 1.3 87.2 - - - +
2056B THR* 4.0 0.3 + - - -
2062B LEU* 4.4 1.6 - - - -
2063B GLN* 3.6 18.8 - - - -
2066B TRP* 3.5 28.5 - - + -
2086B PHE 3.1 8.5 + - - -
2087B GLY* 3.3 20.6 - - - -
2088B THR* 4.1 3.0 - - - +
2099B GLN* 4.7 0.7 - - - +
2101B ALA* 3.9 15.5 - - + +
2102B ILE* 4.0 8.3 - - + +
2105B LEU* 3.7 17.5 - - + -
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Residues in contact with PRO2055 (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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2009B GLY 3.2 20.9 - - - +
2010B THR* 4.5 0.2 - - - -
2015B THR* 3.3 9.4 - - - +
2054B CYS* 1.3 104.3 - - - +
2056B THR* 1.3 61.0 + - - +
2057B LEU* 3.7 14.5 + - + -
2063B GLN* 3.8 22.6 + - + +
2088B THR* 3.0 26.0 - - - +
2101B ALA* 3.5 3.5 - - - +
2170B FMN 3.4 27.4 - - - +
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Residues in contact with THR2056 (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 4.9 0.2 + - - -
2055B PRO* 1.3 72.1 - - - +
2057B LEU* 1.3 57.6 + - - +
2060B GLY* 3.5 28.3 - - - -
2061B GLU 3.5 3.6 - - - +
2088B THR 3.3 7.7 + - - -
2097B ASN 3.7 6.3 - - - +
2099B GLN* 3.2 8.5 + - - -
2100B ASP* 3.1 15.3 + - + -
2101B ALA* 2.9 25.1 + - - +
2170B FMN 2.6 70.5 + - + +
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Residues in contact with LEU2057 (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* 3.7 41.7 - - + +
2055B PRO* 3.9 19.7 - - + +
2056B THR* 1.3 84.8 - - - +
2058B ASN* 1.3 73.7 + - + +
2059B ILE 3.0 3.7 + - - -
2061B GLU* 2.8 34.8 + - + +
2062B LEU 5.4 0.2 - - - +
2063B GLN* 3.9 28.0 - - + -
2064B SER 5.1 1.1 - - - +
2170B FMN 3.8 37.0 - - + +
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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