Contacts of the helix formed by residues 2099 - 2112 (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 GLN2099 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2054B CYS 4.7 0.3 - - - +
2056B THR* 3.2 7.7 + - - -
2087B GLY* 3.0 34.1 + - - -
2088B THR 3.3 5.0 + - - +
2089B GLY 3.3 10.9 - - - +
2098B PHE* 1.3 104.7 - - + +
2100B ASP* 1.3 64.4 + - - +
2101B ALA 3.1 3.9 + - - -
2102B ILE* 3.4 15.5 + - + +
2130B SER* 4.1 1.1 - - - +
2132B ALA* 3.4 25.4 - - + +
2138B PHE* 4.8 3.6 - - + -
2142B ALA* 3.8 14.5 - - + +
2143B LEU 2.9 33.5 + - - +
2170B FMN 3.0 13.1 + - - -
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Residues in contact with ASP2100 (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 THR* 3.1 11.8 + - + -
2060B GLY* 3.7 12.8 - - - +
2096B ASP 4.4 1.1 - - - +
2097B ASN* 2.9 52.7 + - - +
2099B GLN* 1.3 77.0 - - - +
2101B ALA* 1.3 64.0 + - - +
2103B GLY* 2.9 13.2 + - - -
2104B ILE* 3.0 16.5 + - + +
2130B SER* 3.5 2.6 - - - -
2131B LYS* 2.9 52.2 + - + +
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Residues in contact with ALA2101 (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* 3.9 18.6 - - - +
2055B PRO 3.5 22.4 - - - +
2056B THR* 2.9 21.1 + - - +
2061B GLU 4.2 5.2 - - - +
2062B LEU* 3.4 20.6 - - + +
2100B ASP* 1.3 78.0 - - - +
2102B ILE* 1.3 62.8 + - - +
2104B ILE* 3.2 4.4 + - - -
2105B LEU* 3.0 23.1 + - - +
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Residues in contact with ILE2102 (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 4.5 2.2 - - - +
2054B CYS* 4.0 13.9 + - + +
2085B TYR* 4.0 14.2 - - + -
2086B PHE 3.4 32.3 - - - +
2087B GLY* 3.7 21.3 - - - +
2099B GLN* 3.4 25.3 + - + +
2101B ALA* 1.3 76.6 - - - +
2103B GLY* 1.3 58.2 + - - +
2105B LEU* 4.0 6.4 - - + +
2106B GLU* 2.9 31.4 + - - +
2132B ALA* 3.9 7.2 - - + -
2138B PHE* 5.6 0.9 - - + -
2139B VAL* 3.8 20.2 - - + +
2140B GLY* 4.2 15.5 - - - +
2141B LEU 4.2 9.0 - - - +
2142B ALA* 5.4 0.4 - - - -
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Residues in contact with GLY2103 (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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2099B GLN 3.7 0.6 + - - -
2100B ASP 2.9 7.5 + - - -
2102B ILE* 1.3 82.0 - - - +
2104B ILE* 1.3 58.5 + - - +
2107B GLU* 3.0 19.1 + - - +
2131B LYS* 3.3 24.9 - - - -
2132B ALA* 3.7 8.5 - - - -
2134B ARG* 3.0 25.3 + - - -
2139B VAL* 4.3 1.8 - - - -
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Residues in contact with ILE2104 (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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2060B GLY 3.8 22.2 - - - +
2062B LEU* 3.9 25.6 - - + +
2070B TYR* 3.8 33.5 + - + +
2100B ASP 3.0 21.9 + - - +
2101B ALA* 3.6 7.0 - - - +
2103B GLY* 1.3 79.1 - - - +
2105B LEU* 1.3 61.8 + - - +
2107B GLU* 3.5 11.8 + - - +
2108B LYS* 3.4 13.7 + - - +
2131B LYS* 4.0 29.8 - - + +
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Residues in contact with LEU2105 (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* 3.7 23.3 - - + -
2054B CYS* 3.7 28.7 - - + -
2062B LEU* 3.7 16.8 - - + -
2066B TRP* 3.9 34.1 - - + -
2070B TYR* 4.1 21.3 - - + -
2073B LEU* 4.6 6.1 - - + -
2085B TYR* 4.1 11.0 - - + -
2101B ALA 3.0 18.4 + - - +
2102B ILE* 4.0 5.8 - - + +
2104B ILE* 1.3 76.6 - - - +
2106B GLU* 1.3 59.5 + - - +
2108B LYS* 3.3 3.8 + - - +
2109B ILE* 3.0 34.1 + - + +
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Residues in contact with GLU2106 (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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2085B TYR* 3.4 23.3 - - + +
2102B ILE 2.9 19.0 + - - +
2103B GLY 4.0 2.5 - - - +
2105B LEU* 1.3 74.0 - - - +
2107B GLU* 1.3 69.2 + - - +
2110B SER* 2.7 34.8 + - - -
2116B THR* 2.7 29.5 + - - +
2119B TYR* 4.1 5.8 + - - -
2134B ARG* 2.8 29.9 + - - +
2139B VAL* 3.0 30.6 - - + +
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Residues in contact with GLU2107 (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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2070B TYR* 5.0 6.1 + - - -
2103B GLY 3.0 17.8 + - - +
2104B ILE* 3.7 11.7 - - - +
2105B LEU 3.3 0.4 - - - -
2106B GLU* 1.3 82.9 + - - +
2108B LYS* 1.3 62.3 + - - +
2110B SER* 4.1 2.9 - - - -
2111B GLN* 3.2 27.3 + - - +
2134B ARG* 4.2 5.6 - - - +
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Residues in contact with LYS2108 (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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2070B TYR* 3.6 44.0 - - + +
2073B LEU* 3.6 31.9 - - + -
2074B ASP* 3.4 32.1 + - - +
2104B ILE 3.4 1.4 + - - -
2105B LEU 3.3 5.9 + - - +
2106B GLU 3.2 0.2 - - - -
2107B GLU* 1.3 79.0 - - - +
2109B ILE* 1.3 65.0 + - - +
2111B GLN* 3.1 29.8 + - - +
2112B ARG* 3.0 32.5 + - + +
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Residues in contact with ILE2109 (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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2044B LEU* 5.8 0.2 - - + -
2052B ILE* 4.2 21.1 - - + -
2066B TRP* 5.3 4.5 - - + -
2073B LEU* 4.2 18.2 - - + -
2078B PHE* 3.8 41.6 - - + +
2083B VAL* 4.1 15.3 - - + -
2085B TYR* 3.2 36.1 - - + +
2105B LEU* 3.0 21.9 + - + +
2108B LYS* 1.3 75.5 - - - +
2110B SER* 1.3 59.8 + - - +
2112B ARG* 3.1 15.0 + - - +
2113B GLY 3.3 0.7 + - - -
2114B GLY* 3.0 23.4 + - - -
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Residues in contact with SER2110 (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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2085B TYR* 4.8 0.9 + - - -
2106B GLU* 2.7 41.5 + - - +
2107B GLU* 4.1 3.1 - - - -
2109B ILE* 1.3 74.1 - - - +
2111B GLN* 1.3 66.5 + - - +
2113B GLY* 2.9 14.7 + - - -
2114B GLY 3.4 19.1 + - - +
2116B THR* 3.2 11.4 + - - -
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Residues in contact with GLN2111 (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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2074B ASP* 4.2 8.5 + - - -
2107B GLU* 3.2 18.6 + - + +
2108B LYS* 3.1 38.2 + - - +
2110B SER* 1.3 77.3 - - - +
2112B ARG* 1.3 79.7 + - - +
2113B GLY 3.4 2.8 + - - -
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Residues in contact with ARG2112 (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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2073B LEU 3.3 24.7 - - - +
2074B ASP* 3.2 43.4 + - - +
2076B VAL 3.9 7.4 + - - +
2077B ASP* 4.0 6.8 - - - +
2078B PHE* 3.1 42.3 + - + -
2079B ASN* 3.6 3.8 + - - +
2108B LYS* 3.0 24.1 + - + +
2109B ILE* 3.5 5.2 - - - +
2110B SER 3.0 0.6 - - - -
2111B GLN* 1.3 101.7 + - - +
2113B GLY* 1.3 54.3 + - - +
2114B GLY 3.7 0.4 - - - -
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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