Contacts of the helix formed by residues 2131 - 2136 (chain C) in PDB entry 1G24
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 ASP2131 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2130C ASP* 1.3 77.5 + - - +
2132C PRO* 1.3 79.3 - - + +
2133C ALA* 3.2 7.0 - - + +
2134C TYR* 3.0 21.6 + - - +
2186C ARG* 3.7 31.0 + - - +
2187C PRO* 4.1 6.4 - - - +
2188C ILE* 3.7 4.6 - - - +
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Residues in contact with PRO2132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2131C ASP* 1.3 89.0 - - + +
2133C ALA* 1.3 63.6 + - - +
2134C TYR 2.8 2.3 + - - -
2135C LEU* 2.8 21.7 + - - +
2136C GLY 3.9 1.6 + - - -
2139C PHE* 3.5 26.4 - - - +
2140C GLN* 3.7 17.9 - - + +
2143C LEU* 3.6 32.1 - - + -
2144C LEU* 4.2 9.0 - - + -
2187C PRO* 3.6 17.7 - - + -
2188C ILE* 4.3 0.4 - - + -
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Residues in contact with ALA2133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2131C ASP* 3.1 6.7 + - + +
2132C PRO* 1.3 77.9 - - - +
2134C TYR* 1.3 56.5 + - - +
2135C LEU 3.1 0.2 - - - -
2136C GLY* 2.8 32.2 + - - -
2137C THR* 4.2 3.2 + - + +
2140C GLN* 4.1 29.4 - - + +
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Residues in contact with TYR2134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2128C ARG* 6.0 0.7 - - - -
2130C ASP* 3.7 34.8 - - + +
2131C ASP 3.0 16.5 + - - +
2132C PRO 2.8 0.6 + - - -
2133C ALA* 1.3 78.0 - - - +
2135C LEU* 1.3 72.3 + - + +
2136C GLY 3.5 0.2 + - - -
2167C ARG* 2.9 65.2 + - - +
2169C GLU* 5.2 4.9 - - - -
2188C ILE* 4.1 11.0 - - + -
2190C THR* 4.6 13.6 + - - +
2192C PHE* 5.6 0.6 - + - -
2223C TYR* 2.7 33.9 + - - -
2225C ILE* 4.4 8.3 - - + +
2239C ILE* 3.9 22.9 - - + +
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Residues in contact with LEU2135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2132C PRO 2.8 7.3 + - - +
2134C TYR* 1.3 95.5 - - + +
2136C GLY* 1.3 57.7 + - - +
2139C PHE* 3.4 20.3 - - + -
2143C LEU* 3.4 41.1 - - + -
2158C ALA* 4.0 19.7 - - + -
2161C LYS* 3.0 20.4 + - - -
2162C PHE* 3.4 35.8 - - + -
2188C ILE* 3.6 16.4 - - + -
2228C MET* 4.8 3.6 - - + -
2237C ILE* 4.2 6.5 - - + -
2239C ILE* 4.6 10.3 - - + -
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Residues in contact with GLY2136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2132C PRO 4.0 1.2 - - - +
2133C ALA* 2.8 16.8 + - - +
2134C TYR 3.2 1.2 + - - -
2135C LEU* 1.3 80.7 - - - +
2137C THR* 1.3 58.1 + - - -
2138C GLU* 3.0 7.4 - - - -
2139C PHE* 2.8 23.0 + - - +
2140C GLN 3.4 6.6 + - - -
2161C LYS* 4.2 9.6 - - - -
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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