Contacts of the strand formed by residues 2124 - 2130 (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 ILE2124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2046C TYR* 3.7 5.0 - - - -
2047C GLN* 3.5 10.5 - - + +
2049C PHE* 4.5 14.6 - - + -
2058C TRP* 4.1 13.5 - - + -
2120C THR* 3.3 27.8 - - + +
2122C GLU* 3.4 22.2 - - + +
2123C ASN* 1.3 80.5 - - - +
2125C MET* 1.3 64.8 + - - +
2126C LEU* 3.9 26.2 - - + -
2177C LEU* 4.5 2.7 - - + -
2192C PHE 3.5 0.9 - - - +
2194C VAL* 2.8 46.6 + - + +
2200C ALA* 5.3 0.4 - - + -
2215C MET* 3.9 16.2 - - + -
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Residues in contact with MET2125 (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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2046C TYR* 3.6 28.5 - - + +
2047C GLN 2.9 21.5 + - - +
2048C GLU* 4.2 18.0 - - + +
2049C PHE* 5.4 2.1 - - - -
2124C ILE* 1.3 74.6 - - - +
2126C LEU* 1.3 67.3 + - - +
2127C PHE* 3.7 24.0 - - + -
2177C LEU* 4.0 7.8 - - - +
2191C LYS* 3.6 39.3 - - + +
2192C PHE 3.3 15.0 - - - +
2193C LYS* 3.6 29.2 - - + -
2240C THR* 5.1 3.1 - - + -
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Residues in contact with LEU2126 (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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2124C ILE* 3.9 15.9 - - + -
2125C MET* 1.3 83.8 - - - +
2127C PHE* 1.3 63.6 + - - +
2175C THR* 3.4 25.4 - - + +
2176C SER 3.7 6.5 - - - +
2177C LEU* 3.8 26.7 - - + -
2190C THR 3.6 0.3 - - - +
2191C LYS* 3.3 4.7 - - - -
2192C PHE* 2.8 42.9 + - + +
2194C VAL* 3.7 26.5 - - + -
2200C ALA* 4.9 1.8 - - + -
2215C MET* 3.9 16.2 - - + -
2217C LEU* 3.9 22.4 - - + -
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Residues in contact with PHE2127 (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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2048C GLU* 3.6 35.2 - - + -
2049C PHE 5.6 0.4 - - - -
2125C MET* 3.7 23.6 - - + -
2126C LEU* 1.3 75.8 - - - +
2128C ARG* 1.3 62.6 + - - +
2175C THR* 3.2 7.5 - - - -
2176C SER* 2.8 47.5 + - - +
2177C LEU 3.8 11.0 - - - -
2178C MET* 3.7 22.4 - - - +
2179C ASN* 3.9 32.5 - - + +
2189C ILE* 4.7 4.7 - - + -
2190C THR 3.3 4.7 - - - +
2191C LYS* 3.5 42.0 - - + -
2192C PHE* 5.4 0.4 - - - -
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Residues in contact with ARG2128 (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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2127C PHE* 1.3 78.7 - - - +
2129C GLY* 1.3 70.8 + - - +
2130C ASP* 2.7 39.2 + - - +
2134C TYR* 6.0 1.1 - - - -
2173C ILE* 4.2 9.3 - - - +
2174C SER* 2.5 52.1 + - - +
2175C THR* 4.3 2.5 - - + +
2179C ASN* 6.0 1.1 - - - -
2186C ARG* 4.4 7.6 - - - +
2189C ILE* 3.5 5.9 - - - +
2190C THR* 2.9 38.1 + - - -
2192C PHE* 3.9 28.7 - - + -
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Residues in contact with GLY2129 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2128C ARG* 1.3 82.1 + - - +
2130C ASP* 1.3 70.2 + - - -
2183C PHE* 6.4 1.1 - - - -
2186C ARG* 3.0 38.6 + - - +
2188C ILE 3.2 8.7 - - - -
2189C ILE* 4.6 3.8 - - - -
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Residues in contact with ASP2130 (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* 2.7 44.4 + - - +
2129C GLY* 1.3 75.8 - - - +
2131C ASP* 1.3 66.3 + - - +
2134C TYR* 3.7 42.1 - - + +
2186C ARG* 3.6 6.9 - - - +
2187C PRO* 3.4 7.8 - - - +
2188C ILE* 2.8 40.8 + - + +
2190C THR* 4.5 6.6 + - - -
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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