Contacts of the helix formed by residues 2187 - 2196 (chain C) in PDB entry 4ILG
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 LYS2187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A LEU* 6.3 0.2 - - + -
2166C LEU* 5.1 8.7 - - + -
2169C ILE* 4.1 20.2 - - + -
2185C LEU 3.4 1.9 + - - -
2186C PRO* 1.3 72.1 - - - +
2188C ASN* 1.3 63.9 + - - +
2190C LEU* 3.1 6.7 + - + +
2191C LYS* 2.9 31.7 + - + +
2341C LEU* 4.0 30.1 - - + -
2342C SER 2.8 19.4 + - - +
2343C ASP* 3.9 31.2 + - + +
2345C ILE 4.6 1.0 + - - -
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Residues in contact with ASN2188 (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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2186C PRO* 3.2 8.4 - - - +
2187C LYS* 1.3 77.6 - - - +
2189C LEU* 1.3 70.6 + - - +
2191C LYS* 3.5 7.9 + - - +
2192C LYS* 3.2 24.4 + - - +
2343C ASP* 5.9 0.4 - - - +
2345C ILE 4.3 1.4 + - - +
2346C THR* 3.6 18.1 - - - +
2347C GLY 2.9 42.3 + - - -
2349C PHE* 4.9 3.1 - - - -
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Residues in contact with LEU2189 (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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2185C LEU* 4.5 6.3 - - + -
2186C PRO* 3.2 32.3 + - + +
2187C LYS 3.1 0.8 - - - -
2188C ASN* 1.3 84.9 + - - +
2190C LEU* 1.3 67.0 + - - +
2193C PHE* 3.0 25.9 + - - +
2221C ILE* 4.1 10.8 - - + -
2222C LYS 4.2 7.2 - - - +
2224C VAL* 3.7 26.6 - - + +
2347C GLY* 3.7 22.4 - - - +
2348C ASN 3.6 15.5 - - - +
2349C PHE* 3.5 33.3 - - + -
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Residues in contact with LEU2190 (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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2166C LEU* 4.1 12.8 - - + -
2169C ILE* 4.1 15.3 - - + -
2185C LEU* 4.2 17.6 - - + +
2186C PRO 3.4 5.3 + - - +
2187C LYS* 3.1 9.7 + - + +
2189C LEU* 1.3 78.5 - - - +
2191C LYS* 1.3 63.6 + - - +
2193C PHE* 3.3 4.3 + - + -
2194C ILE* 2.9 40.0 + - + +
2259C ILE* 6.1 1.3 - - - -
2293C ILE* 3.7 32.1 - - + -
2300C VAL* 4.6 1.1 - - + -
2302C LEU* 4.0 26.9 - - + -
2341C LEU* 3.9 33.2 - - + -
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Residues in contact with LYS2191 (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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2163C TYR* 5.9 2.0 - - - -
2166C LEU* 3.7 25.8 - - + +
2187C LYS* 2.9 27.8 + - + +
2188C ASN* 3.8 8.7 - - - +
2190C LEU* 1.3 78.5 - - - +
2192C LYS* 1.3 62.4 + - - +
2194C ILE* 3.4 3.3 + - - +
2195C GLU* 3.0 57.0 + - - +
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Residues in contact with LYS2192 (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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2188C ASN 3.2 11.2 + - - +
2191C LYS* 1.3 76.4 - - - +
2193C PHE* 1.3 66.6 + - - +
2195C GLU* 3.1 22.0 + - - +
2196C ILE* 3.0 34.1 + - - +
2349C PHE* 3.7 33.9 - - + -
2378C ILE* 3.7 23.8 - - + +
2379C PRO* 3.7 29.9 + - + -
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Residues in contact with PHE2193 (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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2189C LEU 3.0 20.6 + - - +
2190C LEU* 3.8 4.5 - - - +
2192C LYS* 1.3 78.4 - - - +
2194C ILE* 1.3 62.3 + - + +
2196C ILE* 3.3 32.0 - - + +
2197C SER* 3.3 12.0 + - - -
2203C VAL* 3.6 33.9 - - + -
2204C ALA* 3.9 12.8 - - - -
2205C ALA* 3.8 25.4 - - + -
2224C VAL* 4.7 10.3 - - + -
2226C LEU* 4.2 4.0 - - + -
2259C ILE* 3.9 16.8 - - + -
2260C HIS* 4.3 6.3 - - - -
2261C THR* 4.0 23.3 - - + -
2293C ILE* 3.9 26.0 - - + -
2349C PHE* 4.3 5.8 - + + -
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Residues in contact with ILE2194 (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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2162C LEU* 3.6 40.9 - - + +
2163C TYR* 4.6 0.4 - - - +
2165C ARG* 5.2 0.7 - - + -
2166C LEU* 3.9 26.7 - - + -
2190C LEU* 2.9 29.2 + - + +
2191C LYS 3.7 3.8 - - - +
2193C PHE* 1.3 76.9 - - - +
2195C GLU* 1.3 62.5 + - - +
2197C SER* 2.6 25.3 + - - +
2261C THR* 4.3 17.0 - - + -
2293C ILE* 3.9 29.2 - - + -
2295C SER* 4.7 6.5 - - - +
2300C VAL* 4.0 13.5 - - + -
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Residues in contact with GLU2195 (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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2159C ASN* 4.6 6.9 - - - +
2162C LEU* 4.6 9.6 - - - +
2163C TYR* 4.1 28.6 - - + +
2191C LYS* 3.0 57.1 + - + +
2192C LYS* 3.1 30.7 + - + +
2194C ILE* 1.3 76.8 - - - +
2196C ILE* 1.3 58.9 + - + +
2197C SER 3.7 3.3 + - - +
2381C GLU* 4.4 8.3 - - - +
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Residues in contact with ILE2196 (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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2192C LYS* 3.0 33.1 + - - +
2193C PHE* 3.3 32.5 - - + +
2195C GLU* 1.3 75.8 - - + +
2197C SER* 1.3 63.8 + - - +
2203C VAL* 5.1 1.8 - - + -
2226C LEU* 3.6 32.5 - - + -
2349C PHE* 5.0 2.5 - - + -
2357C TRP* 3.7 10.3 - - + -
2379C PRO* 3.7 33.4 - - + +
2380C LEU 3.7 14.1 - - - +
2381C GLU* 3.9 8.7 - - + +
2382C PHE* 3.1 23.6 + - - +
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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