Contacts of the strand formed by residues 2182 - 2186 (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 VAL2182 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2176C PHE* 3.6 21.8 - - + -
2180C GLN 4.2 2.9 - - - +
2181C ASN* 1.3 77.2 - - - +
2183C TYR* 1.3 67.0 + - - +
2184C VAL* 4.0 5.1 + - + -
2217C LYS* 2.7 11.7 + - + +
2218C VAL* 3.5 15.6 - - + +
2219C LYS* 2.8 31.9 + - - +
2338C GLN* 3.6 29.6 - - + +
2340C LEU* 3.8 36.1 - - + -
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Residues in contact with TYR2183 (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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2181C ASN* 3.4 40.3 + - + -
2182C VAL* 1.3 75.6 - - - +
2184C VAL* 1.3 55.8 + - - +
2219C LYS* 3.4 27.0 - - + +
2221C ILE* 4.8 7.2 - - + -
2256C LEU* 4.4 24.6 + - + -
2287C ASP* 4.3 10.9 + - - -
2289C ILE* 3.7 51.8 - - + +
2304C ALA* 5.8 0.2 - - + -
2306C ASN* 5.2 3.0 + - - -
2337C ALA* 4.7 9.2 - - + -
2338C GLN 3.0 20.2 + - - +
2339C LEU* 3.4 15.7 - - + +
2340C LEU 2.7 33.1 + - - +
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Residues in contact with VAL2184 (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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2182C VAL* 4.5 7.2 - - + +
2183C TYR* 1.3 77.8 - - - +
2185C LEU* 1.3 59.1 + - - +
2186C PRO* 3.5 3.8 - - - +
2218C VAL* 3.9 27.8 - - + -
2219C LYS 2.9 12.4 + - - +
2220C GLU* 4.0 13.0 - - + +
2221C ILE* 3.0 27.7 + - - +
2340C LEU* 3.3 19.7 - - + +
2342C SER* 3.6 30.5 - - - -
2345C ILE* 3.8 14.2 - - + +
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Residues in contact with LEU2185 (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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2183C TYR 4.0 0.4 + - - -
2184C VAL* 1.3 73.4 - - - +
2186C PRO* 1.3 82.5 - - + +
2187C LYS 3.4 0.3 + - - -
2189C LEU* 4.5 11.7 - - + -
2190C LEU* 4.2 13.0 - - + +
2207C ILE* 5.2 0.9 - - + -
2221C ILE* 3.8 29.2 - - + -
2224C VAL* 5.2 3.6 - - + -
2259C ILE* 4.2 23.8 - - + -
2291C ILE* 5.2 1.8 - - + -
2302C LEU* 4.0 21.5 - - + -
2339C LEU* 4.3 11.0 - - + -
2340C LEU 2.7 15.5 + - - +
2341C LEU* 3.5 23.5 - - + +
2342C SER 3.0 21.3 + - - -
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Residues in contact with PRO2186 (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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2184C VAL 3.5 5.4 - - - +
2185C LEU* 1.3 91.5 - - + +
2187C LYS* 1.3 66.0 + - - +
2188C ASN* 3.4 21.1 - - - +
2189C LEU* 3.2 24.6 + - + +
2190C LEU 3.4 8.5 + - - -
2221C ILE* 3.1 34.5 - - + +
2342C SER 3.4 8.7 - - - +
2345C ILE* 3.7 25.8 - - + +
2346C THR 4.3 0.9 - - - -
2347C GLY* 3.8 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