Contacts of the strand formed by residues 2314 - 2317 (chain F) in PDB entry 2ZLE
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 LEU2314 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2279F ILE* 5.7 5.4 - - + -
2281F LEU* 5.5 7.0 - - + -
2287F ILE* 4.8 13.2 - - + -
2291F ASN* 4.8 6.1 - - + +
2301F LEU* 4.8 13.2 - - + -
2305F LEU* 4.5 11.2 - - + -
2312F LEU* 3.4 36.1 - - + -
2313F ALA* 1.3 68.1 - - - +
2315F ASN* 1.3 53.3 + - - +
2316F ILE* 2.5 39.9 + - + +
2323F ILE 3.5 8.1 - - - +
2324F TYR* 3.6 8.2 - - - -
2325F LEU* 2.7 19.8 + - + +
2326F LEU 3.0 29.8 - - - +
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Residues in contact with ASN2315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2287F ILE* 4.1 0.6 - - - -
2288F ILE 3.9 1.0 + - - -
2289F GLY* 3.2 32.5 + - - -
2291F ASN* 3.1 15.1 + - - -
2292F GLN* 3.1 23.2 + - - +
2313F ALA* 2.7 17.6 - - - +
2314F LEU* 1.3 65.2 - - - +
2316F ILE* 1.3 54.2 + - - +
2317F GLN* 2.6 33.7 + - - +
2323F ILE 4.0 0.2 - - - -
2324F TYR* 3.7 30.4 - - + -
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Residues in contact with ILE2316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2280F GLY 3.4 15.0 - - - +
2281F LEU* 3.4 32.8 - - + -
2285F ASP* 3.7 18.8 - - + +
2286F VAL 3.2 13.9 - - - +
2287F ILE* 3.5 22.2 - - + +
2314F LEU* 2.5 40.4 + - + +
2315F ASN* 1.3 72.9 - - - +
2317F GLN* 1.3 63.4 + - - +
2318F ARG* 5.1 1.1 - - + +
2322F THR* 3.5 2.3 - - - -
2323F ILE* 2.9 41.7 + - + +
2325F LEU* 4.3 2.5 - - + -
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Residues in contact with GLN2317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2286F VAL* 3.0 24.1 + - + +
2287F ILE* 3.9 1.2 - - - +
2288F ILE* 3.0 43.2 - - + +
2289F GLY 3.8 1.2 - - - +
2315F ASN* 2.6 30.7 + - - +
2316F ILE* 1.3 73.2 - - - +
2318F ARG* 1.3 57.5 + - - +
2319F GLY 2.8 14.4 + - - +
2320F ASP 4.7 1.8 - - - +
2321F SER 2.9 15.0 - - - +
2322F THR* 3.2 33.2 - - + +
2324F TYR* 5.1 0.2 - - - -
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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