Contacts of the strand formed by residues 4690 - 4693 (chain L) 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 LEU4690 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4655L ILE* 5.7 5.6 - - + -
4657L LEU* 5.5 7.4 - - + -
4663L ILE* 4.8 13.2 - - + -
4667L ASN* 4.8 6.1 - - + +
4677L LEU* 4.7 13.0 - - + -
4681L LEU* 4.5 11.9 - - + -
4688L LEU* 3.4 35.9 - - + -
4689L ALA* 1.3 67.5 - - - +
4691L ASN* 1.3 53.2 + - - +
4692L ILE* 2.5 40.4 + - + +
4699L ILE 3.5 8.1 - - - +
4700L TYR* 3.6 7.4 - - - -
4701L LEU* 2.7 20.7 + - + +
4702L LEU 3.0 29.6 - - - +
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Residues in contact with ASN4691 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4663L ILE* 4.1 1.1 - - - -
4664L ILE 3.9 0.9 + - - -
4665L GLY* 3.2 33.5 + - - -
4667L ASN* 3.1 15.5 + - - -
4668L GLN* 3.1 22.5 + - - +
4689L ALA* 2.7 17.2 - - - +
4690L LEU* 1.3 65.6 - - - +
4692L ILE* 1.3 52.6 - - - +
4693L GLN* 2.6 34.4 + - - +
4699L ILE 4.0 0.4 - - - -
4700L TYR* 3.7 31.0 - - + -
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Residues in contact with ILE4692 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4656L GLY 3.4 14.8 - - - +
4657L LEU* 3.4 32.5 - - + -
4661L ASP* 3.7 18.8 - - + +
4662L VAL 3.2 13.7 - - - +
4663L ILE* 3.5 23.3 - - + +
4690L LEU* 2.5 40.8 + - + +
4691L ASN* 1.3 73.4 - - - +
4693L GLN* 1.3 62.9 + - - +
4694L ARG* 5.1 1.3 - - + +
4697L SER 3.8 0.2 - - - +
4698L THR* 3.5 2.4 - - - -
4699L ILE* 2.9 42.3 + - + +
4701L LEU* 4.3 3.1 - - + -
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Residues in contact with GLN4693 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4662L VAL* 3.0 24.3 + - + +
4663L ILE* 3.9 1.6 - - - +
4664L ILE* 3.0 43.6 - - + +
4665L GLY 3.8 0.8 - - - +
4691L ASN* 2.6 29.9 + - - +
4692L ILE* 1.3 72.1 - - - +
4694L ARG* 1.3 57.5 + - - +
4695L GLY* 2.8 15.5 + - - +
4696L ASP 4.7 1.3 - - - +
4697L SER 2.9 14.8 - - - +
4698L THR* 3.2 33.4 - - + +
4700L 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