Contacts of the strand formed by residues 4482 - 4487 (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 LEU4482 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4360L VAL* 4.5 6.1 - - + -
4362L ILE* 3.9 19.3 - - + -
4370L VAL* 4.9 0.9 - - + -
4419L ILE* 3.9 12.9 - - + +
4420L LYS 2.9 17.4 + - - +
4421L MET* 3.6 26.2 - - + -
4422L ALA* 2.9 26.2 + - - +
4474L ALA* 4.2 17.3 - - + -
4475L LEU 3.6 15.7 - - - +
4476L VAL* 4.0 6.0 - - + +
4480L GLY 4.0 0.8 + - - -
4481L GLU* 1.3 69.2 - - - +
4483L ILE* 1.3 58.7 + - - +
4484L GLY 3.6 14.1 - - - +
4485L ILE* 3.6 27.6 - - + -
4505L SER* 3.2 13.7 + - - -
4508L VAL* 5.1 4.0 - - + -
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Residues in contact with ILE4483 (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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4422L ALA* 4.2 6.7 - - + -
4423L ASP 6.3 0.2 - - - -
4424L SER* 3.6 4.3 + - - +
4427L LEU* 4.1 33.1 - - + +
4432L TYR 4.8 2.2 - - - +
4433L THR* 3.5 25.1 - - - +
4451L VAL* 5.0 2.7 - - + -
4460L ILE* 3.7 7.0 - - - +
4475L LEU* 2.8 33.7 + - + +
4476L VAL 3.9 13.7 - - - +
4477L ASN* 3.7 27.8 - - + +
4481L GLU 3.6 10.8 - - - +
4482L LEU* 1.3 76.7 - - - +
4484L GLY* 1.3 55.3 + - - +
4504L PRO* 3.5 5.7 - - - +
4505L SER* 2.6 31.7 + - - -
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Residues in contact with GLY4484 (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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4460L ILE* 4.8 0.4 - - - -
4475L LEU* 2.8 37.2 + - - +
4482L LEU* 3.6 2.3 - - - +
4483L ILE* 1.3 81.6 - - - +
4485L ILE* 1.3 70.2 + - - +
4502L ALA* 4.3 5.4 - - - -
4503L ILE 2.8 16.2 - - - -
4505L SER* 3.7 6.0 - - - -
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Residues in contact with ILE4485 (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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4360L VAL* 4.9 5.4 - - + -
4370L VAL* 3.9 32.5 - - + +
4371L THR* 5.0 6.7 - - - -
4372L ASN* 3.9 14.6 - - - +
4405L ILE* 3.8 25.4 - - + -
4473L GLY* 3.1 13.5 - - - +
4474L ALA* 5.0 0.4 - - - -
4482L LEU* 3.6 35.2 - - + -
4484L GLY* 1.3 76.9 - - - +
4486L ASN* 1.3 74.7 + - - +
4487L THR* 3.6 0.8 + - - -
4502L ALA* 3.8 1.8 - - - -
4503L ILE* 2.9 30.7 + - + +
4508L VAL* 4.2 10.4 - - + +
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Residues in contact with ASN4486 (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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4372L ASN* 2.7 27.1 + - - -
4435L ALA* 3.9 11.8 - - - +
4462L THR* 4.3 13.1 - - - +
4464L ALA 4.9 4.4 + - - -
4471L SER* 4.8 1.6 - - - -
4472L GLY* 3.3 17.6 - - - +
4473L GLY 2.3 43.7 + - - +
4474L ALA 3.3 18.9 - - - +
4475L LEU* 3.8 14.9 - - - +
4484L GLY 4.0 0.2 - - - -
4485L ILE* 1.3 69.4 - - - +
4487L THR* 1.3 54.2 + - - +
4500L GLY* 4.9 2.6 - - - -
4501L PHE 3.7 10.6 + - - +
4502L ALA* 3.8 14.9 - - - +
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Residues in contact with THR4487 (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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4372L ASN* 3.7 6.7 - - - +
4403L SER 4.2 4.2 + - - -
4404L ASP* 2.6 30.3 + - - +
4459L PHE* 3.6 26.9 - - + -
4471L SER* 3.0 18.1 - - - -
4485L ILE* 4.5 3.1 - - - -
4486L ASN* 1.3 76.4 - - - +
4488L ALA* 1.3 77.4 + - - +
4489L ILE* 4.2 4.8 + - + +
4496L ASN* 6.1 1.2 - - - +
4501L PHE* 2.7 48.8 + - + +
4502L ALA* 4.3 3.4 - - - -
4503L ILE* 4.6 4.3 - - + +
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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