Contacts of the strand formed by residues 1688 - 1690 (chain E) 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 ILE1688 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1655E LEU* 3.2 31.6 - - + -
1679E VAL* 4.6 9.4 - - + -
1681E ALA 3.9 2.7 - - - -
1682E LEU* 4.1 20.0 - - + -
1686E ASN* 3.3 3.1 + - - +
1687E PHE* 1.3 75.1 - - - +
1689E GLN* 1.3 74.4 + - - +
1690E THR* 4.7 2.7 - - - +
1703E LEU* 4.4 23.6 - - + -
1711E ILE 3.7 17.7 - - - +
1712E GLY* 4.8 1.3 - - - -
1728E GLY 3.3 0.5 - - - +
1729E PHE* 3.2 8.0 - - - -
1730E ALA* 2.7 47.5 + - + +
1732E PRO* 4.2 17.7 - - + -
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Residues in contact with GLN1689 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1679E VAL 3.5 1.4 - - - -
1680E SER* 2.6 32.6 + - - -
1681E ALA* 2.9 40.5 + - + +
1683E GLY* 5.2 4.3 + - - -
1687E PHE 3.9 1.3 + - - +
1688E ILE* 1.3 76.4 - - - +
1690E THR* 1.3 55.9 + - - +
1727E ILE* 4.1 17.7 - - + +
1728E GLY 3.1 8.7 - - - +
1729E PHE* 4.1 26.4 - - + -
2460G PHE* 5.2 5.1 - - - -
2462G LEU* 4.6 21.0 - - - +
2465G THR* 3.8 27.1 + - - +
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Residues in contact with THR1690 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1661E THR* 3.0 27.8 - - + +
1678E ILE 2.6 24.4 + - - -
1679E VAL* 4.7 1.8 - - - -
1680E SER* 3.9 3.1 - - - -
1688E ILE* 4.8 6.3 - - + +
1689E GLN* 1.3 75.4 - - - +
1691E ASP* 1.3 60.3 + - - +
1692E ALA 3.4 18.2 + - - +
1703E LEU* 4.4 9.9 - - + -
1714E ASN* 4.3 17.0 - - - +
1727E ILE* 2.9 6.3 - - - +
1728E GLY* 2.8 48.1 + - - +
1730E ALA* 5.7 0.7 - - + -
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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
------------------------------------------------------------
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