Contacts of the helix formed by residues 388 - 391 (chain E) in PDB entry 5UQ9
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 ASN 388 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E ALA* 4.0 8.0 + - - +
340E MET* 3.2 40.2 - - - +
380E PHE* 5.9 0.9 - - - -
386E LEU* 3.2 21.8 - - - +
387E GLN* 1.3 81.9 + - - +
389E LEU* 1.3 66.5 + - - +
390E LEU* 2.7 39.8 + - - +
391E LEU* 3.1 18.9 + - + +
429E PHE* 5.1 1.8 - - - -
433E TYR* 3.3 36.8 + - + +
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Residues in contact with LEU 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E ILE* 5.1 4.5 - - + +
335E TYR* 4.2 22.7 - - + +
336E ALA* 4.1 17.0 + - + +
339E PHE* 4.5 5.6 - - + +
372E PHE* 5.9 0.7 - - + -
376E ILE* 3.8 36.1 - - + -
379E ALA* 4.0 4.5 - - + -
380E PHE* 3.6 30.8 - - + -
386E LEU* 3.9 15.0 - - + -
388E ASN* 1.3 76.3 + - - +
390E LEU* 1.3 62.4 + - - +
391E LEU 3.3 0.9 + - - -
392E ASP* 3.3 12.0 + - - +
395E PHE* 3.5 46.7 - - + +
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Residues in contact with LEU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E ILE* 4.0 22.0 - - + -
333E ILE* 3.7 33.9 - - + -
336E ALA* 4.2 6.3 - - + -
388E ASN* 2.7 22.8 + - - +
389E LEU* 1.3 72.2 - - - +
391E LEU* 1.3 58.5 + - - +
392E ASP 3.3 2.7 + - - -
395E PHE* 5.0 2.7 - - + +
396E LYS* 3.9 12.9 - - - +
399E VAL* 4.4 12.6 - - + -
429E PHE* 4.3 13.7 - - + -
430E TYR* 4.2 10.5 - - + -
433E TYR* 3.7 25.8 - - + -
303F LYS* 5.8 0.3 - - - +
304F LEU* 3.2 38.0 - - + +
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Residues in contact with LEU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386E LEU* 4.2 11.5 - - + +
387E GLN* 4.6 13.2 - - + +
388E ASN* 3.1 24.0 + - + +
390E LEU* 1.3 80.3 - - - +
392E ASP* 1.3 59.4 - - - +
393E ASP* 4.0 2.4 + - - +
396E LYS* 5.4 0.7 - - - -
433E TYR* 4.0 20.0 - - + +
296F GLU* 5.5 2.7 - - + +
299F GLN* 3.3 40.2 - - - +
300F ALA* 4.0 28.0 - - + -
303F LYS* 4.4 15.8 - - + +
304F LEU* 4.8 1.6 - - + -
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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