Contacts of the helix formed by residues 388 - 391 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296C GLU* 3.4 11.1 + - - +
336D ALA* 4.0 5.2 - - - +
340D MET* 3.0 41.3 - - - +
343D ARG* 3.7 5.4 - - - +
380D PHE* 6.4 0.4 - - - -
386D LEU* 3.2 22.1 - - - +
387D GLN* 1.3 79.6 - - - +
389D LEU* 1.3 65.6 + - - +
390D LEU* 2.9 38.4 + - - +
391D LEU* 3.1 22.0 + - + +
429D PHE* 5.3 0.4 - - - -
433D TYR* 3.3 28.5 + - - +
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Residues in contact with LEU 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D ILE* 4.8 7.2 - - + -
335D TYR 5.2 1.8 - - - +
336D ALA* 3.9 29.3 + - + +
339D PHE* 5.3 6.6 - - + +
343D ARG* 4.9 1.8 - - - +
372D PHE* 5.1 1.3 - - + -
376D ILE* 4.0 21.8 - - + -
379D ALA* 3.8 27.6 - - + -
380D PHE* 4.3 19.8 - - + -
386D LEU* 4.0 10.8 - - + -
388D ASN* 1.3 75.7 + - - +
390D LEU* 1.3 62.0 + - - +
391D LEU 3.3 0.5 + - - -
392D ASP* 3.4 12.8 + - - +
395D PHE* 3.5 59.6 - - + +
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Residues in contact with LEU 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LEU* 3.8 29.4 - - + +
332D ILE* 3.9 22.2 - - + -
333D ILE* 3.7 34.5 - - + -
336D ALA* 4.0 8.1 - - + -
388D ASN* 2.9 17.7 + - - +
389D LEU* 1.3 77.0 - - - +
391D LEU* 1.3 59.5 + - - +
392D ASP 3.2 2.8 + - - +
395D PHE* 4.9 3.8 - - - +
396D LYS* 3.9 14.4 - - - +
399D VAL* 4.2 12.8 - - + -
429D PHE* 4.2 14.4 - - + -
430D TYR* 4.4 15.5 - - + -
433D TYR* 3.9 24.9 - - + -
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Residues in contact with LEU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C GLU* 5.4 4.3 - - + +
299C GLN* 4.8 12.3 - - + +
300C ALA* 4.2 29.4 - - + +
303C LYS* 4.7 19.1 - - + -
304C LEU* 5.0 3.8 - - + -
386D LEU* 4.3 12.9 - - + +
387D GLN* 4.8 10.5 - - + -
388D ASN* 3.1 28.5 + - + +
390D LEU* 1.3 79.3 - - - +
392D ASP* 1.3 60.6 + - - +
393D ASP* 4.0 2.6 + - - +
396D LYS* 5.3 3.4 - - - +
433D TYR* 4.1 16.4 - - + +
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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