Contacts of the helix formed by residues 293 - 302 (chain F) 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 LEU 293 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E GLY 5.8 3.6 - - - +
277E PRO* 4.6 4.9 - - + -
340E MET* 3.6 30.7 - - + -
387E GLN* 5.5 4.3 - - - +
433E TYR* 4.6 9.6 - - + -
289F CYS 3.7 15.5 - - - +
290F LEU* 3.2 20.4 + - + +
291F SER 3.1 1.6 - - - -
292F SER* 1.3 78.8 - - - +
294F LYS* 1.3 59.2 + - - +
295F ASP 3.4 2.2 - - - -
296F GLU* 3.2 30.7 + - + +
297F ARG* 2.9 34.5 + - + +
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Residues in contact with LYS 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E GLU* 3.4 18.8 - - - +
437E MET* 4.3 4.0 - - - -
458E LEU* 3.1 27.7 - - - +
255F ARG* 3.4 45.3 - - + +
256F ASP* 2.5 29.3 + - - +
257F SER* 4.8 1.8 - - - -
291F SER 3.5 4.2 + - - +
292F SER 3.0 8.1 + - - +
293F LEU* 1.3 75.6 - - - +
295F ASP* 1.3 58.0 + - - +
297F ARG* 3.1 27.6 + - - +
298F ILE* 2.8 56.5 + - + +
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Residues in contact with ASP 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F ARG* 3.8 17.9 + - - -
293F LEU 3.4 0.2 - - - -
294F LYS* 1.3 75.7 - - - +
296F GLU* 1.3 74.3 + - - +
298F ILE* 3.3 14.4 + - - +
299F GLN* 3.1 23.7 + - - +
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Residues in contact with GLU 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E GLN* 3.3 40.8 + - + +
391E LEU* 5.5 2.0 - - + +
433E TYR* 3.9 23.3 + - + +
293F LEU* 3.2 41.1 - - + +
294F LYS 3.3 0.4 - - - -
295F ASP* 1.3 85.7 + - - +
297F ARG* 1.3 58.1 + - - +
299F GLN* 3.5 6.1 + - - +
300F ALA* 2.9 29.6 + - - +
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Residues in contact with ARG 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432E GLY 3.4 19.1 - - - +
433E TYR* 3.7 29.4 - - + +
435E HIS 3.2 19.3 + - - +
436E GLU* 3.0 31.6 + - - -
438E LEU* 3.7 20.7 - - - +
256F ASP* 2.8 28.6 + - - -
290F LEU* 3.2 26.4 + - + +
291F SER* 2.8 24.2 + - - +
293F LEU* 2.9 15.7 + - + +
294F LYS* 3.3 16.1 - - - +
296F GLU* 1.3 74.8 - - - +
298F ILE* 1.3 61.0 + - - +
300F ALA* 4.0 0.2 - - - +
301F SER* 2.9 31.2 + - - -
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Residues in contact with ILE 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436E GLU* 3.6 33.7 - - + +
458E LEU* 6.2 0.7 - - + -
294F LYS* 2.8 48.3 + - + +
295F ASP* 3.7 15.3 - - - +
297F ARG* 1.3 77.4 - - - +
299F GLN* 1.3 60.4 + - - +
301F SER* 2.7 22.2 + - - -
302F LYS* 3.6 16.7 - - + +
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Residues in contact with GLN 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E GLN* 5.8 0.7 - - - +
391E LEU* 3.3 32.4 - - - +
295F ASP 3.1 16.6 + - - +
296F GLU* 4.1 4.7 - - - +
298F ILE* 1.3 79.5 - - - +
300F ALA* 1.3 61.6 + - - +
301F SER 3.4 0.2 - - - -
302F LYS* 3.6 22.4 + - + +
303F LYS* 3.7 34.0 + - - +
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Residues in contact with ALA 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E LEU* 4.0 13.2 - - + -
433E TYR* 3.4 41.1 - - + +
434E ARG 4.5 0.7 - - - -
296F GLU 2.9 18.5 + - - +
297F ARG 4.0 0.2 - - - +
298F ILE 3.3 0.2 - - - -
299F GLN* 1.3 74.7 - - - +
301F SER* 1.3 57.2 + - - +
302F LYS 3.1 1.8 - - - -
303F LYS 3.0 1.0 + - - -
304F LEU* 2.5 46.0 + - + +
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Residues in contact with SER 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E ARG 3.2 25.0 + - - +
436E GLU* 3.4 28.6 + - - +
297F ARG 2.9 14.1 + - - -
298F ILE 2.7 22.0 + - - -
300F ALA* 1.3 76.0 - - - +
302F LYS* 1.3 61.5 + - - +
304F LEU 3.5 11.3 - - - +
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Residues in contact with LYS 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F ILE* 3.6 24.0 - - + +
299F GLN* 3.6 17.5 + - - +
300F ALA 3.1 0.8 - - - -
301F SER* 1.3 81.2 - - - +
303F LYS* 1.3 81.5 + - - +
305F LYS* 6.2 0.4 - - - +
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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