Contacts of the helix formed by residues 278 - 288 (chain V) in PDB entry 5IJO
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 ASP 278 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226V GLU* 5.9 7.4 - - + -
227V MET 6.3 0.4 - - - +
274V VAL 2.8 13.0 + - - -
275V GLU* 3.1 15.2 + - - +
276V GLY 3.1 4.6 - - - +
277V MET* 1.3 79.2 - - - +
279V ILE* 1.3 65.7 + - - +
280V GLU 3.2 2.9 - - - -
281V SER* 3.2 16.2 + - - +
282V LEU* 2.8 18.7 + - - +
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Residues in contact with ILE 279 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274V VAL 4.3 2.0 + - - -
277V MET* 3.3 7.8 - - + +
278V ASP* 1.3 74.1 - - - +
280V GLU* 1.3 64.5 + - - +
282V LEU* 3.8 4.2 - - - +
283V HIS* 2.8 27.7 + - - +
325V ALA* 4.5 28.5 - - + +
328V LEU* 5.9 3.1 - - + -
329V LEU* 6.2 4.5 - - + +
383V GLY 5.6 2.5 - - - +
384V LEU* 5.5 9.2 - - - -
387V PHE* 5.5 10.3 - - + -
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Residues in contact with GLU 280 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278V ASP* 3.2 1.0 - - - -
279V ILE* 1.3 80.8 - - - +
281V SER* 1.3 63.1 + - - +
283V HIS* 3.5 3.5 + - - +
284V LYS* 3.2 19.9 + - - +
383V GLY* 5.1 18.2 + - - +
386V SER* 6.3 2.0 - - - -
387V PHE* 5.8 5.4 - - - -
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Residues in contact with SER 281 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278V ASP* 3.2 18.7 + - - +
280V GLU* 1.3 79.3 - - - +
282V LEU* 1.3 57.0 + - - +
284V LYS* 3.2 8.1 + - - +
285V CYS* 2.8 28.8 + - - +
289V ASP* 5.1 1.4 - - - +
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Residues in contact with LEU 282 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277V MET 4.0 10.5 - - - +
278V ASP* 2.8 18.5 + - + +
279V ILE* 3.8 5.6 - - - +
281V SER* 1.3 77.6 - - - +
283V HIS* 1.3 62.1 + - - +
285V CYS* 3.0 9.5 + - - +
286V ALA* 2.8 21.7 + - - +
297V ALA* 6.0 6.7 - - + -
329V LEU* 5.9 7.6 - - + -
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Residues in contact with HIS 283 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279V ILE 2.8 17.7 + - - +
280V GLU* 4.0 4.0 - - - +
282V LEU* 1.3 75.6 - - - +
284V LYS* 1.3 64.8 + - - +
286V ALA* 3.1 9.9 + - - +
287V LEU* 3.0 20.4 + - - +
329V LEU* 6.3 2.9 - - - +
332V THR* 5.1 13.1 - - - -
387V PHE* 5.9 7.0 - - + -
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Residues in contact with LYS 284 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280V GLU 3.2 11.9 + - - +
281V SER* 3.4 11.4 - - - +
282V LEU 3.2 0.2 - - - -
283V HIS* 1.3 77.9 - - - +
285V CYS* 1.3 52.2 + - - +
287V LEU* 3.0 9.3 + - - +
288V ASP 2.6 36.8 + - - +
289V ASP* 4.1 13.0 - - + -
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Residues in contact with CYS 285 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281V SER 2.8 13.1 + - - +
282V LEU* 3.0 12.5 + - - +
284V LYS* 1.3 77.0 - - - +
286V ALA* 1.3 63.1 + - - +
288V ASP* 2.8 16.1 + - - -
289V ASP* 3.7 18.4 + - + +
295V GLN* 6.0 6.5 - - + -
297V ALA* 6.2 3.8 - - + -
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Residues in contact with ALA 286 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282V LEU 2.8 13.0 + - - +
283V HIS* 3.1 11.4 + - - +
285V CYS* 1.3 76.9 - - - +
287V LEU* 1.3 65.7 + - - +
332V THR* 4.5 21.1 - - - +
333V LEU* 6.3 0.4 - - - -
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Residues in contact with LEU 287 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283V HIS 3.0 12.4 + - - +
284V LYS* 3.4 9.9 - - - +
286V ALA* 1.3 78.7 - - - +
288V ASP* 1.4 68.9 + - - +
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Residues in contact with ASP 288 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284V LYS* 2.6 15.1 + - - +
285V CYS 2.8 9.8 + - - -
286V ALA 4.2 0.2 - - - -
287V LEU* 1.4 79.3 - - - +
289V ASP* 1.3 58.9 + - - +
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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