Contacts of the helix formed by residues 282 - 289 (chain N) in PDB entry 2JA7
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 ILE 282 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256N VAL* 4.5 5.6 - - + -
269N ILE* 3.3 38.4 + - + +
271N ALA* 4.7 8.3 - - + -
280N ILE 3.2 4.2 + - - -
281N PRO* 1.3 67.4 - - - +
283N VAL* 1.3 69.9 + - + +
285N ILE* 3.2 14.5 + - - +
286N PHE* 2.8 24.9 + - + +
297N ILE* 6.2 1.1 - - + -
301N ILE* 4.2 6.7 - - + -
314N LEU* 4.2 9.2 - - + -
317N CYS* 3.4 27.1 - - - -
378N LEU* 4.1 10.0 - - + +
382N ILE* 3.3 46.7 - - + -
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Residues in contact with VAL 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281N PRO* 2.4 16.5 + - + +
282N ILE* 1.3 67.2 - - + +
284N ILE* 1.3 55.0 + - + +
286N PHE* 2.4 41.9 + - - +
287N ARG* 3.0 34.8 + - - +
297N ILE* 4.0 18.2 - - + -
317N CYS* 3.4 43.5 - - - +
318N VAL* 4.2 11.7 - - + +
321N GLY* 4.1 19.3 - - - +
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Residues in contact with ILE 284 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280N ILE* 3.9 12.8 - - + -
281N PRO* 2.9 33.6 + - + -
283N VAL* 1.3 77.5 - - - +
285N ILE* 1.3 52.0 + - - +
287N ARG* 3.0 10.3 + - - +
288N ALA* 2.7 33.6 + - - +
321N GLY* 4.6 12.3 - - - -
324N ILE* 3.3 39.5 - - + -
330N ALA* 3.6 18.3 - - - +
333N PHE* 4.2 28.5 - - + -
334N ILE* 4.7 4.5 - - + -
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Residues in contact with ILE 285 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271N ALA* 4.2 17.0 - - + -
273N LEU* 4.4 14.4 - - + -
280N ILE* 3.3 43.7 - - + +
281N PRO 4.3 0.2 - - - +
282N ILE* 3.3 12.1 - - - +
283N VAL 2.7 3.0 + - - -
284N ILE* 1.3 73.8 - - - +
286N PHE* 1.3 54.8 + - - +
288N ALA* 2.8 28.9 + - - +
289N LEU* 2.9 22.1 + - + +
334N ILE* 4.4 7.9 - - + -
356N LEU* 5.1 2.2 - - + -
360N PHE* 3.6 22.2 - - + -
378N LEU* 3.4 30.1 - - + -
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Residues in contact with PHE 286 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282N ILE* 2.8 21.4 + - + -
283N VAL 2.4 16.6 + - - +
285N ILE* 1.3 72.3 - - - +
287N ARG* 1.3 55.5 + - - +
289N LEU* 3.3 13.5 + - + +
291N ILE* 3.1 44.0 + - + +
297N ILE* 3.6 33.9 - - + -
300N HIS* 3.9 19.7 - + + -
301N ILE* 3.6 27.1 - - + -
375N ALA* 3.2 40.8 - - + -
378N LEU* 4.1 9.0 - - + -
379N GLY* 3.9 15.0 - - - -
382N ILE* 3.8 11.0 - - + -
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Residues in contact with ARG 287 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283N VAL* 3.0 31.1 + - - +
284N ILE* 3.0 9.0 + - - +
286N PHE* 1.3 72.5 - - - +
288N ALA* 1.3 61.3 + - - +
289N LEU 2.9 5.4 - - - -
290N GLY* 3.0 12.3 + - - -
291N ILE 3.7 13.1 + - - +
292N ILE* 2.9 32.6 + - + +
294N ASP* 2.7 32.5 + - - +
297N ILE* 4.3 5.0 - - + +
318N VAL* 4.9 4.4 - - - +
321N GLY 3.2 18.6 + - - -
322N PHE* 5.0 2.8 - - - +
324N ILE* 2.4 49.5 + - + +
325N GLN* 3.7 18.0 + - - +
326N ASP 5.1 1.3 - - - -
327N ARG* 3.6 17.2 + - - +
330N ALA* 3.5 12.8 - - + -
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Residues in contact with ALA 288 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284N ILE 2.7 12.2 + - - +
285N ILE 2.8 9.8 + - - +
287N ARG* 1.3 77.9 - - - +
289N LEU* 1.3 58.8 + - - +
290N GLY 3.3 1.9 + - - -
327N ARG* 4.0 9.0 + - - -
330N ALA* 3.4 7.6 - - + +
331N LEU* 3.3 40.9 - - + +
334N ILE* 3.9 24.9 - - + -
356N LEU* 4.1 12.5 - - + +
371N GLU* 5.6 0.5 - - - +
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Residues in contact with LEU 289 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285N ILE* 2.9 26.2 + - + +
286N PHE* 3.5 19.5 - - + +
287N ARG 2.9 0.8 - - - -
288N ALA* 1.3 81.5 - - - +
290N GLY* 1.3 59.1 + - - +
291N ILE* 3.5 5.2 - - + +
327N ARG* 4.7 2.6 + - - -
356N LEU* 4.8 23.3 - - + +
360N PHE* 5.0 6.7 - - + -
371N GLU* 3.5 46.0 - - + +
374N LYS* 4.4 14.4 - - + +
375N ALA* 3.6 38.4 - - + +
378N LEU* 4.8 4.5 - - + -
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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