Contacts of the helix formed by residues 326 - 337 (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 ASP 326 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287N ARG* 4.7 2.1 - - - +
292N ILE* 3.7 16.3 - - + +
324N ILE* 4.1 2.4 - - - +
325N GLN* 1.3 81.6 + - - +
327N ARG* 1.3 67.7 + - - +
328N GLU* 2.7 25.6 + - + +
329N THR* 2.8 29.5 + - - -
330N ALA* 2.8 18.4 + - - +
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Residues in contact with ARG 327 (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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287N ARG 3.6 18.2 - - - +
288N ALA 4.0 10.9 + - - +
289N LEU 4.7 0.8 + - - -
290N GLY* 4.3 22.0 - - - +
292N ILE* 3.6 18.2 - - + +
326N ASP* 1.3 71.4 - - - +
328N GLU* 1.3 66.9 + - - +
330N ALA* 3.8 0.7 - - - -
331N LEU* 2.9 47.9 + - + +
353N LYS* 6.1 5.1 - - - +
371N GLU* 3.7 30.1 + - - +
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Residues in contact with GLU 328 (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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326N ASP* 2.7 24.5 + - + +
327N ARG* 1.3 80.2 - - - +
329N THR* 1.3 64.5 + - - +
331N LEU* 3.5 1.9 + - - +
332N ASP* 3.2 17.3 + - - +
349N ILE* 4.9 15.7 - - + +
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Residues in contact with THR 329 (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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323N VAL 4.8 4.3 - - - +
324N ILE* 4.0 29.6 - - + +
325N GLN 4.9 2.0 - - - -
326N ASP* 2.8 23.3 + - - -
328N GLU* 1.3 77.1 - - - +
330N ALA* 1.3 64.9 + - - +
332N ASP* 2.9 28.9 - - - +
333N PHE* 3.4 3.8 + - - +
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Residues in contact with ALA 330 (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* 3.6 8.9 - - - +
287N ARG* 3.5 16.4 - - + -
288N ALA* 3.4 32.5 - - + +
324N ILE* 4.0 13.8 - - + +
326N ASP 2.8 12.9 + - - +
327N ARG 3.3 10.1 - - - +
328N GLU 3.1 0.2 - - - -
329N THR* 1.3 78.6 - - - +
331N LEU* 1.3 65.3 + - - +
332N ASP 3.1 0.3 + - - -
333N PHE* 3.1 16.5 + - - +
334N ILE* 3.9 3.1 + - - +
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Residues in contact with LEU 331 (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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288N ALA* 3.3 42.2 - - + +
327N ARG* 2.9 42.5 + - + +
328N GLU 4.2 1.8 - - - +
330N ALA* 1.3 79.3 - - - +
332N ASP* 1.3 63.6 + - - +
333N PHE 3.1 0.3 + - - -
334N ILE* 3.4 3.9 + - - -
335N GLY* 3.1 20.6 + - - -
348N ARG 4.7 1.2 - - - +
349N ILE* 4.0 23.8 - - + +
352N ALA* 3.7 19.1 - - + +
353N LYS* 3.8 36.6 - - + +
356N LEU* 4.5 3.6 - - + -
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Residues in contact with ASP 332 (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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328N GLU 3.2 10.5 + - - +
329N THR* 2.9 31.4 - - - +
330N ALA 3.0 0.2 - - - -
331N LEU* 1.3 78.7 - - - +
333N PHE* 1.3 56.9 + - - +
335N GLY* 4.0 0.3 - - - -
336N ARG* 2.4 82.2 + - - +
345N LYS* 5.2 1.0 - - - +
348N ARG* 4.7 3.3 - - - +
349N ILE* 4.7 16.9 - - + +
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Residues in contact with PHE 333 (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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278N GLN* 4.6 3.8 - - - -
279N ASP 4.5 12.3 - - - -
280N ILE* 4.8 8.7 - - + -
281N PRO* 5.8 2.0 - - + -
284N ILE* 4.2 33.4 - - + -
324N ILE* 4.4 7.0 - - + -
329N THR 3.4 3.7 + - - +
330N ALA 3.1 12.3 + - - +
332N ASP* 1.3 76.6 + - - +
334N ILE* 1.3 72.5 + - - +
335N GLY 2.8 3.5 + - - -
336N ARG* 2.9 4.8 + - - +
337N ARG* 2.9 70.5 + - + +
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Residues in contact with ILE 334 (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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273N LEU* 4.2 4.9 - - + -
276N ILE* 3.3 33.5 - - + +
280N ILE* 3.3 26.9 - - + -
284N ILE* 4.7 6.3 - - + -
285N ILE* 4.4 12.6 - - - -
288N ALA* 3.9 26.7 - - + -
330N ALA 4.2 8.1 - - - +
331N LEU* 3.4 5.8 + - - +
333N PHE* 1.3 76.4 - - - +
335N GLY* 1.3 56.9 + - - +
337N ARG* 4.0 4.2 + - - +
338N GLY* 2.9 21.1 + - - -
351N TYR* 5.3 0.9 - - - -
352N ALA* 4.1 16.8 - - + -
355N ILE* 5.1 4.6 - - + +
356N LEU* 4.2 22.7 - - + -
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Residues in contact with GLY 335 (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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331N LEU 3.1 10.9 + - - -
332N ASP 4.0 0.7 - - - -
333N PHE 2.8 4.8 + - - -
334N ILE* 1.3 74.5 - - - +
336N ARG* 1.3 57.6 + - - +
338N GLY 2.7 16.7 + - - -
340N ALA* 3.8 8.1 - - - +
348N ARG* 3.4 28.2 - - - +
351N TYR* 3.7 20.7 - - - -
352N ALA* 4.0 5.8 - - - +
355N ILE* 5.7 0.2 - - - -
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Residues in contact with ARG 336 (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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332N ASP* 2.4 56.6 + - - +
333N PHE* 2.9 6.2 + - - +
335N GLY* 1.3 72.2 - - - +
337N ARG* 1.3 68.4 + - - +
338N GLY 3.6 0.7 + - - -
340N ALA* 3.7 26.8 + - - +
345N LYS* 2.8 57.9 - - - +
348N ARG* 2.9 45.8 - - + +
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Residues in contact with ARG 337 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276N ILE* 4.8 6.7 - - + -
277N LYS* 4.5 10.1 - - - +
278N GLN* 2.7 58.3 + - + +
279N ASP 5.0 2.2 - - - +
280N ILE* 6.0 0.7 - - + -
333N PHE* 2.9 51.0 + - + +
334N ILE* 4.1 4.5 - - - +
336N ARG* 1.3 79.9 - - - +
338N GLY* 2.6 45.5 - - - +
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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