Contacts of the helix formed by residues 345 - 359 (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 LYS 345 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332N ASP* 5.5 0.4 - - - +
336N ARG* 2.8 35.6 - - - +
343N ILE* 3.4 7.3 + - - +
344N LYS* 1.3 86.4 - - - +
346N GLU* 1.3 66.4 + - + +
347N LYS 3.1 0.9 - - - -
348N ARG* 3.6 12.6 - - - +
349N ILE* 3.0 38.7 + - + +
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Residues in contact with GLU 346 (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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344N LYS* 3.7 3.2 - - + +
345N LYS* 1.3 81.6 - - + +
347N LYS* 1.3 59.7 + - + +
349N ILE* 3.8 9.8 + - + +
350N GLN* 3.1 30.1 + - - +
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Residues in contact with LYS 347 (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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342N GLY 5.1 5.6 + - - +
343N ILE* 3.0 37.5 - - + +
344N LYS* 4.7 19.0 - - + +
345N LYS 3.1 0.4 - - - -
346N GLU* 1.3 80.5 - - + +
348N ARG* 1.3 57.8 + - - +
350N GLN* 3.4 6.1 + - - +
351N TYR* 2.9 28.4 + - - +
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Residues in contact with ARG 348 (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 5.1 0.9 - - - -
332N ASP* 4.7 2.9 - - - +
335N GLY* 3.4 12.1 - - - -
336N ARG* 2.9 70.9 - - + +
340N ALA* 3.5 19.4 + - + +
341N LEU* 3.5 32.5 + - - +
343N ILE* 2.7 55.2 + - + +
344N LYS 5.1 0.2 - - - -
345N LYS* 3.3 11.6 + - - +
347N LYS* 1.3 74.9 - - - +
349N ILE* 1.3 62.6 + - - +
351N TYR* 3.1 18.5 + - - +
352N ALA 3.3 5.0 + - - -
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Residues in contact with ILE 349 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328N GLU* 4.9 17.0 - - + +
331N LEU* 4.0 26.6 - - + +
332N ASP* 4.7 20.9 - - + +
345N LYS* 3.0 23.4 + - + +
346N GLU* 4.0 8.3 - - + +
348N ARG* 1.3 76.1 - - + +
350N GLN* 1.3 64.8 + - - +
352N ALA* 3.2 9.0 + - - +
353N LYS* 3.1 31.0 + - - +
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Residues in contact with GLN 350 (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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346N GLU 3.1 18.6 + - - +
347N LYS* 3.7 6.7 - - - +
349N ILE* 1.3 81.0 - - - +
351N TYR* 1.3 59.9 - - - +
353N LYS* 3.5 36.0 + - - +
354N ASP* 2.7 47.6 + - - +
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Residues in contact with TYR 351 (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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275N TYR* 3.6 32.3 + + - +
335N GLY* 3.7 20.2 - - - -
338N GLY* 4.4 1.8 - - - -
339N THR* 3.2 45.5 + - - -
343N ILE* 4.9 10.1 - - + -
347N LYS 2.9 14.7 + - - +
348N ARG* 3.1 12.8 + - - +
350N GLN* 1.3 77.5 - - - +
352N ALA* 1.3 60.5 + - - +
354N ASP* 3.7 6.6 + - + +
355N ILE* 2.8 54.5 + - + +
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Residues in contact with ALA 352 (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* 3.7 35.0 - - + +
334N ILE* 4.1 13.7 - - + -
335N GLY* 4.0 10.2 - - - +
348N ARG 3.3 2.1 + - - +
349N ILE 3.2 9.0 + - - +
351N TYR* 1.3 76.8 - - - +
353N LYS* 1.3 68.3 + - - +
355N ILE* 2.9 13.1 + - - +
356N LEU* 2.6 29.0 + - + +
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Residues in contact with LYS 353 (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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327N ARG* 6.1 5.2 - - - +
331N LEU* 3.8 26.8 - - + +
349N ILE* 3.1 15.2 + - - +
350N GLN* 3.5 37.0 + - - +
352N ALA* 1.3 77.0 - - - +
354N ASP* 1.3 53.6 + - - +
356N LEU* 2.9 8.5 + - - +
357N GLN* 2.7 56.8 + - - +
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Residues in contact with ASP 354 (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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350N GLN* 2.7 36.9 + - - +
351N TYR* 3.8 6.6 + - + +
352N ALA 3.3 0.2 - - - -
353N LYS* 1.3 77.8 - - - +
355N ILE* 1.3 55.4 + - + +
357N GLN* 2.7 12.0 + - - +
358N LYS* 2.4 50.6 + - + +
359N GLU* 5.3 0.2 - - - -
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Residues in contact with ILE 355 (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* 5.2 2.5 - - + -
274N PRO* 3.7 27.4 - - + +
275N TYR* 4.7 3.8 - - + -
276N ILE* 4.5 23.1 - - + -
334N ILE* 5.1 4.3 - - + +
351N TYR* 2.8 61.7 - - + +
352N ALA* 2.9 14.3 + - - +
354N ASP* 1.3 73.3 - - + +
356N LEU* 1.3 57.8 + - + +
359N GLU* 2.8 27.6 + - + +
360N PHE* 2.6 35.2 + - + +
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Residues in contact with LEU 356 (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* 4.4 8.3 - - + -
285N ILE* 5.1 2.7 - - + -
288N ALA* 4.1 35.2 - - + +
289N LEU* 4.8 16.2 - - + +
331N LEU* 4.5 5.4 - - + -
334N ILE* 4.2 22.0 - - + -
352N ALA* 2.6 30.2 + - + +
353N LYS* 3.4 9.2 - - - +
355N ILE* 1.3 76.0 - - + +
357N GLN* 1.3 52.5 + - + +
360N PHE* 3.6 36.2 - - + +
371N GLU* 5.7 1.0 - - - +
374N LYS* 2.7 31.2 + - - +
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Residues in contact with GLN 357 (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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353N LYS* 2.7 42.3 + - - +
354N ASP* 2.7 7.5 + - - +
356N LEU* 1.3 78.2 - - + +
358N LYS* 1.3 56.9 + - + +
366N GLN* 2.7 40.8 - - - +
367N LEU 2.9 22.5 - - - +
368N GLU* 3.3 31.9 + - - +
371N GLU* 4.8 14.2 + - - +
374N LYS* 3.0 11.3 + - - +
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Residues in contact with LYS 358 (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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250N PHE* 4.8 5.5 - - + -
354N ASP* 2.4 34.3 + - + +
357N GLN* 1.3 77.8 - - + +
359N GLU* 1.3 69.9 + - + +
362N PRO* 3.9 10.2 - - - +
366N GLN* 3.3 39.5 - - + +
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Residues in contact with GLU 359 (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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250N PHE* 3.7 26.4 - - - -
252N SER* 3.9 11.0 + - - -
274N PRO* 3.4 28.1 - - + +
275N TYR* 3.1 42.3 + - + -
354N ASP 5.3 0.2 - - - -
355N ILE* 2.8 39.6 + - + +
358N LYS* 1.3 86.3 - - + +
360N PHE* 1.3 56.8 + - - +
361N LEU 3.4 0.3 + - - -
362N PRO* 3.0 23.7 - - - +
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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