Contacts of the helix formed by residues 341 - 354 (chain A) in PDB entry 5JZU
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 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PHE* 3.8 15.7 - - + +
338A ASP* 3.0 34.3 + - - +
340A THR* 1.3 89.3 - - - +
342A LYS* 1.3 64.7 + - - +
343A ALA* 3.1 5.8 + - - +
344A GLU* 3.3 16.4 + - + +
345A LEU* 3.1 34.6 + - + +
367A LEU* 6.0 0.4 - - + -
371A TYR* 3.7 52.5 - - + +
374A SER* 4.4 4.9 - - - -
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU* 4.1 24.0 - - + +
338A ASP 3.1 8.7 + - - +
339A LYS* 3.7 15.9 + - + +
340A THR 3.6 1.4 - - - -
341A ILE* 1.3 78.1 - - - +
343A ALA* 1.3 53.4 + - - +
345A LEU* 3.7 7.9 - - + +
346A ASP* 2.8 64.0 + - - +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ILE* 3.1 2.2 + - - -
342A LYS* 1.3 79.1 - - - +
344A GLU* 1.3 61.1 + - + +
346A ASP* 3.2 7.1 + - - +
347A ALA* 2.8 30.6 + - - +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 3.3 17.0 + - + +
343A ALA* 1.3 79.1 - - + +
345A LEU* 1.3 62.1 + - + +
347A ALA* 3.2 9.3 + - - +
348A ALA* 3.0 23.9 + - - +
367A LEU* 3.8 25.4 - - + +
370A LYS* 3.1 23.8 + - - -
371A TYR* 2.5 31.7 + - - -
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU* 4.5 4.3 - - + -
338A ASP* 3.7 30.3 - - + +
341A ILE* 3.1 29.8 + - + +
342A LYS* 3.7 6.1 - - - +
344A GLU* 1.3 79.1 - - - +
346A ASP* 1.3 63.2 + - - +
348A ALA* 3.3 3.5 + - - +
349A GLU* 3.0 24.4 + - - +
364A PHE* 4.1 7.8 - - + -
367A LEU* 3.9 15.0 - - + -
376A ARG* 3.9 31.7 + - + -
377A ALA* 3.6 39.9 - - + +
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LYS* 2.8 63.7 + - - +
343A ALA* 3.5 7.1 + - - +
345A LEU* 1.3 75.0 - - - +
347A ALA* 1.3 63.0 + - - +
349A GLU* 3.3 7.4 + - - +
350A LYS* 3.0 25.9 + - - +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA 2.8 14.7 + - - +
344A GLU* 3.3 13.5 - - - +
346A ASP* 1.3 77.7 - - - +
348A ALA* 1.3 63.8 + - - +
350A LYS* 3.4 16.5 + - - +
351A LEU* 3.6 14.3 + - - +
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A GLU 3.0 12.9 + - - +
345A LEU 3.7 4.5 - - - +
347A ALA* 1.3 74.5 - - - +
349A GLU* 1.3 66.7 + - - +
351A LEU* 3.1 18.3 + - - +
352A ARG 3.4 7.3 + - - -
360A ALA* 4.1 6.6 - - - +
363A ALA* 4.0 26.0 - - + -
364A PHE* 3.6 32.8 - - + -
367A LEU* 4.0 6.7 - - + -
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Residues in contact with GLU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU 3.0 17.0 + - - +
346A ASP* 3.8 9.2 - - - +
348A ALA* 1.3 76.2 - - - +
350A LYS* 1.3 63.0 + - - +
352A ARG* 3.0 52.5 + - - +
353A LYS* 3.0 24.3 + - + +
364A PHE* 3.6 15.1 - - + -
376A ARG* 3.2 29.3 + - - +
380A GLY* 5.1 0.2 - - - -
383A GLN* 3.9 4.7 - - - +
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Residues in contact with LYS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ASP 3.0 16.6 + - - +
347A ALA* 3.5 8.5 - - - +
348A ALA 3.1 0.2 - - - -
349A GLU* 1.3 76.7 - - - +
351A LEU* 1.3 65.6 + - + +
353A LYS* 3.3 9.2 + - + +
354A ARG* 3.1 41.8 + - + +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ALA 3.6 15.7 - - - +
348A ALA* 3.1 9.4 + - - +
350A LYS* 1.3 78.6 - - + +
352A ARG* 1.3 62.2 + - - +
354A ARG* 3.3 17.8 + - - +
356A LYS* 3.2 32.8 + - + +
359A GLU* 4.2 32.8 - - + +
360A ALA* 3.9 11.7 - - + +
363A ALA* 4.4 20.9 - - + -
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Residues in contact with ARG 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ALA 3.4 3.3 + - - +
349A GLU* 3.0 44.8 + - - +
351A LEU* 1.3 80.3 - - - +
353A LYS* 1.3 72.9 + - - +
355A GLY* 3.0 21.0 + - - -
356A LYS 4.6 2.7 - - - -
357A ILE* 5.0 6.1 + - + +
360A ALA* 3.6 14.5 - - + +
364A PHE* 5.1 0.2 - - - -
380A GLY 4.8 0.4 - - - -
383A GLN* 3.5 41.0 + - - +
384A CYS* 3.5 27.6 - - - +
387A ASP* 2.9 37.6 + - - +
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Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLU* 3.0 26.4 + - + +
350A LYS* 3.3 9.8 + - + +
352A ARG* 1.3 100.9 - - - +
354A ARG* 1.3 59.3 + - + +
355A GLY 3.1 4.3 + - - -
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Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A LYS* 3.1 34.4 + - + +
351A LEU* 3.7 17.7 - - - +
352A ARG 3.1 0.6 - - - -
353A LYS* 1.3 75.3 - - + +
355A GLY* 1.3 55.0 + - - +
356A LYS* 3.0 12.8 + - + +
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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