Contacts of the helix formed by residues 356 - 371 (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 LYS 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A LEU* 3.2 20.5 + - + +
354A ARG* 3.0 11.3 + - + +
355A GLY* 1.3 72.6 - - - +
357A ILE* 1.3 56.1 + - - +
358A GLU* 3.0 14.4 + - + +
359A GLU* 2.8 40.1 - - + +
360A ALA* 3.3 22.5 + - - +
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Residues in contact with ILE 357 (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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352A ARG* 5.0 8.3 - - + +
355A GLY* 2.5 16.8 + - - +
356A LYS* 1.3 69.4 - - - +
358A GLU* 1.3 58.8 + - - +
360A ALA* 4.1 8.9 - - - +
361A VAL* 3.1 29.1 + - - +
384A CYS* 4.7 6.9 - - + +
387A ASP* 4.4 25.1 - - + +
388A LEU* 4.6 14.8 - - + +
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Residues in contact with GLU 358 (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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356A LYS* 3.0 6.0 - - + -
357A ILE* 1.3 81.3 - - - +
359A GLU* 1.3 62.8 + - + +
361A VAL* 3.6 8.3 + - - +
362A ASN* 2.8 21.4 + - - -
388A LEU* 5.3 7.0 - - + -
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.2 27.4 - - + +
356A LYS* 2.8 33.5 + - + +
358A GLU* 1.3 77.1 - - + +
360A ALA* 1.3 61.6 - - - +
361A VAL 3.3 0.7 - - - -
362A ASN* 3.5 13.1 + - + +
363A ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 360 (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 4.1 3.8 - - - +
351A LEU* 3.9 8.1 - - + -
352A ARG* 3.6 26.5 - - + +
356A LYS 3.3 18.6 + - - +
357A ILE* 4.3 3.6 - - - -
358A GLU 3.3 0.6 - - - -
359A GLU* 1.3 76.8 - - - +
361A VAL* 1.3 65.5 + - - +
363A ALA* 3.3 8.3 + - - +
364A PHE* 3.0 28.1 + - - -
384A CYS* 3.7 18.8 - - - -
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Residues in contact with VAL 361 (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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357A ILE 3.1 19.5 + - - +
358A GLU* 3.6 8.9 + - - +
359A GLU 3.3 0.2 - - - -
360A ALA* 1.3 76.4 - - - +
362A ASN* 1.3 55.0 + - - +
364A PHE* 3.0 5.7 + - - +
365A LYS* 2.6 59.8 + - + +
381A LYS* 5.6 3.8 - - + +
384A CYS* 3.4 32.3 - - + +
385A GLU* 4.6 11.0 - - + +
388A LEU* 4.9 16.8 - - + -
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Residues in contact with ASN 362 (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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358A GLU 2.8 30.5 + - - -
359A GLU* 3.8 9.9 - - + +
360A ALA 3.4 0.2 - - - -
361A VAL* 1.3 81.0 - - - +
363A ALA* 1.3 56.4 + - - +
365A LYS* 3.6 13.9 - - - +
366A GLU* 2.9 29.3 + - - +
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Residues in contact with ALA 363 (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* 4.0 19.5 - - + -
351A LEU* 4.4 11.7 - - + -
359A GLU 3.0 18.4 + - - +
360A ALA* 3.4 10.3 - - - +
361A VAL 3.0 0.2 - - - -
362A ASN* 1.3 77.0 - - - +
364A PHE* 1.3 58.4 + - - +
366A GLU* 3.2 8.3 + - - +
367A LEU* 3.1 30.5 + - - +
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Residues in contact with PHE 364 (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* 4.1 18.6 - - + -
348A ALA* 3.6 30.7 - - + -
349A GLU* 3.6 32.3 - - + -
352A ARG* 5.1 0.4 - - - -
360A ALA 3.0 21.7 + - - +
361A VAL* 3.0 4.3 + - - +
363A ALA* 1.3 73.3 - - - +
365A LYS* 1.3 61.5 + - - +
367A LEU* 3.2 10.4 + - + +
368A VAL* 2.8 36.4 + - - +
376A ARG* 4.1 12.8 - - - -
377A ALA* 3.5 15.4 - - - +
380A GLY* 3.5 34.3 - - - -
381A LYS* 3.6 17.9 - - - +
384A CYS* 3.7 12.1 - - - -
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Residues in contact with LYS 365 (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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361A VAL* 2.6 43.8 + - + +
362A ASN* 3.6 14.1 - - - +
364A PHE* 1.3 72.5 - - - +
366A GLU* 1.3 56.8 + - - +
368A VAL* 3.5 8.3 + - - +
369A ARG* 3.0 27.9 + - - +
381A LYS* 4.2 25.4 - - + -
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Residues in contact with GLU 366 (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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362A ASN 2.9 17.5 + - - +
363A ALA* 3.4 7.9 - - - +
365A LYS* 1.3 75.6 - - - +
367A LEU* 1.3 63.1 + - + +
369A ARG* 3.3 9.1 + - - +
370A LYS* 2.9 46.5 + - - +
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Residues in contact with LEU 367 (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* 3.8 54.1 - - + +
345A LEU* 3.9 23.1 - - + -
348A ALA* 4.0 17.9 - - + -
363A ALA 3.1 10.7 + - - +
364A PHE* 3.7 12.3 - - + +
366A GLU* 1.3 77.2 - - + +
368A VAL* 1.3 58.3 + - - +
370A LYS* 4.3 4.3 - - - -
371A TYR* 2.6 57.2 + - + +
377A ALA* 4.0 13.0 - - + -
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PHE 2.8 20.7 + - - +
365A LYS* 3.7 7.9 - - - +
367A LEU* 1.3 76.8 - - - +
369A ARG* 1.3 62.8 + - - +
371A TYR 4.1 5.6 - - - -
372A PRO* 3.0 30.4 - - + +
374A SER 5.8 0.2 - - - +
377A ALA* 3.6 26.9 - - + +
378A ARG* 3.9 35.4 - - - +
381A LYS* 4.1 22.2 - - + -
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Residues in contact with ARG 369 (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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365A LYS 3.0 17.9 + - - +
366A GLU* 3.6 13.5 - - - +
368A VAL* 1.3 78.9 - - - +
370A LYS* 1.3 62.1 + - - +
372A PRO* 3.8 9.3 - - - +
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Residues in contact with LYS 370 (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* 3.1 23.6 + - - -
366A GLU* 2.9 33.2 + - - +
367A LEU* 3.8 8.1 - - - +
369A ARG* 1.3 79.2 - - - +
371A TYR* 1.3 100.7 + - + +
372A PRO* 3.3 7.6 - - - +
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Residues in contact with TYR 371 (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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337A PHE* 3.5 36.6 - + + -
341A ILE* 3.7 26.2 - - + +
344A GLU* 2.5 29.4 + - - -
367A LEU* 2.6 36.1 + - + +
368A VAL* 3.2 8.0 - - - +
370A LYS* 1.3 114.7 + - + +
372A PRO* 1.3 57.6 - - - +
373A GLN 2.9 11.9 + - - -
374A SER* 2.9 29.4 + - - +
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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