Contacts of the helix formed by residues 358 - 365 (chain A) in PDB entry 2ZJ4
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 HIS 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A GLY 5.1 1.8 + - - -
355A LEU 3.3 5.3 + - - +
357A ASP* 1.3 84.7 - - + +
359A ILE* 1.3 63.3 + - - +
360A LYS 3.2 2.0 + - - -
361A GLU* 3.4 14.2 + - + +
362A ILE* 3.1 27.6 + - + +
441A LEU* 4.2 23.6 - - + -
458A ASP* 3.3 31.1 + - + +
459A CYS* 3.6 28.7 - - + +
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Residues in contact with ILE 359 (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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355A LEU* 2.9 28.8 + - + +
356A LYS* 4.3 6.7 - - - +
357A ASP 3.2 2.6 + - - -
358A HIS* 1.3 72.9 - - - +
360A LYS* 1.3 69.1 + - + +
362A ILE* 3.3 8.9 + - + +
363A GLN* 3.1 41.1 + - - +
487A PHE* 4.0 16.8 - - + -
490A MET* 3.8 40.8 - - + +
491A MET* 4.0 23.3 - - - +
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Residues in contact with LYS 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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356A LYS 5.7 2.2 - - - +
357A ASP 4.1 8.9 + - - +
358A HIS 3.3 0.6 - - - -
359A ILE* 1.3 81.4 - - + +
361A GLU* 1.3 65.6 + - - +
363A GLN* 3.1 23.7 + - - +
364A ARG* 3.2 32.7 + - - +
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Residues in contact with GLU 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 ASP 5.2 0.4 + - - -
358A HIS* 3.4 20.7 + - + +
360A LYS* 1.3 76.8 - - - +
362A ILE* 1.3 60.9 + - - +
364A ARG* 3.1 29.3 + - - +
365A CYS* 3.5 12.2 + - - -
441A LEU* 4.4 18.2 - - + -
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Residues in contact with ILE 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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355A LEU* 4.5 14.4 - - + -
358A HIS* 3.1 25.9 + - + +
359A ILE* 3.5 11.9 - - - +
360A LYS 3.3 0.2 - - - -
361A GLU* 1.3 75.7 - - - +
363A GLN* 1.3 59.0 + - - +
365A CYS* 3.0 23.7 + - - +
368A LEU* 4.8 3.5 - - + +
393A LEU* 4.9 2.4 - - - +
415A VAL* 4.3 18.3 - - + +
441A LEU* 3.3 28.5 - - + -
443A VAL* 4.4 16.8 - - + -
459A CYS* 4.7 0.9 - - - -
487A PHE* 3.7 39.0 - - + -
491A MET* 3.8 14.8 - - + +
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Residues in contact with GLN 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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359A ILE* 3.1 37.2 + - - +
360A LYS* 3.1 15.7 + - - +
362A ILE* 1.3 76.0 - - - +
364A ARG* 1.3 62.0 + - - +
365A CYS 3.3 5.1 + - - +
366A ARG* 5.1 2.4 + - - -
393A LEU* 5.5 4.1 - - - +
490A MET 4.4 6.8 - - - +
491A MET* 3.6 42.4 - - + +
493A ASP* 5.0 3.8 - - - +
494A ASP* 6.3 0.8 - - - +
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Residues in contact with ARG 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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360A LYS* 3.2 30.8 + - - +
361A GLU* 3.1 23.7 + - - +
363A GLN* 1.3 76.7 - - - +
365A CYS* 1.3 65.2 + - - +
366A ARG* 3.5 17.3 + - - +
413A ASP* 5.2 2.4 - - - +
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Residues in contact with CYS 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 GLU* 3.6 17.3 - - - -
362A ILE* 3.0 9.2 + - - +
363A GLN 3.9 5.2 - - - +
364A ARG* 1.3 83.6 - - - +
366A ARG* 1.3 68.9 + - - +
367A ARG 3.7 3.1 - - - +
368A LEU* 5.7 1.8 - - + -
393A LEU* 3.9 15.8 - - + +
412A ARG 5.4 0.9 - - - -
413A ASP* 3.2 27.4 - - - +
414A ASP 4.3 1.8 - - - -
415A VAL* 2.8 40.4 - - + +
441A LEU* 4.7 7.9 - - - -
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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