Contacts of the helix formed by residues 357 - 365 (chain A) in PDB entry 2J2C
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 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A TYR* 3.9 13.5 - - + +
350A GLY 4.2 9.0 - - - +
352A HIS 3.1 6.4 + - - +
353A ILE* 3.7 14.8 - - + +
355A GLY 3.8 0.4 - - - -
356A ASP* 1.3 86.9 - - + +
358A LEU* 1.3 70.8 + - - +
359A LYS 3.2 0.4 - - - -
360A SER* 3.3 2.8 + - - -
361A LYS* 3.0 26.3 + - - +
368A THR* 3.7 10.6 - - + +
369A PHE 3.5 28.5 - - - +
370A LEU* 3.5 25.6 - - + -
457A TYR* 3.4 33.7 - - + +
458A ALA* 3.8 13.9 - - + +
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Residues in contact with LEU 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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353A ILE 2.9 22.1 + - - +
354A PHE* 3.6 26.9 - - + +
357A ILE* 1.3 73.7 - - - +
359A LYS* 1.3 74.2 + - + +
361A LYS* 3.5 0.7 + - - +
362A LYS* 2.8 60.1 + - + +
453A GLN* 4.1 20.4 - - + +
457A TYR* 3.5 48.0 - - + +
1490A SO4 4.1 8.5 - - - +
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Residues in contact with LYS 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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293A PRO* 3.4 32.8 - - + +
296A PHE* 4.1 10.5 - - + +
354A PHE* 3.1 54.1 + - + +
355A GLY 4.2 1.8 - - - +
357A ILE 3.2 0.6 - - - +
358A LEU* 1.3 85.6 - - + +
360A SER* 1.3 61.7 + - - +
362A LYS* 4.9 1.7 - - + +
363A ARG* 2.9 63.3 + - + +
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Residues in contact with SER 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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296A PHE* 3.5 34.8 - - - -
348A TYR* 4.7 2.5 - - - +
356A ASP 2.8 26.8 + - - -
357A ILE 3.3 4.6 + - - -
359A LYS* 1.3 76.8 - - - +
361A LYS* 1.3 64.6 + - - +
364A GLN* 3.1 19.9 + - - +
365A GLY 3.2 6.9 + - - -
366A TRP* 3.3 25.5 + - - +
368A THR* 3.5 13.3 - - - +
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Residues in contact with LYS 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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39A ARG* 4.9 4.7 - - - +
357A ILE 3.0 15.3 + - - +
358A LEU 3.6 2.9 - - - +
360A SER* 1.3 81.2 + - - +
362A LYS* 1.3 62.1 + - + +
365A GLY* 3.0 30.1 + - - -
366A TRP 3.3 23.3 + - - +
367A ARG* 3.8 10.1 - - - +
368A THR* 3.9 4.7 - - + +
456A ARG 5.2 1.8 - - - +
457A TYR* 3.9 36.6 - - + +
459A ASP* 2.8 41.3 + - - -
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Residues in contact with LYS 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 LEU* 2.8 46.4 + - + +
359A LYS* 4.5 1.8 - - + +
361A LYS* 1.3 75.3 - - + +
363A ARG* 1.3 68.5 + - + +
365A GLY 4.9 0.3 + - - -
457A TYR* 3.7 36.5 + - + +
1490A SO4 4.3 6.1 + - - -
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Residues in contact with ARG 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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293A PRO 5.9 0.4 - - - +
296A PHE* 3.5 25.8 + - + +
297A GLY* 3.8 22.0 - - - +
359A LYS* 2.9 51.1 + - + +
362A LYS* 1.3 82.8 - - + +
364A GLN* 1.3 71.8 + - + +
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Residues in contact with GLN 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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296A PHE* 2.9 35.6 + - + +
297A GLY* 4.9 3.6 + - - -
332A SER* 3.4 24.5 + - - +
333A ASP* 4.2 16.6 + - - +
336A CYS* 5.9 2.0 - - - -
343A GLY* 4.1 6.8 - - - -
360A SER* 3.1 12.4 + - - +
363A ARG* 1.3 91.1 + - + +
365A GLY* 1.3 63.1 + - - +
366A TRP* 3.4 26.2 + - + +
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Residues in contact with GLY 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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343A GLY 3.5 4.6 - - - -
344A LYS* 3.4 32.2 + - - +
360A SER 3.2 0.4 + - - -
361A LYS* 3.0 24.4 + - - -
362A LYS 4.7 0.4 - - - -
363A ARG 3.9 0.2 - - - -
364A GLN* 1.3 77.3 - - - +
366A TRP* 1.3 64.9 + - - +
367A ARG* 4.8 1.2 - - - -
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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