Contacts of the helix formed by residues 353 - 364 (chain A) in PDB entry 1A4Y
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 GLU 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A ALA* 4.3 9.9 - - + -
351A ARG* 3.4 30.1 + - - +
352A LEU* 1.3 91.6 - - - +
354A ASP* 1.3 67.4 + - - +
355A ALA* 4.0 7.0 - - + +
357A VAL* 3.2 20.1 + - - +
379A CYS 3.0 8.8 + - - -
380A ASP* 2.3 52.0 - - - +
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Residues in contact with ASP 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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353A GLU* 1.3 75.3 - - - +
355A ALA* 1.3 61.3 + - - +
357A VAL* 4.4 0.4 - - - -
358A ARG* 3.0 25.3 + - - +
380A ASP 3.8 4.7 - - - +
381A VAL* 3.7 0.6 - - - +
382A SER* 2.5 48.6 + - - -
384A SER* 3.6 14.8 - - - -
385A SER* 2.5 36.0 + - - +
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Residues in contact with ALA 355 (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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326A ALA* 4.2 15.0 - - + -
352A LEU 4.5 0.4 - - - +
353A GLU* 3.1 5.0 - - + +
354A ASP* 1.3 78.0 - - - +
356A GLY* 1.3 64.2 + - - +
358A ARG* 3.1 13.4 + - - +
359A GLU* 3.1 24.1 + - - +
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Residues in contact with GLY 356 (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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326A ALA* 3.8 4.6 - - - +
329A CYS* 3.2 41.3 - - - +
352A LEU* 3.0 16.0 + - - -
355A ALA* 1.3 78.7 - - - +
357A VAL* 1.3 57.0 + - - +
359A GLU* 3.4 6.7 + - - -
360A LEU* 3.0 24.8 + - - +
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Residues in contact with VAL 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 LEU* 4.5 11.4 - - + -
353A GLU 3.2 18.6 + - - +
356A GLY* 1.3 74.7 - - - +
358A ARG* 1.3 65.6 + - - +
360A LEU* 3.3 7.5 + - + +
361A CYS* 3.0 26.1 + - - +
376A LEU* 4.5 26.0 - - + -
379A CYS 5.0 0.2 - - - +
381A VAL* 3.6 24.7 - - + -
385A SER* 3.7 27.8 - - - +
389A LEU* 4.3 19.5 - - + -
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Residues in contact with ARG 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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354A ASP 3.0 18.7 + - - +
355A ALA* 3.1 6.9 + - - +
357A VAL* 1.3 76.4 - - - +
359A GLU* 1.3 59.7 + - + +
361A CYS* 3.0 24.4 - - - +
362A GLN* 3.1 12.4 + - - +
385A SER* 5.0 2.4 + - - -
388A SER* 4.4 18.5 - - - +
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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
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326A ALA* 3.5 20.1 - - - +
329A CYS* 4.0 15.3 - - - +
330A SER* 3.6 25.2 - - - -
333A SER* 2.8 21.4 + - - -
355A ALA* 3.1 17.7 - - - +
356A GLY* 3.5 11.2 + - - +
357A VAL 3.2 0.2 - - - -
358A ARG* 1.3 72.3 - - + +
360A LEU* 1.3 67.6 + - - +
361A CYS 2.9 1.6 - - - -
362A GLN* 2.7 27.5 + - + +
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Residues in contact with LEU 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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329A CYS* 3.6 19.7 - - + +
332A PHE* 3.5 34.1 - - + -
333A SER* 4.1 6.1 - - - +
336A LEU* 3.9 16.7 - - + +
345A LEU* 5.9 0.2 - - + -
347A ILE* 3.5 31.0 - - + -
352A LEU* 4.1 14.4 - - + -
356A GLY 3.0 17.7 + - - +
357A VAL* 3.6 10.5 - - + +
359A GLU* 1.3 75.2 - - - +
361A CYS* 1.3 64.3 + - - +
363A GLY* 3.4 2.3 + - - -
364A LEU* 3.1 24.7 + - + +
374A LEU* 5.4 6.7 - - + -
376A LEU* 4.1 14.4 - - + -
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Residues in contact with CYS 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 VAL* 3.0 18.3 + - - +
358A ARG 3.0 15.0 - - - +
360A LEU* 1.3 76.5 - - - +
362A GLN* 1.3 62.3 + - - +
364A LEU* 3.9 6.5 - - - -
365A GLY* 3.0 19.6 + - - -
376A LEU* 6.4 0.2 - - - -
388A SER* 3.6 27.8 - - - -
389A LEU* 3.9 26.0 - - - -
392A THR* 3.3 31.1 + - - +
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Residues in contact with GLN 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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333A SER* 3.9 4.0 - - - +
358A ARG* 3.1 14.0 + - - +
359A GLU* 2.7 30.6 + - + +
361A CYS* 1.3 74.5 - - - +
363A GLY* 1.3 63.8 + - - +
365A GLY* 3.1 9.0 + - - -
366A GLN* 3.6 11.9 + - - +
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Residues in contact with GLY 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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333A SER* 3.0 34.4 + - - -
336A LEU* 3.9 1.7 - - - +
337A ALA* 3.5 23.9 - - - -
359A GLU 3.4 1.0 + - - -
360A LEU 3.9 1.3 - - - -
362A GLN* 1.3 79.1 - - - +
364A LEU* 1.3 62.0 + - - +
366A GLN* 3.2 21.4 + - - +
369A SER* 4.3 0.5 - - - -
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Residues in contact with LEU 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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336A LEU* 4.1 22.6 - - + +
360A LEU 3.1 16.1 + - - +
361A CYS* 3.9 3.8 - - - +
363A GLY* 1.3 76.7 - - - +
365A GLY* 1.3 57.1 + - - +
366A GLN 3.1 0.7 + - - -
369A SER* 2.9 31.3 + - - +
371A LEU* 3.8 29.2 - - + -
374A LEU* 4.3 16.2 - - + -
392A THR* 3.8 24.7 - - + -
396A ASN* 3.3 26.1 + - - +
399A LEU* 4.2 26.5 - - + -
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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