Contacts of the helix formed by residues 385 - 396 (chain W) in PDB entry 2Q4G
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 SER 385 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354W ASP* 2.9 33.8 + - - -
357W VAL* 3.8 14.8 - - - +
358W ARG* 3.0 29.6 - - - +
381W VAL* 3.2 21.0 - - - +
382W SER 3.8 0.2 + - - -
383W ASP 3.4 0.2 - - - -
384W SER* 1.3 76.1 - - - +
386W CYS* 1.3 60.1 + - - +
387W SER 3.4 1.1 - - - -
388W SER* 3.6 4.2 - - - -
389W LEU* 3.5 22.5 + - - +
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Residues in contact with CYS 386 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382W SER 3.2 21.3 - - - -
383W ASP* 2.8 15.8 + - - +
385W SER* 1.3 77.4 - - - +
387W SER* 1.3 63.2 + - - +
388W SER 3.2 0.4 - - - -
389W LEU* 3.5 15.2 + - - +
390W ALA* 3.1 22.2 + - - +
409W LEU* 3.4 23.1 - - - -
413W GLY* 3.6 35.9 - - - +
416W GLN* 3.9 4.6 - - - +
417W LEU* 4.0 11.0 - - + +
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Residues in contact with SER 387 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358W ARG* 4.4 3.3 + - - -
384W SER 3.9 10.0 + - - -
385W SER 3.4 0.2 - - - -
386W CYS* 1.3 76.0 - - - +
388W SER* 1.3 70.2 + - - +
390W ALA* 3.0 8.9 + - - +
391W ALA* 2.9 21.9 + - - +
416W GLN* 3.1 24.9 + - - -
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Residues in contact with SER 388 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358W ARG* 3.2 34.3 + - - +
361W CYS* 4.0 21.1 - - - -
385W SER 3.6 10.7 + - - -
387W SER* 1.3 82.7 + - - +
389W LEU* 1.3 54.6 + - - +
391W ALA* 2.8 9.2 + - - +
392W THR* 2.7 38.2 + - - -
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Residues in contact with LEU 389 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357W VAL* 4.4 5.4 - - + -
361W CYS* 3.5 23.3 - - - -
374W LEU* 5.4 2.9 - - + -
376W LEU* 4.3 19.5 - - + -
381W VAL* 4.5 3.6 - - + -
385W SER* 3.5 24.6 + - - +
386W CYS* 3.5 16.5 + - - +
387W SER 3.4 0.4 - - - -
388W SER* 1.3 77.9 - - - +
390W ALA* 1.3 61.5 + - - +
392W THR* 3.4 5.3 + - + -
393W LEU* 3.1 34.5 + - + +
402W LEU* 4.6 18.2 - - + -
404W LEU* 4.1 27.1 - - + -
417W LEU* 3.6 15.0 - - + -
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Residues in contact with ALA 390 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386W CYS 3.1 12.1 + - - +
387W SER* 3.0 12.1 + - - +
389W LEU* 1.3 79.5 - - - +
391W ALA* 1.3 58.9 + - - +
393W LEU* 3.7 6.6 + - - -
394W LEU* 3.6 6.4 - - - +
416W GLN* 3.1 36.6 - - + +
417W LEU* 4.0 2.8 - - - +
420W SER* 2.3 35.1 + - - +
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Residues in contact with ALA 391 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387W SER 2.9 10.1 + - - +
388W SER* 2.8 13.1 + - - +
390W ALA* 1.3 70.2 - - - +
392W THR* 1.3 62.1 + - - +
393W LEU 3.1 1.6 - - - -
394W LEU* 2.8 26.6 + - - +
395W ALA* 2.9 16.1 + - + +
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Residues in contact with THR 392 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361W CYS* 3.4 32.5 + - + +
364W LEU* 3.8 40.2 - - + -
365W GLY* 4.2 7.9 - - - +
388W SER* 2.7 22.5 + - - -
389W LEU* 3.7 10.1 - - + -
391W ALA* 1.3 72.1 - - - +
393W LEU* 1.3 60.1 + - + +
395W ALA* 4.4 6.5 - - - +
396W ASN* 2.9 32.4 + - + +
399W LEU* 6.0 0.7 - - + -
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Residues in contact with LEU 393 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389W LEU* 3.1 22.7 + - + +
390W ALA* 3.8 11.7 - - - +
391W ALA 3.1 0.6 - - - -
392W THR* 1.3 76.7 - - + +
394W LEU* 1.3 58.6 + - - +
396W ASN* 3.7 10.8 - - - +
397W HIS* 5.1 0.7 + - - -
399W LEU* 4.2 18.2 - - + -
402W LEU* 4.3 17.5 - - + -
417W LEU* 4.3 12.1 - - + +
420W SER* 4.3 4.9 - - - -
421W VAL* 4.1 17.9 - - + -
426W CYS* 3.1 33.9 - - - +
427W LEU 4.8 1.0 + - - -
428W LEU* 3.7 39.0 - - + -
431W LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 394 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390W ALA 3.6 11.9 - - - +
391W ALA* 2.8 12.3 + - - +
393W LEU* 1.3 83.7 - - - +
395W ALA* 1.3 58.3 + - - +
397W HIS* 3.0 25.3 + - - -
420W SER* 3.5 37.9 - - - +
423W GLN* 4.1 27.8 - - + +
425W GLY* 5.1 2.0 - - - -
426W CYS* 4.0 13.0 - - + +
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Residues in contact with ALA 395 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365W GLY* 4.2 20.2 - - - +
367W PRO* 6.0 1.6 - - - +
391W ALA* 2.9 15.4 + - + +
392W THR* 4.1 4.7 - - - +
394W LEU* 1.3 76.1 - - - +
396W ASN* 1.3 60.6 + - - +
397W HIS* 2.9 19.1 + - - -
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Residues in contact with ASN 396 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364W LEU* 3.2 38.4 + - + +
365W GLY* 4.5 1.8 - - - -
366W GLN 5.7 0.9 - - - -
367W PRO* 6.5 0.4 - - - -
369W SER* 2.7 29.2 + - - -
392W THR* 2.9 20.6 + - + +
393W LEU* 3.7 13.3 - - - +
395W ALA* 1.3 79.1 - - - +
397W HIS* 1.3 62.8 + - - +
398W SER* 3.1 18.0 + - - +
399W LEU* 3.0 33.3 + - - +
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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