Contacts of the helix formed by residues 368 - 383 (chain A) in PDB entry 1QZ2
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 ASP 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A ILE* 5.4 0.9 - - - +
363A HIS* 2.7 39.5 + - + +
366A VAL* 3.2 20.0 - - + +
367A ASN* 1.3 71.6 - - - +
369A PHE* 1.3 58.1 + - - +
370A GLU* 3.4 6.0 - - - +
371A LEU* 3.4 27.4 + - + +
372A ALA* 2.8 28.8 + - - +
3C HIS* 5.0 6.8 - - - +
145C GLU* 4.2 16.0 - - - +
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Residues in contact with PHE 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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364A LEU* 3.5 30.1 - - + -
367A ASN* 3.1 48.3 + - + -
368A ASP* 1.3 73.1 - - - +
370A GLU* 1.3 60.0 + - - +
372A ALA* 2.9 6.5 + - - +
373A ARG* 2.6 35.7 + - - +
396A CYS* 4.3 7.0 - - - +
399A ARG* 3.6 54.1 - - + -
400A ILE* 3.6 21.5 - - + -
403A GLN* 4.0 28.7 - - + -
3C HIS* 4.6 3.1 - + - -
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Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASN 4.9 1.9 - - - +
368A ASP* 4.4 3.8 - - - +
369A PHE* 1.3 84.3 + - - +
371A LEU* 1.3 67.1 + - + +
373A ARG* 3.0 27.4 + - - +
374A ALA* 2.9 21.4 + - - +
400A ILE* 4.3 12.1 - - + +
403A GLN* 3.3 24.0 + - - +
3C HIS* 5.8 1.4 - - - -
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Residues in contact with LEU 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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363A HIS* 3.1 40.8 + - + +
368A ASP* 3.4 33.2 + - - +
369A PHE 3.4 0.4 - - - -
370A GLU* 1.3 79.7 - - + +
372A ALA* 1.3 61.1 + - - +
374A ALA* 3.3 11.4 + - + +
375A ASP* 3.2 19.4 + - - +
145C GLU* 6.1 0.2 - - - +
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Residues in contact with ALA 372 (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 GLY* 3.7 23.1 - - - +
363A HIS* 3.7 7.5 - - - +
364A LEU* 3.9 11.7 - - + +
368A ASP 2.8 15.0 + - - +
369A PHE* 3.2 9.6 - - - +
371A LEU* 1.3 73.6 - - - +
373A ARG* 1.3 68.5 + - - +
375A ASP* 2.7 15.3 + - - +
376A PHE* 2.9 18.2 + - + -
396A CYS* 3.9 16.4 - - - -
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Residues in contact with ARG 373 (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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369A PHE 2.6 16.0 + - - +
370A GLU* 3.2 24.1 + - - +
372A ALA* 1.3 71.4 - - - +
374A ALA* 1.3 58.4 + - - +
376A PHE* 4.7 2.2 - - - +
377A GLN* 2.7 46.5 + - + +
393A LEU* 4.6 14.5 - - + +
396A CYS* 4.0 12.7 - - + -
397A GLN* 3.9 23.3 + - - +
400A ILE* 3.7 39.3 - - + +
421B GLU* 5.9 0.8 + - - -
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Residues in contact with ALA 374 (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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370A GLU 2.9 11.0 + - - +
371A LEU* 3.3 16.2 - - + +
372A ALA 3.0 0.2 - - - -
373A ARG* 1.3 78.1 - - - +
375A ASP* 1.3 60.6 + - - +
377A GLN* 3.7 14.0 - - - +
378A LYS* 3.0 29.6 + - - +
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Residues in contact with ASP 375 (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 LEU* 3.6 24.3 - - - +
359A ARG* 2.5 65.1 + - - +
360A GLY* 3.7 10.8 - - - -
363A HIS* 3.6 8.2 + - - -
371A LEU 3.2 6.7 + - - +
372A ALA 2.7 12.7 + - - +
374A ALA* 1.3 74.5 - - - +
376A PHE* 1.3 60.1 + - - +
378A LYS* 3.4 6.3 + - - +
379A VAL* 3.0 33.4 + - - +
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Residues in contact with PHE 376 (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 PHE* 4.0 32.1 - + - -
360A GLY* 3.4 31.4 - - - -
361A GLU* 3.2 29.6 - - - -
364A LEU* 4.2 12.3 - - + -
372A ALA* 2.9 21.6 + - + +
373A ARG 4.1 1.6 - - - +
375A ASP* 1.3 75.1 - - - +
377A GLN* 1.3 67.1 + - - +
378A LYS 3.0 1.7 + - - -
379A VAL* 3.1 3.2 + - - +
380A LEU* 3.0 31.6 + - - +
389A ALA* 3.9 22.4 - - - +
392A GLN* 3.4 28.3 - - + -
393A LEU* 4.1 9.4 - - + -
396A CYS* 3.9 14.1 - - - -
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Residues in contact with GLN 377 (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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373A ARG* 2.7 29.9 + - + +
374A ALA* 3.7 14.2 - - - +
376A PHE* 1.3 76.6 - - - +
378A LYS* 1.3 62.1 + - - +
380A LEU* 3.8 3.6 + - - +
381A GLN* 3.5 22.7 + - - +
393A LEU* 4.1 20.1 - - + +
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Residues in contact with LYS 378 (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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350A SER* 3.4 21.9 + - - -
351A ASN* 4.8 1.7 + - - -
356A LEU* 3.4 31.7 - - + +
374A ALA 3.0 18.0 + - - +
375A ASP* 3.9 5.8 - - - +
376A PHE 3.0 0.2 - - - -
377A GLN* 1.3 78.7 - - - +
379A VAL* 1.3 65.6 + - - +
380A LEU 3.1 1.6 - - - -
381A GLN* 3.2 22.9 + - - +
382A LEU* 3.1 36.2 + - + +
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Residues in contact with VAL 379 (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* 4.2 6.1 - - + +
356A LEU* 3.6 31.0 - - + -
357A PHE* 3.7 28.9 - - + +
375A ASP 3.0 21.9 + - - +
376A PHE* 3.1 5.8 + - - +
378A LYS* 1.3 76.6 - - - +
380A LEU* 1.3 51.6 + - - +
382A LEU* 3.4 0.7 + - - -
383A TYR* 2.7 45.6 + - + +
386A ASN* 3.7 32.1 - - + +
389A ALA* 3.9 6.3 - - + -
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Residues in contact with LEU 380 (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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376A PHE 3.0 30.7 + - - +
377A GLN* 3.9 6.1 - - - +
379A VAL* 1.3 74.7 - - - +
381A GLN* 1.3 66.7 + - - +
383A TYR 3.8 2.7 - - - +
384A PRO* 2.9 53.9 - - + +
386A ASN 4.2 4.0 - - - +
389A ALA* 3.1 45.1 - - + +
390A LYS* 3.6 17.7 - - + +
393A LEU* 4.0 16.2 - - + -
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Residues in contact with GLN 381 (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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377A GLN* 3.5 12.4 + - - +
378A LYS* 3.2 27.9 + - - +
380A LEU* 1.3 80.5 - - - +
382A LEU* 1.3 77.7 + - + +
384A PRO* 4.3 7.6 - - - +
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Residues in contact with LEU 382 (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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351A ASN* 2.9 52.9 - - + +
356A LEU* 4.5 11.4 - - + -
378A LYS* 3.1 20.7 + - + +
379A VAL* 5.0 0.2 - - - -
381A GLN* 1.3 107.2 - - + +
383A TYR* 1.3 84.7 + - + +
384A PRO* 3.8 4.9 - - - +
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Residues in contact with TYR 383 (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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349A ASP* 5.4 0.2 + - - -
351A ASN* 3.1 30.6 + - - +
352A ASN* 4.4 0.9 - - - -
353A GLU* 2.9 53.9 + - + +
356A LEU* 5.9 1.1 - - + -
379A VAL* 2.7 25.8 + - + +
380A LEU* 3.1 5.9 - - - +
382A LEU* 1.3 100.9 - - + +
384A PRO* 1.3 67.2 - - - +
385A ASN 3.2 3.8 - - - +
386A ASN* 3.2 26.6 + - + +
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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