Contacts of the helix formed by residues 379 - 389 (chain A) in PDB entry 3QJQ
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 ALA 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 4.5 14.8 - - + -
378A THR* 1.3 73.6 - - - +
380A TRP* 1.3 59.0 + - - +
382A PRO* 3.0 13.2 - - - +
383A GLY 3.0 22.2 + - - -
439A LEU* 3.0 41.3 - - + +
442A ALA* 4.2 7.6 - - + -
443A GLY* 3.7 8.2 - - - +
447A VAL* 3.1 11.5 + - + +
449A ARG* 3.9 3.5 - - - +
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Residues in contact with TRP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLY* 4.0 12.7 + - - -
365A VAL* 4.1 17.0 - - + +
366A ASN* 3.5 25.9 + - - -
375A VAL* 3.8 27.8 - - + +
378A THR* 3.0 17.1 + - - +
379A ALA* 1.3 74.2 - - - +
381A VAL* 1.3 59.8 + - + +
384A HIS* 2.6 40.7 + - + +
439A LEU 3.3 9.7 + - - -
440A HIS* 3.4 41.5 + + + +
443A GLY* 3.7 2.9 - - - -
444A LEU* 3.8 31.0 - - + -
22C PHE* 3.8 38.1 - + - -
26C VAL* 4.1 14.6 - - + -
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ASN* 4.8 0.9 - - - +
375A VAL 3.7 22.4 - - - +
377A ASN* 4.1 12.1 - - - +
378A THR 3.8 6.5 - - - +
380A TRP* 1.3 83.8 - - + +
382A PRO* 1.4 62.4 - - + +
384A HIS* 3.4 6.2 - - + +
385A PHE* 2.7 37.7 + - + -
449A ARG* 4.8 8.3 - - - +
801A HAS 3.5 66.2 - - + +
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Residues in contact with PRO 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TYR* 6.2 0.2 - - + -
378A THR 3.1 13.0 - - - +
379A ALA* 3.0 22.0 - - + +
381A VAL* 1.4 90.5 - - + +
383A GLY* 1.4 52.0 + - - +
385A PHE* 3.2 25.8 + - + -
386A HIS* 2.8 48.6 + - - +
439A LEU* 4.1 11.9 - - + -
449A ARG* 4.0 17.7 - - + -
800A HEM 4.3 19.5 - - + +
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Residues in contact with GLY 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ALA 3.0 10.7 + - - -
380A TRP 3.5 3.4 - - - -
382A PRO* 1.4 76.9 - - - +
384A HIS* 1.3 65.1 + - - +
386A HIS* 3.5 6.7 + - - +
387A LEU* 3.5 11.1 + - - +
436A ALA* 4.2 6.3 - - - +
439A LEU* 3.6 26.3 - - - +
440A HIS* 3.1 22.9 - - - -
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Residues in contact with HIS 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLY* 3.0 31.7 + - - -
362A GLY* 3.9 2.0 - - - -
363A GLY* 3.3 20.2 + - - -
366A ASN* 3.5 16.8 - - - +
380A TRP* 2.6 27.1 + - + +
381A VAL* 3.4 5.2 - - - +
383A GLY* 1.3 73.8 - - - +
385A PHE* 1.3 78.6 + - - +
386A HIS 2.9 0.3 + - - -
387A LEU* 3.1 15.6 + - - +
388A GLN* 3.6 11.6 + - + +
440A HIS* 3.2 16.8 - - - +
801A HAS 2.3 69.7 + + + -
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Residues in contact with PHE 385 (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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381A VAL* 2.7 29.4 + - + -
382A PRO* 3.2 28.7 - - + -
384A HIS* 1.3 76.4 - - + +
386A HIS* 1.3 77.9 + + - +
388A GLN* 2.8 20.4 + - - +
389A VAL* 2.9 24.2 + - + +
449A ARG* 4.5 8.3 - - - -
800A HEM 3.3 58.1 - + + -
801A HAS 3.3 63.7 - + + -
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Residues in contact with HIS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PRO* 2.8 33.8 + - + +
383A GLY* 4.1 4.9 - - - +
384A HIS 2.9 0.4 + - - -
385A PHE* 1.3 79.9 - + - +
387A LEU* 1.3 56.8 + - - +
388A GLN 3.3 0.3 + - - -
390A ALA* 3.2 31.6 + - + +
391A SER* 2.8 34.2 + - - -
432A MET* 4.4 10.1 - - + +
435A MET* 3.6 22.5 - - + +
436A ALA* 6.0 2.7 - - + +
439A LEU* 4.7 1.2 - - + +
800A HEM 2.1 83.6 + + + -
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Residues in contact with LEU 387 (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 GLY* 3.1 31.0 - - - +
356A PHE* 4.1 3.1 + - - -
358A PRO* 3.8 15.3 - - + -
359A GLY* 3.5 26.5 - - - +
383A GLY 3.5 2.1 + - - +
384A HIS 3.1 8.3 + - - +
386A HIS* 1.3 78.0 - - - +
388A GLN* 1.3 67.3 + - - +
391A SER* 3.6 17.0 + - - -
392A LEU* 4.0 2.1 + - - +
432A MET* 5.0 3.1 - - + +
433A MET* 3.7 33.2 - - + +
436A ALA* 3.7 21.7 - - + +
440A HIS* 3.9 22.9 - - + -
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Residues in contact with GLN 388 (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 PHE* 3.0 33.0 - - + +
359A GLY* 3.0 37.6 - - - +
360A GLY* 3.4 4.7 + - - -
384A HIS* 3.7 15.9 - - + +
385A PHE* 2.8 13.1 + - - +
386A HIS 4.3 0.2 - - - -
387A LEU* 1.3 83.2 + - - +
389A VAL* 1.3 58.2 + - - +
392A LEU* 3.4 14.3 - - - +
393A VAL* 3.4 23.0 + - - +
801A HAS 3.5 55.7 - - + +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 5.3 1.3 - - + -
81A THR* 4.4 9.2 - - + -
239A TRP* 3.7 29.8 - - + -
385A PHE* 2.9 36.9 + - + +
388A GLN* 1.3 72.0 - - - +
390A ALA* 1.3 65.0 + - + +
391A SER 3.2 1.3 - - - -
393A VAL* 3.4 12.7 - - + +
394A THR* 2.7 34.5 + - - -
800A HEM 3.5 27.3 - - + +
801A HAS 3.6 18.2 - - + -
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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