Contacts of the helix formed by residues 386 - 397 (chain A) in PDB entry 1PJS
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 GLN 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A THR 5.3 0.4 + - - -
358A GLY* 4.2 26.9 - - - -
365A GLU* 3.9 19.5 + - - +
366A LEU* 6.0 3.2 - - - +
368A TRP* 5.6 8.3 - - - -
383A GLY* 3.3 14.9 + - - +
385A ASN* 1.3 77.7 - - - +
387A ALA* 1.3 62.2 + - - +
388A ALA 3.4 2.7 - - - -
389A THR* 2.9 47.9 + - + +
390A ILE* 3.2 17.2 - - + +
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Residues in contact with ALA 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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383A GLY 3.2 10.1 + - - +
384A LEU 3.6 18.8 - - - +
385A ASN 3.3 1.0 - - - -
386A GLN* 1.3 77.3 - - - +
388A ALA* 1.3 65.3 + - - +
390A ILE* 3.3 16.5 + - - +
391A GLN* 3.5 9.4 + - - +
426A LEU* 3.7 27.4 - - + +
427A GLY* 4.4 1.3 + - - -
430A ALA* 3.7 21.5 - - + -
439A ILE* 4.2 5.8 - - + -
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Residues in contact with ALA 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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385A ASN 5.2 0.8 - - - -
386A GLN* 3.4 1.0 - - - +
387A ALA* 1.3 78.3 - - - +
389A THR* 1.3 63.3 + - + +
391A GLN* 3.5 7.7 - - - +
392A GLU* 3.2 28.8 + - - +
427A GLY* 4.2 16.9 - - - -
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Residues in contact with THR 389 (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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365A GLU* 5.3 3.4 + - - -
368A TRP* 4.3 7.0 - - - -
385A ASN 5.8 0.2 - - - +
386A GLN* 2.9 42.5 + - + +
387A ALA 3.2 0.2 - - - -
388A ALA* 1.3 78.4 - - + +
390A ILE* 1.3 61.2 + - - +
392A GLU* 4.4 8.3 - - - +
393A LYS* 2.9 44.5 + - - +
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Residues in contact with ILE 390 (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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368A TRP* 3.7 26.9 - - + -
380A PHE* 3.5 44.9 - - + -
383A GLY* 4.7 8.3 - - - +
386A GLN* 3.2 24.0 - - + +
387A ALA* 3.3 15.0 + - + +
388A ALA 3.2 0.6 - - - -
389A THR* 1.3 78.0 - - - +
391A GLN* 1.3 55.4 + - - +
393A LYS* 4.0 0.5 - - - +
394A LEU* 2.7 61.2 + - + +
426A LEU* 4.3 8.5 - - + -
439A ILE* 5.3 7.0 - - + -
441A VAL* 5.5 0.7 - - + -
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Residues in contact with GLN 391 (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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387A ALA 3.5 6.7 + - - +
388A ALA* 3.5 12.0 - - - +
390A ILE* 1.3 79.1 - - - +
392A GLU* 1.3 66.6 + - + +
394A LEU* 4.2 0.2 - - - -
395A ILE* 2.8 48.5 + - - +
423A LEU* 2.7 41.6 + - + +
424A THR* 3.3 23.6 + - - +
425A GLN 4.1 0.3 - - - -
426A LEU* 3.5 19.2 + - + -
427A GLY* 2.9 26.1 + - - -
428A GLU* 4.6 1.4 + - - +
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Residues in contact with GLU 392 (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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388A ALA 3.2 16.6 + - - +
389A THR* 4.4 7.5 - - - +
391A GLN* 1.3 83.6 - - + +
393A LYS* 1.3 73.4 + - - +
395A ILE* 4.1 4.8 - - - +
396A ALA* 3.1 28.5 + - + +
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Residues in contact with LYS 393 (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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365A GLU* 5.1 7.0 - - - +
368A TRP* 3.5 46.7 - - + +
389A THR* 2.9 31.7 + - - +
392A GLU* 1.3 98.5 + - - +
394A LEU* 1.3 60.8 + - - +
396A ALA* 3.2 4.6 + - + +
397A PHE* 2.8 48.0 + - + +
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Residues in contact with LEU 394 (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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368A TRP* 4.2 15.5 - - + +
371A LEU* 3.6 13.9 - - + +
372A ALA* 3.5 35.6 - - + +
378A LEU* 4.4 6.5 - - + -
390A ILE* 2.7 49.9 + - + +
391A GLN* 4.1 3.6 - - - +
393A LYS* 1.3 73.9 - - - +
395A ILE* 1.3 60.3 + - - +
397A PHE* 3.4 1.1 + - - -
398A GLY 3.4 5.7 + - - -
399A MET* 2.8 53.4 + - + +
423A LEU* 4.2 11.0 - - + -
426A LEU* 5.1 0.2 - - + -
441A VAL* 4.5 12.8 - - + -
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Residues in contact with ILE 395 (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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391A GLN* 2.8 51.0 + - - +
392A GLU* 4.1 4.3 - - - +
394A LEU* 1.3 75.3 - - - +
396A ALA* 1.3 62.3 + - - +
398A GLY* 3.4 9.5 + - - -
399A MET 3.5 15.2 + - - +
401A ALA* 4.6 7.9 - - + +
423A LEU* 3.8 25.6 - - + -
424A THR* 4.2 19.7 - - + -
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Residues in contact with ALA 396 (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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392A GLU* 3.1 21.4 + - + +
393A LYS* 3.5 10.3 - - + +
394A LEU 3.2 0.2 - - - -
395A ILE* 1.3 80.4 - - - +
397A PHE* 1.3 66.5 + - + +
398A GLY 3.1 3.3 + - - -
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Residues in contact with PHE 397 (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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367A ASP* 5.3 1.3 - - - -
368A TRP* 3.5 40.4 - + + +
369A GLU* 3.2 50.3 - - + +
372A ALA* 3.9 10.9 - - + +
393A LYS* 2.8 36.9 + - + +
394A LEU 3.4 2.2 + - - -
395A ILE 3.3 0.2 - - - -
396A ALA* 1.3 82.2 - - + +
398A GLY* 1.3 56.1 + - - +
399A MET 3.9 0.2 - - - -
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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