Contacts of the helix formed by residues 386 - 396 (chain B) in PDB entry 1PJQ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358B GLY* 4.6 0.7 - - - -
359B HIS* 2.8 67.3 + - + +
366B LEU* 5.6 0.2 - - - +
368B TRP* 4.9 5.2 - - - -
383B GLY 3.3 9.6 + - - +
384B LEU 3.2 0.2 - - - -
385B ASN* 1.3 85.6 - - + +
387B ALA* 1.3 55.6 + - - +
388B ALA 3.3 3.1 - - - -
389B THR* 3.7 30.8 - - + +
390B ILE* 2.7 50.7 + - + +
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B GLY 3.4 8.9 + - - +
384B LEU 3.8 9.0 - - - +
385B ASN 3.6 2.0 - - - -
386B GLN* 1.3 76.7 - - - +
388B ALA* 1.3 58.3 + - - +
390B ILE* 3.3 6.4 + - - +
391B GLN* 3.0 25.5 + - - +
426B LEU* 3.6 13.7 - - + +
427B GLY* 3.8 10.8 - - - +
430B ALA* 3.3 34.5 - - + -
439B ILE* 4.7 8.1 - - + -
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B ALA* 1.3 74.4 - - - +
389B THR* 1.3 56.9 + - - +
390B ILE 3.0 5.6 - - - -
391B GLN* 3.0 8.5 + - - +
392B GLU* 3.0 42.6 + - + +
427B GLY* 3.8 17.0 - - - -
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B TRP* 4.0 9.0 - - + -
386B GLN* 3.1 42.9 + - + +
388B ALA* 1.3 78.3 - - - +
390B ILE* 1.3 58.9 + - - +
392B GLU* 4.3 6.2 - - - +
393B LYS* 3.6 31.2 + - + +
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLY* 5.5 3.6 - - - -
366B LEU* 6.1 0.9 - - + -
368B TRP* 3.5 28.7 - - + -
380B PHE* 3.9 39.3 - - + -
383B GLY* 4.1 20.0 - - - +
386B GLN* 2.7 33.7 + - + +
387B ALA 3.5 3.8 - - - +
389B THR* 1.3 77.0 - - - +
391B GLN* 1.3 66.6 + - - +
392B GLU 3.4 0.2 - - - -
393B LYS 4.0 0.4 - - - -
394B LEU* 3.2 35.0 + - + +
426B LEU* 4.0 16.8 - - + -
439B ILE* 4.6 6.1 - - + -
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Residues in contact with GLN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B ALA 3.0 13.1 + - - +
388B ALA* 3.4 11.2 - - - +
390B ILE* 1.3 78.7 - - - +
392B GLU* 1.3 64.1 + - + +
394B LEU* 3.4 6.9 + - - +
395B ILE* 2.9 35.0 + - + +
423B LEU* 3.0 34.9 - - + +
424B THR* 3.1 25.7 + - - +
425B GLN 3.8 0.9 - - - -
426B LEU* 2.9 11.6 + - + -
427B GLY* 2.8 31.5 + - - -
428B GLU 4.4 0.5 + - - -
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Residues in contact with GLU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ALA* 3.0 25.0 + - + +
389B THR* 4.9 4.3 - - - +
391B GLN* 1.3 84.8 - - + +
393B LYS* 1.3 60.5 + - + +
394B LEU 3.2 2.6 + - - -
395B ILE* 3.7 8.0 - - + +
396B ALA* 3.1 27.6 + - - +
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Residues in contact with LYS 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B GLU* 4.7 11.1 + - - -
368B TRP* 3.0 58.7 - - + +
372B ALA* 4.9 0.3 - - - +
389B THR* 3.6 21.8 + - + +
390B ILE 3.7 2.5 + - - -
391B GLN 3.4 0.6 - - - -
392B GLU* 1.3 81.0 - - + +
394B LEU* 1.3 57.0 + - - +
396B ALA* 4.2 7.6 - - + -
397B PHE* 3.4 31.4 - - + +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B TRP* 3.2 38.6 - - + -
371B LEU* 5.0 6.5 - - + -
372B ALA* 3.7 17.0 - - + +
378B LEU* 4.2 15.3 - - + -
380B PHE* 4.9 5.2 - - + -
390B ILE* 3.2 25.8 + - + +
391B GLN 3.8 3.8 - - - +
392B GLU 3.1 1.0 - - - -
393B LYS* 1.3 78.1 - - - +
395B ILE* 1.3 66.9 + - - +
396B ALA 3.1 1.1 - - - -
397B PHE 3.3 6.8 + - - -
398B GLY 3.7 0.3 + - - -
399B MET* 3.1 52.0 + - + +
423B LEU* 4.2 13.9 - - + -
441B VAL* 4.4 11.7 - - + -
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Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B GLN* 2.9 37.5 - - + +
392B GLU* 3.7 9.2 - - + +
394B LEU* 1.3 73.2 - - - +
396B ALA* 1.3 66.6 + - - +
398B GLY* 3.4 10.1 + - - -
399B MET 3.0 24.5 - - - +
401B ALA* 3.8 21.8 - - + +
423B LEU* 3.5 19.7 - - + -
424B THR* 4.5 15.0 - - + -
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B GLU 3.1 20.9 + - - +
393B LYS* 4.2 9.9 - - + +
395B ILE* 1.3 80.9 - - - +
397B PHE* 1.3 65.2 + - + +
398B GLY 3.4 2.3 + - - -
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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