Contacts of the helix formed by residues 366 - 376 (chain B) in PDB entry 1QAS
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 PHE 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B LEU* 3.9 14.8 - - + -
344B CYS* 3.6 34.1 - - + -
352B PRO* 3.1 34.5 + - + +
353B ILE* 4.1 1.1 - - - +
354B ILE* 3.9 20.4 - - + -
364B ILE 3.7 2.2 + - - -
365B LEU* 1.3 70.7 - - - +
367B CYS* 1.3 63.9 + - - +
369B VAL* 3.4 3.5 + - - +
370B LEU* 3.1 47.0 + - + +
389B LEU* 4.3 3.6 - - + -
401B MET* 3.5 43.3 - - + -
404B HIS* 4.0 14.6 - + + -
405B LEU* 3.9 20.9 - - + -
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Residues in contact with CYS 367 (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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351B GLU* 4.7 8.0 + - - -
352B PRO 4.9 0.4 + - - -
365B LEU* 3.2 23.5 - - - -
366B PHE* 1.3 85.8 - - - +
368B ASP* 1.3 64.3 + - - +
370B LEU* 3.3 1.3 + - - -
371B ARG* 3.0 52.5 + - - +
404B HIS* 3.6 36.2 - - + +
408B ILE* 3.2 18.6 - - + +
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Residues in contact with ASP 368 (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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494A ASP* 4.9 12.1 - - - +
326B THR* 3.8 17.2 - - + +
364B ILE* 5.7 1.1 - - + +
365B LEU* 3.2 38.5 + - + +
367B CYS* 1.3 74.9 - - - +
369B VAL* 1.3 65.3 + - - +
371B ARG* 2.9 38.2 + - - +
372B ALA* 3.0 13.3 + - - +
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Residues in contact with VAL 369 (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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326B THR* 3.8 10.1 - - + +
329B TYR* 3.7 33.0 - - + -
342B LEU* 4.0 7.9 - - + -
354B ILE* 3.8 20.4 - - + -
364B ILE* 3.3 34.8 - - + -
365B LEU 3.1 9.5 + - - +
366B PHE 3.5 7.9 - - - +
368B ASP* 1.3 79.9 - - - +
370B LEU* 1.3 57.1 + - - +
372B ALA* 3.5 3.0 + - - +
373B ILE* 3.0 44.2 + - + +
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Residues in contact with LEU 370 (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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342B LEU* 4.2 15.9 - - + -
366B PHE* 3.1 41.0 + - + +
367B CYS 3.6 8.1 - - - +
368B ASP 3.1 0.6 - - - -
369B VAL* 1.3 72.8 - - - +
371B ARG* 1.3 61.4 + - - +
373B ILE* 3.9 5.2 - - + +
374B ARG* 2.9 28.8 + - - +
387B LEU* 4.0 21.1 - - + -
404B HIS* 3.7 10.1 - - + +
405B LEU* 3.5 46.4 - - + +
408B ILE* 3.6 13.7 - - + +
409B LEU* 4.0 11.9 - - + +
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Residues in contact with ARG 371 (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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367B CYS* 3.0 45.3 + - - +
368B ASP* 2.9 35.2 + - - +
370B LEU* 1.3 73.8 - - - +
372B ALA* 1.3 65.5 + - - +
374B ARG* 3.3 19.1 + - - +
375B ASP* 3.0 32.1 + - - +
404B HIS* 5.0 4.9 - - - -
408B ILE* 3.8 28.3 - - + +
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Residues in contact with ALA 372 (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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326B THR* 3.8 27.4 - - - +
329B TYR* 4.9 3.6 - - + -
330B ILE* 4.0 23.3 - - + -
333B LEU* 5.0 0.7 - - - -
368B ASP 3.0 10.7 + - - +
369B VAL* 3.7 8.7 - - - +
371B ARG* 1.3 76.6 - - - +
373B ILE* 1.3 62.3 + - - +
375B ASP* 3.2 7.0 + - - -
376B TYR* 3.1 30.7 + - - +
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Residues in contact with ILE 373 (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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329B TYR* 3.9 24.7 - - + -
333B LEU* 3.9 8.3 - - + -
340B LEU* 3.9 16.4 - - + -
342B LEU* 4.3 2.7 - - + -
369B VAL* 3.0 34.9 + - + +
370B LEU* 3.9 7.6 - - + +
372B ALA* 1.3 74.8 - - - +
374B ARG* 1.3 59.1 + - - +
377B ALA* 2.9 39.9 + - + +
385B VAL* 4.8 1.3 - - + -
387B LEU* 3.9 39.0 - - + -
409B LEU* 4.8 2.2 - - + -
435B ILE* 4.1 21.3 - - + -
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Residues in contact with ARG 374 (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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370B LEU 2.9 19.3 + - - +
371B ARG* 3.5 21.2 + - - +
372B ALA 3.2 0.4 - - - -
373B ILE* 1.3 77.3 - - - +
375B ASP* 1.3 93.9 + - - +
377B ALA* 4.1 9.8 + - - +
378B PHE* 5.4 1.4 + - - -
408B ILE* 3.3 33.4 + - + +
409B LEU* 4.0 14.6 - - + +
412B ILE* 4.0 27.5 - - + +
435B ILE* 5.3 0.4 - - - -
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Residues in contact with ASP 375 (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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371B ARG* 3.0 20.0 + - - +
372B ALA* 3.5 6.6 - - - +
374B ARG* 1.3 111.0 + - - +
376B TYR* 1.3 71.6 - - + +
377B ALA 3.7 0.2 - - - -
378B PHE 5.3 0.3 + - - -
379B LYS* 2.6 31.0 + - - +
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Residues in contact with TYR 376 (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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330B ILE* 3.6 43.3 - - + +
333B LEU* 3.7 29.5 - - + +
334B CYS* 3.6 25.8 - - - -
372B ALA* 3.1 19.8 + - - +
375B ASP* 1.3 90.3 - - + +
377B ALA* 1.3 65.7 + - - +
378B PHE 3.1 4.1 + - - -
379B LYS* 3.2 39.2 + - + +
380B ALA 4.6 1.2 + - - -
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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