Contacts of the helix formed by residues 364 - 376 (chain B) in PDB entry 2QUH
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 THR 364 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B THR 4.8 4.0 - - - +
363B ASP* 1.3 74.6 - - - +
365B ALA* 1.3 65.7 + - - +
366B LYS* 3.5 9.3 + - - +
367B GLN* 2.8 49.6 + - - +
368B ILE* 2.9 23.6 + - - +
446B GLN* 5.5 0.9 - - - +
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Residues in contact with ALA 365 (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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363B ASP 4.0 0.4 + - - -
364B THR* 1.3 71.7 - - - +
366B LYS* 1.3 61.9 + - - +
368B ILE* 3.4 6.8 + - - +
369B LYS* 3.1 13.9 + - - +
439B GLN* 3.1 42.7 - - + +
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Residues in contact with LYS 366 (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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364B THR* 3.1 8.0 + - - +
365B ALA* 1.3 78.9 - - - +
367B GLN* 1.3 56.8 + - + +
369B LYS* 3.1 10.6 + - - +
370B THR* 2.6 37.9 + - + +
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Residues in contact with GLN 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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362B THR 4.4 1.6 - - - +
363B ASP* 3.4 25.6 + - + +
364B THR* 2.8 53.3 + - - +
366B LYS* 1.3 76.1 - - + +
368B ILE* 1.3 56.8 + - - +
370B THR* 3.4 8.3 + - - +
371B LYS* 2.8 42.5 + - + +
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Residues in contact with ILE 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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359B ILE* 4.3 14.8 - - + -
363B ASP* 4.0 24.0 - - + +
364B THR 2.9 19.7 + - - +
365B ALA* 3.6 12.3 - - - +
367B GLN* 1.3 75.2 - - - +
369B LYS* 1.3 64.3 + - - +
371B LYS* 3.3 5.2 + - - +
372B VAL* 3.0 33.2 + - + +
435B ILE* 5.0 3.1 - - + -
438B LEU* 4.0 28.7 - - + -
439B GLN* 4.1 23.6 - - + +
442B ILE* 3.6 32.1 - - + -
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Residues in contact with LYS 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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365B ALA 3.1 10.3 + - - +
366B LYS* 3.4 11.4 - - - +
368B ILE* 1.3 80.6 - - - +
370B THR* 1.3 60.6 + - + +
373B ASN* 2.9 50.3 + - - +
435B ILE* 3.6 22.5 - - + +
439B GLN* 3.9 11.8 + - - +
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Residues in contact with THR 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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366B LYS* 2.6 34.3 - - + +
367B GLN* 3.8 8.1 + - - +
369B LYS* 1.3 77.6 - - + +
371B LYS* 1.3 61.9 + - - +
373B ASN* 4.5 5.6 - - - +
374B LYS* 2.9 36.2 + - - +
375B HIS* 4.6 0.5 - - - -
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Residues in contact with LYS 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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343B LEU* 4.1 16.5 - - + +
355B PRO 3.5 15.5 - - - +
356B ASN* 5.1 3.6 - - - +
358B SER 2.9 29.1 + - - +
359B ILE* 4.2 8.5 - - + -
360B PHE* 4.4 6.4 - - - -
363B ASP* 2.7 37.4 + - - +
367B GLN* 2.8 30.9 + - + +
368B ILE* 3.7 4.0 - - - +
369B LYS 3.2 0.4 - - - -
370B THR* 1.3 75.6 - - - +
372B VAL* 1.3 63.3 + - - +
375B HIS* 2.8 46.8 + - + +
376B ALA 3.5 1.4 + - - -
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Residues in contact with VAL 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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343B LEU* 4.8 3.6 - - + -
359B ILE* 4.1 20.9 - - + -
368B ILE* 3.0 21.9 + - + +
369B LYS 3.7 0.2 - - - +
371B LYS* 1.3 76.7 - - - +
373B ASN* 1.3 61.8 + - - +
376B ALA* 3.0 35.2 + - + +
399B SER* 4.1 4.7 - - - +
431B LYS* 3.2 28.6 + - + +
434B LEU* 4.1 26.5 - - + -
435B ILE* 3.6 27.8 - - + -
438B LEU* 4.3 7.4 - - + -
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Residues in contact with ASN 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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369B LYS* 2.9 49.4 + - - +
370B THR* 4.3 4.4 - - - +
372B VAL* 1.3 77.2 - - - +
374B LYS* 1.3 58.8 + - + +
428B GLY* 5.0 1.2 - - - +
431B LYS* 3.1 43.4 + - - +
432B LYS* 5.0 0.7 + - - -
435B ILE* 3.7 9.0 - - - +
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Residues in contact with LYS 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 THR* 2.9 27.2 + - - +
373B ASN* 1.3 75.1 - - + +
375B HIS* 1.3 78.7 + - + +
376B ALA 5.5 0.2 - - - -
431B LYS* 5.5 0.2 - - - -
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Residues in contact with HIS 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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343B LEU* 3.0 34.0 - - + +
344B GLN* 4.1 11.7 + - - +
356B ASN* 3.5 44.2 + - - +
370B THR* 4.6 0.7 - - - -
371B LYS* 2.8 36.4 + - + +
374B LYS* 1.3 93.6 + - + +
376B ALA* 1.3 63.2 + - - +
377B PHE* 3.0 2.3 + - - -
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Residues in contact with ALA 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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343B LEU* 3.6 17.9 - - + +
371B LYS 3.5 2.6 + - - -
372B VAL* 3.0 28.1 + - + +
374B LYS 5.5 0.3 - - - -
375B HIS* 1.3 74.0 - - - +
377B PHE* 1.3 66.3 + - - +
378B SER* 3.4 2.4 + - - -
398B VAL* 4.7 2.2 - - + -
399B SER* 3.2 32.3 - - - +
431B LYS* 3.4 17.3 + - - -
434B LEU* 5.5 1.1 - - + -
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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