Contacts of the helix formed by residues 334 - 347 (chain A) in PDB entry 1QSA
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 ARG 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A LEU* 2.9 36.7 + - + +
330A LEU* 5.0 0.4 - - - -
332A ARG* 4.3 14.6 - - + +
333A GLY* 1.3 79.6 - - - +
335A GLU* 1.3 63.3 + - - +
336A ALA 3.5 1.8 - - - -
337A GLU* 3.2 32.6 + - + +
338A ALA* 3.1 24.2 + - - +
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Residues in contact with GLU 335 (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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330A LEU* 4.6 11.4 - - + +
333A GLY 3.3 7.0 + - - +
334A ARG* 1.3 74.3 - - - +
336A ALA* 1.3 58.6 + - - +
338A ALA* 3.4 1.4 + - - +
339A LYS* 2.9 70.9 + - + +
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Residues in contact with ALA 336 (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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334A ARG 3.5 0.4 - - - -
335A GLU* 1.3 80.5 - - - +
337A GLU* 1.3 63.1 + - - +
339A LYS* 3.9 2.5 - - - +
340A GLU* 3.0 26.0 + - - +
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Residues in contact with GLU 337 (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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325A GLN* 4.9 3.5 + - - -
329A LEU* 3.7 29.1 - - + +
334A ARG* 3.2 45.8 + - + +
335A GLU 3.4 0.4 - - - -
336A ALA* 1.3 79.5 - - - +
338A ALA* 1.3 63.6 + - - +
340A GLU* 3.5 5.6 + - - +
341A ILE* 3.4 26.1 + - + +
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Residues in contact with ALA 338 (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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326A ALA* 3.5 29.4 - - + +
329A LEU* 3.7 14.3 - - + +
330A LEU* 3.5 22.7 - - + -
334A ARG 3.1 18.6 + - - +
335A GLU 3.8 0.2 - - - +
337A GLU* 1.3 77.8 - - - +
339A LYS* 1.3 58.2 + - - +
341A ILE* 3.1 7.7 + - - +
342A LEU* 3.0 29.2 + - - +
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Residues in contact with LYS 339 (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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330A LEU* 4.2 18.2 - - + -
335A GLU* 2.9 55.4 + - + +
336A ALA* 4.3 3.1 - - - +
338A ALA* 1.3 74.3 - - - +
340A GLU* 1.3 59.4 + - - +
342A LEU* 3.8 6.5 - - + +
343A HIS* 2.8 50.0 + - + +
360A ILE* 4.1 28.6 - - + +
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Residues in contact with GLU 340 (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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336A ALA 3.0 18.3 + - - +
337A GLU* 3.8 6.5 - - - +
338A ALA 3.2 0.2 - - - -
339A LYS* 1.3 73.8 - - - +
341A ILE* 1.3 61.7 + - + +
343A HIS* 3.3 10.3 + - - +
344A GLN* 2.9 62.2 + - + +
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Residues in contact with ILE 341 (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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322A ARG* 3.4 44.1 + - + +
325A GLN* 4.0 17.9 - - + -
326A ALA* 4.0 11.2 - - + +
329A LEU* 3.9 28.3 - - + -
337A GLU* 3.5 12.3 - - + +
338A ALA 3.1 7.1 + - - +
340A GLU* 1.3 79.9 - - + +
342A LEU* 1.3 57.9 + - - +
344A GLN* 3.2 8.0 + - - +
345A LEU* 2.9 31.4 + - + +
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Residues in contact with LEU 342 (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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323A TYR* 3.7 32.8 - - + -
326A ALA* 3.8 14.8 - - + -
330A LEU* 4.3 16.4 - - + -
338A ALA 3.0 17.6 + - - +
339A LYS* 3.8 10.8 - - + +
341A ILE* 1.3 75.8 - - - +
343A HIS* 1.3 56.6 + - - +
345A LEU* 3.2 8.3 + - + +
346A MET* 3.0 33.3 + - - +
356A ALA* 3.6 16.9 - - + +
359A ARG* 4.2 16.4 - - + -
360A ILE* 3.2 37.5 - - + -
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Residues in contact with HIS 343 (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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339A LYS* 2.8 36.1 + - + +
340A GLU* 3.8 15.2 + - - +
341A ILE 3.3 0.2 - - - -
342A LEU* 1.3 76.9 - - - +
344A GLN* 1.3 64.2 + - - +
346A MET* 3.4 18.6 + - + +
347A GLN* 3.5 18.4 + - - +
360A ILE* 3.4 15.2 - - + +
362A GLU* 2.9 40.7 + - - -
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Residues in contact with GLN 344 (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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322A ARG* 3.3 23.7 + - - +
340A GLU* 2.9 42.7 + - + +
341A ILE* 3.2 3.8 + - - +
343A HIS* 1.3 78.3 - - - +
345A LEU* 1.3 62.9 + - - +
347A GLN* 3.1 52.8 + - - +
348A GLN* 3.8 10.6 - - - +
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Residues in contact with LEU 345 (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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319A ASP* 3.9 32.3 - - + +
322A ARG* 3.6 28.7 - - + +
323A TYR* 3.9 37.9 - - + +
341A ILE* 2.9 19.1 + - + +
342A LEU* 3.2 11.0 + - + +
344A GLN* 1.3 77.8 - - - +
346A MET* 1.3 57.4 + - - +
348A GLN* 2.9 25.1 + - - +
352A TYR* 4.7 5.8 - - + +
353A PRO* 3.0 25.2 - - + +
356A ALA* 4.0 18.2 - - + -
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Residues in contact with MET 346 (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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342A LEU 3.0 12.7 + - - +
343A HIS* 3.6 20.0 - - + +
344A GLN 3.3 0.2 - - - -
345A LEU* 1.3 75.8 - - - +
347A GLN* 1.3 59.8 + - + +
348A GLN 3.1 2.5 + - - +
353A PRO* 3.8 11.9 - - - +
356A ALA* 4.0 0.7 - - + -
357A ALA* 3.6 37.0 - - + +
360A ILE* 3.4 30.3 - - - -
362A GLU* 3.5 32.3 - - + +
363A GLU 4.0 11.2 - - - +
364A TYR* 3.5 21.8 - - + -
365A GLU* 4.7 8.7 + - + +
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Residues in contact with GLN 347 (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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343A HIS* 3.5 13.2 - - - +
344A GLN* 3.1 45.3 + - - +
345A LEU 3.1 1.0 - - - -
346A MET* 1.3 76.5 - - - +
348A GLN* 1.3 61.4 + - + +
367A LYS* 5.8 5.4 - - - +
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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