Contacts of the helix formed by residues 326 - 334 (chain A) 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 THR 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A SER* 1.3 76.3 + - - +
327A GLU* 1.3 61.5 + - - +
329A TYR* 2.9 29.7 + - - +
330A ILE* 3.0 18.8 + - - +
364A ILE* 4.1 7.4 - - + +
368A ASP* 3.9 18.8 - - + +
369A VAL* 3.8 33.4 - - + +
372A ALA* 3.8 14.3 - - + +
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Residues in contact with GLU 327 (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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316A LEU* 4.2 10.2 - - + +
325A SER* 3.1 15.1 + - - +
326A THR* 1.3 85.6 + - - +
328A ALA* 1.3 56.0 + - - +
330A ILE* 3.2 13.0 + - + +
331A ARG* 2.8 67.7 + - + +
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Residues in contact with ALA 328 (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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313A THR* 3.0 26.7 - - - +
314A TYR 3.3 10.3 - - - +
315A LEU 3.6 11.2 - - - +
316A LEU* 3.9 19.1 - - + +
325A SER 3.1 14.6 + - - +
326A THR 3.1 0.4 - - - -
327A GLU* 1.3 75.5 - - - +
329A TYR* 1.3 63.4 + - - +
331A ARG* 4.2 4.3 - - - +
332A ALA* 3.2 23.2 + - - +
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Residues in contact with TYR 329 (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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313A THR* 3.6 20.9 - - + -
314A TYR* 3.4 40.1 - - + +
325A SER 3.8 11.2 - - - -
326A THR* 2.9 10.7 + - - +
328A ALA* 1.3 80.0 - - - +
330A ILE* 1.3 63.5 + - - +
332A ALA* 3.1 3.6 + - - +
333A LEU* 2.9 29.9 + - + +
340A LEU* 4.0 8.9 - - + +
341A GLU 2.7 28.9 + - - -
342A LEU* 3.5 27.1 - - + +
354A ILE* 4.0 3.3 - - - +
369A VAL* 3.7 30.5 - - + +
372A ALA* 5.0 4.7 - - + -
373A ILE* 3.8 30.5 - - + -
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Residues in contact with ILE 330 (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 THR* 3.0 18.4 + - - +
327A GLU* 3.6 17.0 - - + +
329A TYR* 1.3 72.5 - - - +
331A ARG* 1.3 69.5 + - + +
333A LEU* 3.3 1.4 + - - +
334A CYS* 2.9 31.1 + - - +
372A ALA* 4.1 18.6 - - + +
376A TYR* 3.6 60.6 - - + +
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Residues in contact with ARG 331 (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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316A LEU* 3.9 24.6 - - - +
327A GLU* 2.8 60.4 + - + +
328A ALA* 4.2 4.0 - - - +
330A ILE* 1.3 76.5 - - + +
332A ALA* 1.3 64.0 + - - +
334A CYS* 3.3 5.8 + - - +
335A LYS* 3.2 32.3 + - + +
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Residues in contact with ALA 332 (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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310A SER* 4.4 4.3 - - - +
313A THR* 4.0 17.0 - - + -
328A ALA 3.2 18.3 + - - +
329A TYR 3.1 4.8 + - - +
331A ARG* 1.3 80.0 - - - +
333A LEU* 1.3 59.1 + - - +
335A LYS* 3.2 10.8 + - - +
337A CYS* 3.0 38.1 + - + +
340A LEU* 4.6 2.7 - - + -
579A PHE* 4.2 22.7 - - + -
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Residues in contact with LEU 333 (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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329A TYR 2.9 22.8 + - - +
330A ILE 3.9 3.4 - - - +
332A ALA* 1.3 72.0 - - - +
334A CYS* 1.3 58.6 + - - +
335A LYS 3.0 4.9 - - - -
336A GLY* 2.8 20.6 + - - -
337A CYS 3.4 20.9 - - - +
338A ARG* 3.8 17.0 + - - +
340A LEU* 3.9 28.0 - - + -
372A ALA 4.6 0.4 - - - +
373A ILE* 3.9 20.9 - - + -
376A TYR* 3.7 23.1 - - + +
377A ALA* 3.8 30.5 - - + +
380A ALA* 3.6 9.4 - - - +
385A VAL* 4.7 7.0 - - + -
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Residues in contact with CYS 334 (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 ILE* 2.9 19.3 + - - +
331A ARG* 3.7 7.6 - - - +
332A ALA 3.3 0.4 - - - -
333A LEU* 1.3 77.0 - - - +
335A LYS* 1.3 59.0 + - + +
336A GLY 3.1 3.3 + - - -
376A TYR* 3.5 35.4 - - - -
379A LYS* 4.8 10.8 - - - -
380A ALA* 3.8 14.5 - - - +
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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