Contacts of the helix formed by residues 326 - 338 (chain A) in PDB entry 1A4Y
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 ALA 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 THR* 1.3 74.3 - - - +
327A ALA* 1.3 63.2 + - - +
329A CYS* 3.2 20.3 + - - +
351A ARG 3.2 6.9 + - - -
352A LEU* 3.2 27.4 - - - +
353A GLU* 4.3 8.3 - - + +
355A ALA* 4.2 11.2 - - + -
356A GLY* 3.8 12.6 - - - +
359A GLU* 3.5 10.3 - - - +
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Residues in contact with ALA 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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297A ASP* 3.9 12.3 - - + +
325A THR* 2.8 15.2 + - - +
326A ALA* 1.3 78.5 - - - +
328A CYS* 1.3 58.4 + - - +
330A SER* 3.5 15.1 + - - -
331A HIS* 4.3 5.4 + - - -
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Residues in contact with CYS 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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297A ASP* 3.3 18.7 + - + +
300A ALA* 3.6 20.0 - - + -
324A PHE* 3.6 26.2 - - - -
325A THR 3.1 18.5 + - - -
327A ALA* 1.3 77.1 - - - +
329A CYS* 1.3 66.2 + - - +
330A SER 3.3 1.6 - - - -
331A HIS* 3.1 23.2 + - + +
332A PHE* 3.2 32.0 + - - -
352A LEU* 4.3 7.9 - - - -
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Residues in contact with CYS 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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326A ALA* 3.2 14.1 + - - +
328A CYS* 1.3 78.1 - - - +
330A SER* 1.3 59.9 + - - +
332A PHE* 4.3 2.2 - - - +
333A SER* 2.8 32.1 + - - -
352A LEU* 3.9 31.4 - - - -
356A GLY* 3.2 43.7 - - - +
359A GLU* 3.8 6.6 - - - +
360A LEU* 3.6 21.4 - - + +
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Residues in contact with SER 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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327A ALA 3.5 10.9 + - - -
329A CYS* 1.3 77.0 - - - +
331A HIS* 1.3 78.9 + - - +
333A SER* 3.5 7.8 - - - -
334A SER* 3.2 24.9 + - - -
359A GLU* 3.6 20.9 + - - -
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Residues in contact with HIS 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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300A ALA 5.1 1.1 - - - +
301A ARG* 4.2 31.1 - - + +
304A CYS* 3.7 26.3 - - + +
305A GLU* 5.6 5.2 - - + -
308A LEU* 5.0 0.7 - - - +
327A ALA 4.3 7.2 + - - -
328A CYS* 3.1 13.9 + - + +
330A SER* 1.3 90.6 + - - +
332A PHE* 1.3 64.2 + - - +
333A SER 3.2 0.2 - - - -
334A SER* 3.2 16.3 + - - -
335A VAL* 3.2 17.0 + - - +
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Residues in contact with PHE 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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300A ALA* 3.7 28.0 - - + -
303A LEU* 5.2 4.3 - - + -
304A CYS* 3.7 19.5 - - - -
307A LEU* 5.1 4.9 - - + -
317A LEU* 4.6 12.6 - - + -
319A VAL* 4.8 5.4 - - + -
324A PHE* 4.1 23.3 - + - -
328A CYS* 3.2 34.3 + - - -
329A CYS* 3.3 2.9 + - - +
331A HIS* 1.3 76.2 - - - +
333A SER* 1.3 65.8 + - - +
335A VAL* 3.2 9.8 + - + +
336A LEU* 3.0 31.2 + - + +
345A LEU* 4.2 32.1 - - + -
347A ILE* 4.8 8.7 - - + -
352A LEU* 6.3 0.2 - - + -
360A LEU* 3.5 22.9 - - + -
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Residues in contact with SER 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 CYS 2.8 18.2 + - - -
330A SER* 3.5 10.8 - - - -
332A PHE* 1.3 77.9 - - - +
334A SER* 1.3 61.2 + - - +
336A LEU* 3.4 3.3 + - - -
337A ALA* 3.1 18.7 + - - +
359A GLU* 2.8 31.2 + - - -
360A LEU* 4.1 6.7 - - - +
362A GLN* 3.9 4.0 - - - +
363A GLY* 3.0 25.9 + - - -
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Residues in contact with SER 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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308A LEU* 4.0 19.1 - - - -
330A SER 3.2 12.9 + - - -
331A HIS* 3.2 11.8 + - - -
333A SER* 1.3 76.5 - - - +
335A VAL* 1.3 60.1 + - - +
337A ALA* 3.9 3.7 - - - -
338A GLN* 2.9 46.2 + - - +
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Residues in contact with VAL 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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304A CYS* 3.8 39.0 - - + +
307A LEU* 3.8 26.5 - - + +
308A LEU* 3.9 11.2 - - + -
331A HIS 3.2 15.2 + - - +
332A PHE* 3.6 9.6 - - + +
334A SER* 1.3 75.4 - - - +
336A LEU* 1.3 60.3 + - + +
339A ASN* 2.7 50.8 + - + +
342A LEU* 4.1 17.5 - - + -
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Residues in contact with LEU 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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332A PHE 3.0 21.3 + - - +
333A SER 3.8 4.5 - - - +
334A SER 3.3 0.2 - - - -
335A VAL* 1.3 79.8 - - + +
337A ALA* 1.3 59.0 + - - +
339A ASN 4.6 2.9 - - - +
340A ARG* 4.1 1.4 + - - -
342A LEU* 4.8 8.3 - - + -
345A LEU* 4.4 18.2 - - + -
360A LEU* 3.9 34.5 - - + +
363A GLY 3.9 2.0 - - - -
364A LEU* 4.1 24.2 - - + +
369A SER* 3.6 23.6 - - - -
370A VAL 4.7 1.7 + - - -
371A LEU* 3.7 43.4 + - + +
374A LEU* 5.6 2.9 - - + -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A SER 3.1 14.9 + - - +
334A SER* 4.0 4.9 - - - +
336A LEU* 1.3 76.1 - - - +
338A GLN* 1.3 60.7 + - + +
340A ARG* 2.4 32.2 + - - +
363A GLY* 3.5 22.9 + - - +
366A GLN* 4.1 27.8 + - + +
367A PRO 4.8 2.9 - - - +
369A SER* 5.0 0.4 - - - -
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Residues in contact with GLN 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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308A LEU* 3.7 26.1 + - + +
334A SER* 2.9 28.6 + - - +
337A ALA* 1.3 81.8 - - + +
339A ASN* 1.3 67.7 + - - +
340A ARG* 3.4 21.8 + - - +
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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