Contacts of the helix formed by residues 326 - 338 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325D THR* 1.3 74.7 - - - +
327D ALA* 1.3 62.4 + - - +
328D CYS 3.2 0.2 - - - -
329D CYS* 3.2 21.2 + - - +
330D SER 4.5 0.2 + - - -
351D ARG 3.4 6.8 + - - +
352D LEU 3.1 24.9 - - - +
353D GLU* 4.7 6.5 + - + +
355D ALA* 4.7 8.7 - - + -
356D GLY* 3.8 14.6 - - - +
359D GLU* 3.7 9.4 - - - +
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Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ASP* 3.6 13.9 - - + +
325D THR* 2.9 15.6 + - - +
326D ALA* 1.3 78.2 - - - +
328D CYS* 1.3 59.5 + - - +
329D CYS 3.4 0.2 - - - -
330D SER* 3.5 14.9 + - - -
331D HIS* 4.2 7.3 + - - -
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Residues in contact with CYS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ASP* 3.3 18.5 + - + +
300D ALA* 3.6 22.0 - - + -
324D PHE* 3.7 22.0 - - - -
325D THR 3.2 20.1 + - - -
327D ALA* 1.3 75.6 - - - +
329D CYS* 1.3 67.2 + - - +
330D SER 3.2 3.1 - - - -
331D HIS* 2.9 31.3 + - - +
332D PHE* 3.1 31.4 + - + -
347D ILE* 5.9 0.2 - - - -
352D LEU* 4.5 3.1 - - - -
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Residues in contact with CYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D THR 4.3 0.2 - - - -
326D ALA* 3.2 14.0 + - - +
328D CYS* 1.3 77.1 - - - +
330D SER* 1.3 59.8 + - - +
331D HIS 3.1 0.2 - - - -
332D PHE* 3.9 3.8 - - - +
333D SER* 2.9 28.2 + - - -
352D LEU* 3.8 31.2 - - - -
356D GLY* 3.3 42.6 - - - +
359D GLU* 3.6 10.5 - - + +
360D LEU* 3.9 18.9 - - + +
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Residues in contact with SER 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ALA 4.5 0.2 + - - -
327D ALA 3.5 15.4 + - - -
329D CYS* 1.3 76.8 - - - +
331D HIS* 1.3 76.0 + - - +
333D SER* 3.5 4.8 - - - -
334D SER* 3.3 18.4 + - - -
359D GLU* 3.6 27.0 + - - -
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Residues in contact with HIS 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D ASP 5.8 0.2 + - - -
300D ALA 5.1 1.1 - - - +
301D ARG* 4.2 36.0 - - + +
304D CYS* 3.7 25.2 - - + +
305D GLU* 5.7 4.6 + - + -
327D ALA 4.2 8.6 + - - -
328D CYS* 2.9 15.4 + - + +
330D SER* 1.3 90.0 + - - +
332D PHE* 1.3 60.4 + - - +
333D SER 2.9 1.3 - - - -
334D SER* 2.8 24.0 + - - -
335D VAL* 3.2 14.2 + - - +
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Residues in contact with PHE 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ALA* 4.0 17.9 - - + -
303D LEU* 5.0 4.9 - - + -
304D CYS* 3.4 20.9 - - - -
307D LEU* 4.7 5.8 - - + -
317D LEU* 4.4 13.0 - - + -
319D VAL* 4.6 8.1 - - + -
324D PHE* 4.1 24.7 - + - -
328D CYS* 3.1 38.0 + - + +
329D CYS* 4.4 1.3 - - - -
331D HIS* 1.3 79.0 - - - +
333D SER* 1.3 63.2 + - - +
335D VAL* 3.4 8.6 + - + +
336D LEU* 3.1 29.0 + - + +
342D LEU* 6.2 1.3 - - + -
345D LEU* 4.2 30.5 - - + -
347D ILE* 4.4 10.8 - - + -
360D LEU* 3.5 22.9 - - + -
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Residues in contact with SER 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D CYS 2.9 21.0 + - - -
330D SER* 3.5 10.1 - - - -
332D PHE* 1.3 79.6 - - - +
334D SER* 1.3 61.3 + - - +
336D LEU* 3.6 2.6 + - - +
337D ALA* 3.2 17.3 + - - +
359D GLU* 3.1 27.2 + - - -
360D LEU* 4.0 6.5 - - - +
362D GLN* 4.5 3.3 + - - +
363D GLY* 3.4 23.8 + - - -
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Residues in contact with SER 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D LEU* 4.1 18.5 - - - +
330D SER 3.3 10.2 + - - -
331D HIS* 2.8 15.6 + - - -
333D SER* 1.3 78.3 - - - +
335D VAL* 1.3 58.6 + - - -
337D ALA* 3.2 5.4 + - - +
338D GLN* 2.9 46.9 + - - +
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Residues in contact with VAL 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D CYS* 3.7 40.2 - - + +
307D LEU* 3.9 25.4 - - + +
308D LEU* 3.8 14.6 - - + -
331D HIS 3.2 11.6 + - - +
332D PHE* 3.8 9.6 - - + +
334D SER* 1.3 77.2 - - - +
336D LEU* 1.3 61.2 + - + +
338D GLN 3.0 0.2 + - - -
339D ASN* 2.6 54.1 + - + +
342D LEU* 4.5 13.5 - - + -
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D PHE* 3.1 20.2 + - + +
333D SER* 3.9 4.3 - - - +
334D SER 3.3 0.2 - - - -
335D VAL* 1.3 80.1 - - + +
337D ALA* 1.3 59.5 + - - +
339D ASN 4.8 4.5 - - - +
342D LEU* 4.6 9.6 - - + +
345D LEU* 4.3 17.7 - - + -
360D LEU* 3.9 37.9 - - + +
363D GLY 3.9 9.4 - - - -
364D LEU* 4.1 17.9 - - + +
369D SER* 3.5 24.8 - - - -
370D VAL 4.7 2.1 + - - -
371D LEU* 4.0 40.1 + - + +
374D LEU* 5.7 4.3 - - + -
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Residues in contact with ALA 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D SER 3.2 16.9 + - - +
334D SER* 3.2 6.7 + - - +
335D VAL 3.1 0.8 - - - -
336D LEU* 1.3 77.6 - - - +
338D GLN* 1.3 65.6 + - + +
340D ARG* 3.7 16.5 + - - -
363D GLY* 3.3 12.3 + - - +
366D GLN* 3.4 35.0 + - + +
367D PRO 5.1 1.2 - - - +
369D SER* 5.1 0.2 - - - -
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Residues in contact with GLN 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D LEU* 3.8 24.5 + - + +
334D SER* 2.9 31.4 + - - +
335D VAL 3.0 0.2 + - - -
337D ALA* 1.3 86.2 - - + +
339D ASN* 1.3 67.0 + - - +
340D ARG* 3.3 24.3 + - - +
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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