Contacts of the helix formed by residues 353 - 364 (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 GLU 353 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ALA* 4.7 6.4 + - + +
351D ARG* 3.3 25.0 - - - +
352D LEU* 1.3 85.1 - - - +
354D ASP* 1.3 67.8 + - - +
355D ALA* 4.0 7.2 - - + +
356D GLY 4.5 0.4 - - - +
357D VAL* 3.0 19.4 + - - +
379D CYS 2.8 10.0 + - - -
380D ASP* 2.9 49.4 - - - +
381D VAL* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D GLU* 1.3 75.0 - - - +
355D ALA* 1.3 57.3 + - - +
357D VAL* 4.5 0.2 - - - -
358D ARG* 2.9 30.0 + - - +
380D ASP 3.5 6.2 + - - +
381D VAL* 3.5 1.3 - - - +
382D SER* 2.5 48.1 + - - -
384D SER* 2.9 20.8 + - - -
385D SER* 2.7 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ALA* 4.7 9.9 - - + -
352D LEU 4.9 0.2 - - - +
353D GLU* 3.1 5.4 - - + +
354D ASP* 1.3 77.3 - - - +
356D GLY* 1.3 67.7 + - - +
358D ARG* 3.3 5.9 + - - +
359D GLU* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ALA* 3.8 7.5 - - - +
329D CYS* 3.3 35.4 - - - +
352D LEU 2.9 22.0 + - - -
355D ALA* 1.3 76.4 - - - +
357D VAL* 1.3 63.7 + - - +
359D GLU* 3.0 16.5 + - - +
360D LEU* 3.1 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D LEU* 4.1 13.9 - - + -
353D GLU 3.0 11.7 + - - +
356D GLY* 1.3 77.9 - - - +
358D ARG* 1.3 61.7 + - - +
359D GLU 3.1 0.7 + - - -
360D LEU* 3.1 9.6 + - + +
361D CYS* 3.1 24.4 + - - -
376D LEU* 4.3 25.1 - - + -
379D CYS* 4.9 0.2 - - + -
381D VAL* 3.3 31.0 - - + -
385D SER* 3.8 27.1 - - - +
389D LEU* 4.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D ASP 2.9 19.5 + - - +
355D ALA* 3.3 6.2 + - - +
357D VAL* 1.3 76.3 - - - +
359D GLU* 1.3 59.5 + - - +
361D CYS* 3.7 4.7 + - - +
362D GLN* 3.4 27.2 + - - +
385D SER* 5.0 3.6 - - - +
388D SER* 4.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ALA 3.7 10.2 - - - +
329D CYS* 3.6 24.1 - - - +
330D SER* 3.6 26.8 + - - -
333D SER* 3.1 24.6 + - - +
355D ALA* 3.3 13.9 + - - +
356D GLY* 3.0 8.6 + - - +
357D VAL 3.0 0.8 - - - -
358D ARG* 1.3 76.9 - - - +
360D LEU* 1.3 63.2 + - - +
362D GLN* 3.5 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D CYS* 3.9 15.3 - - + +
332D PHE* 3.5 35.2 - - + -
333D SER* 4.0 5.4 - - - +
336D LEU* 3.9 19.9 - - + +
345D LEU* 5.5 0.2 - - + -
347D ILE* 3.3 31.4 - - + -
352D LEU* 3.9 11.0 - - + -
356D GLY 3.1 15.9 + - - +
357D VAL* 3.1 9.8 + - + +
359D GLU* 1.3 77.9 - - - +
361D CYS* 1.3 62.6 + - - +
363D GLY* 3.3 4.2 + - - -
364D LEU* 3.1 23.4 + - + +
374D LEU* 5.4 6.7 - - + -
376D LEU* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D VAL* 3.1 20.7 + - - +
358D ARG 3.8 6.7 - - - +
359D GLU 3.3 0.2 - - - -
360D LEU* 1.3 78.9 - - - +
362D GLN* 1.3 55.7 + - - +
364D LEU* 3.3 9.6 + - - +
365D GLY* 2.9 25.3 + - - -
388D SER* 4.0 13.5 - - - +
389D LEU* 3.9 43.3 - - - -
392D THR* 3.3 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 362 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D SER* 4.5 3.5 + - - +
358D ARG* 3.4 19.2 + - - +
359D GLU* 3.7 20.8 - - - +
360D LEU 3.3 0.6 - - - -
361D CYS* 1.3 75.5 - - - +
363D GLY* 1.3 65.2 + - - +
365D GLY* 3.3 9.6 + - - -
366D GLN* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D SER* 3.4 32.3 + - - -
336D LEU* 3.8 3.4 - - - +
337D ALA* 3.3 23.1 - - - -
360D LEU 3.3 5.5 + - - -
362D GLN* 1.3 79.9 - - - +
364D LEU* 1.3 59.1 + - - +
366D GLN* 3.1 23.9 + - - +
369D SER* 4.2 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D LEU* 4.1 23.0 - - + +
360D LEU* 3.1 11.1 + - + +
361D CYS* 3.5 14.4 - - - +
362D GLN 3.2 0.2 - - - -
363D GLY* 1.3 77.4 - - - +
365D GLY* 1.3 56.7 + - - +
369D SER* 2.8 28.7 + - - +
371D LEU* 4.0 25.1 - - + -
374D LEU* 4.2 24.0 - - + -
389D LEU* 6.5 0.9 - - + -
392D THR* 3.6 20.0 - - + -
396D ASN* 3.1 29.1 + - - +
399D LEU* 4.4 18.6 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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