Contacts of the helix formed by residues 379 - 393 (chain A) in PDB entry 2FQ6
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 ASP 379 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLN* 5.7 1.6 - - - +
378A GLU* 1.3 75.1 - - - +
380A VAL* 1.3 65.3 + - - +
381A ASP* 2.9 36.6 + - - +
382A ASP* 3.1 43.3 + - - +
383A LEU* 3.2 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLN* 5.9 0.4 - - - +
268A GLU* 6.1 1.3 - - + +
269A SER* 3.4 47.7 + - - +
272A LYS* 3.6 33.9 - - + -
273A VAL* 3.6 16.8 - - + -
378A GLU 3.2 5.6 + - - -
379A ASP* 1.3 74.1 + - - +
381A ASP* 1.3 64.5 + - - +
383A LEU* 3.2 9.3 + - + +
384A ILE* 2.8 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 3.3 30.1 + - - -
379A ASP* 2.9 14.3 + - - +
380A VAL* 1.3 79.6 - - - +
382A ASP* 1.3 62.2 + - - +
384A ILE* 3.8 8.0 - - - +
385A ALA* 2.8 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 3.6 23.8 - - + +
378A GLU* 5.5 0.4 - - + -
379A ASP* 3.1 34.9 + - + +
381A ASP* 1.3 77.3 - - - +
383A LEU* 1.3 58.0 + - - +
385A ALA* 3.4 7.9 + - - +
386A ASP* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER* 5.5 0.2 - - - -
273A VAL* 5.2 4.3 - - + -
333A LEU* 4.3 15.9 - - + -
334A PHE* 3.6 25.0 - - + -
345A SER* 3.4 35.9 - - - +
375A ILE* 4.0 25.6 - - + -
376A GLY 4.6 0.9 - - - +
378A GLU* 3.8 33.7 - - + +
379A ASP 3.2 14.2 + - - +
380A VAL* 3.5 12.8 - - + +
382A ASP* 1.3 74.1 - - - +
384A ILE* 1.3 65.4 + - - +
386A ASP* 3.0 14.0 + - - +
387A LEU* 3.0 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 4.1 35.9 - - + -
273A VAL* 4.2 15.5 - - + -
276A TRP* 3.7 55.1 - - + +
380A VAL* 2.8 21.9 + - + +
381A ASP* 3.9 9.2 - - - +
383A LEU* 1.3 75.5 - - - +
385A ALA* 1.3 59.6 + - - +
387A LEU* 3.2 8.7 + - - +
388A ASP* 2.8 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASP 2.8 19.0 + - - +
382A ASP* 3.6 8.1 - - - +
383A LEU 3.3 0.2 - - - -
384A ILE* 1.3 78.4 - - - +
386A ASP* 1.3 55.1 + - - +
388A ASP* 3.5 7.6 - - - +
389A ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASN 5.1 0.5 - - - +
331A PHE* 3.4 23.4 - - - -
332A SER* 3.0 30.2 + - - -
333A LEU* 2.8 32.2 + - + +
334A PHE* 3.1 19.6 + - + -
382A ASP 3.0 12.7 + - - +
383A LEU* 3.0 11.7 + - - +
385A ALA* 1.3 73.0 - - - +
387A LEU* 1.3 61.2 + - - +
389A ALA* 3.4 7.7 + - - +
390A GLY 3.0 20.8 + - - -
393A ARG* 4.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 3.7 30.3 - - + -
276A TRP* 3.7 17.0 - - + -
277A LEU* 5.0 2.9 - - + -
313A PHE* 4.7 6.5 - - + -
327A TYR* 3.9 22.0 - - - +
331A PHE* 4.0 15.5 - - + -
334A PHE* 3.7 23.3 - - + -
347A ILE* 4.6 0.2 - - + -
373A LEU* 4.0 25.8 - - + -
383A LEU 3.0 15.9 + - - +
384A ILE* 3.6 5.8 - - - +
386A ASP* 1.3 75.2 - - - +
388A ASP* 1.3 58.8 + - - +
390A GLY* 3.1 2.3 + - - -
391A PHE* 2.9 36.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TRP* 3.7 22.3 - - + -
280A HIS* 4.6 8.7 - - - -
384A ILE* 2.8 22.3 + - + +
385A ALA* 3.5 9.9 - - - +
387A LEU* 1.3 71.6 - - - +
389A ALA* 1.3 62.4 + - - +
391A PHE* 3.2 15.6 + - - +
392A ALA* 3.2 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA 3.0 16.9 + - - +
386A ASP* 3.7 9.2 - - - +
387A LEU 3.2 0.4 - - - -
388A ASP* 1.3 76.2 + - - +
390A GLY* 1.3 63.8 + - - +
392A ALA* 3.3 18.0 + - - +
393A ARG* 3.3 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 3.2 30.4 - - - -
331A PHE* 4.3 1.8 - - - -
386A ASP 3.0 13.5 + - - -
387A LEU 3.1 4.6 + - - -
389A ALA* 1.3 77.2 - - - +
391A PHE* 1.3 60.8 + - - +
393A ARG* 3.1 37.1 + - - +
394A ILE* 3.5 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TRP* 3.6 24.9 - + - -
277A LEU* 3.6 17.0 - - + -
280A HIS* 3.4 27.4 - + + +
282A GLN* 2.9 46.8 - - + +
283A VAL* 3.3 27.6 - - + -
313A PHE* 4.2 8.5 - + - -
315A LEU* 3.7 29.2 - - + -
327A TYR* 4.2 6.3 - + - -
387A LEU* 2.9 23.5 + - + -
388A ASP* 3.2 7.1 + - - +
390A GLY* 1.3 76.2 - - - +
392A ALA* 1.3 62.2 + - - +
394A ILE* 3.1 13.9 + - + +
395A VAL* 3.1 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN* 4.7 0.2 - - - +
388A ASP* 3.2 10.7 + - - +
389A ALA* 3.3 13.2 + - - +
391A PHE* 1.3 78.5 - - - +
393A ARG* 1.3 60.3 + - + +
394A ILE 3.3 1.2 + - - -
395A VAL* 3.6 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLU* 5.9 0.9 - - - +
326A ASN* 2.8 66.8 + - - +
327A TYR* 2.9 21.5 + - - +
330A ASN* 3.2 33.9 + - - +
331A PHE* 3.5 19.6 - - - +
386A ASP* 4.8 1.6 + - - -
389A ALA* 3.3 34.3 + - - +
390A GLY* 3.1 27.6 + - - +
392A ALA* 1.3 76.3 - - + +
394A ILE* 1.3 60.3 + - - +
395A VAL* 3.8 0.8 - - - +
----------------------------------------------------------
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