Contacts of the helix formed by residues 383 - 391 (chain B) in PDB entry 2QUH
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 383 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG 3.8 4.2 - - - +
382B ASP* 1.3 83.6 - - + +
384B ILE* 1.3 65.8 + - - +
385B GLU* 3.7 9.2 + - - +
386B GLU* 3.0 36.9 + - - +
387B HIS* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ASP 5.9 0.2 - - - +
383B THR* 1.3 70.7 - - - +
385B GLU* 1.3 64.9 + - + +
387B HIS* 3.4 8.8 - - - +
388B ARG* 2.9 36.3 + - + +
426B LEU* 4.0 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B THR* 3.2 9.9 + - - +
384B ILE* 1.3 84.6 - - + +
386B GLU* 1.3 69.8 + - - +
388B ARG* 3.2 8.8 + - - +
389B GLN* 3.0 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 3.5 36.8 + - + +
382B ASP* 3.9 10.8 - - - +
383B THR* 3.0 39.4 + - - +
385B GLU* 1.3 88.4 - - + +
387B HIS* 1.3 57.9 + - - +
389B GLN* 4.4 2.2 - - - -
390B PHE* 2.8 45.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLY* 3.6 12.5 - - - -
381B ARG* 3.2 26.6 + - + +
383B THR 3.1 13.4 + - - +
384B ILE* 3.4 12.6 - - - +
385B GLU 3.1 0.4 - - - -
386B GLU* 1.3 75.6 - - - +
388B ARG* 1.3 62.1 + - - +
391B GLY* 2.8 30.7 + - - -
392B GLY* 3.5 30.8 + - - -
420B TYR* 3.7 20.1 + + - -
423B GLY* 3.4 9.3 - - - -
425B MET 2.7 29.7 + - - -
426B LEU* 3.6 23.0 - - + -
427B THR* 4.0 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ILE* 2.9 23.6 + - + +
385B GLU* 3.6 7.2 - - - +
387B HIS* 1.3 76.7 - - - +
389B GLN* 1.3 61.4 + - - +
422B SER 3.9 13.0 - - - +
423B GLY 2.8 27.7 + - - +
424B ALA* 2.7 32.3 + - - +
425B MET* 3.7 0.6 - - - +
426B LEU* 3.6 36.7 - - + +
429B GLU* 4.1 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLU* 3.0 27.1 + - + +
386B GLU* 4.4 0.4 - - - -
387B HIS 3.1 0.2 - - - -
388B ARG* 1.3 80.5 - - - +
390B PHE* 1.3 103.1 + - + +
422B SER 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 3.4 43.1 - - - +
386B GLU* 2.8 33.8 + - + +
389B GLN* 1.3 116.1 - - + +
391B GLY* 1.3 63.4 + - - +
421B THR 3.9 4.5 - - - +
422B SER 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 4.0 17.3 + - - +
386B GLU 3.9 0.2 + - - -
387B HIS* 2.8 30.8 + - - -
388B ARG 4.6 0.2 + - - -
389B GLN 3.7 0.8 - - - -
390B PHE* 1.3 78.3 - - - +
392B GLY* 1.3 62.8 + - - -
421B THR 3.2 15.5 - - - -
422B SER 4.0 0.8 - - - -
423B GLY* 3.6 11.8 - - - -
----------------------------------------------------------
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