Contacts of the strand formed by residues 388 - 397 (chain A) in PDB entry 1QU2
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 388 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA* 3.0 7.6 - - - -
207A SER* 2.9 41.2 + - - +
209A TYR* 5.2 5.9 - - - -
386A LYS* 2.8 32.5 + - - +
387A LEU* 1.3 77.7 - - - +
389A PHE* 1.3 67.0 + - - +
390A ILE* 4.7 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 5.5 15.0 - - + -
205A SER 3.9 4.7 - - - +
206A ALA* 4.3 17.0 - - + -
372A LYS* 5.4 16.4 - - + -
387A LEU* 4.1 28.5 - - + -
388A ASP* 1.3 80.8 - - - +
390A ILE* 1.3 72.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS 3.5 0.9 - - - +
204A ARG* 3.8 2.4 - - - -
205A SER* 3.0 36.8 + - - +
207A SER* 3.7 23.1 - - - +
388A ASP* 4.7 8.1 - - + -
389A PHE* 1.3 87.6 - - - +
391A THR* 1.3 84.8 + - - +
392A HIS* 4.4 6.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP* 3.2 38.5 - - + +
203A LYS 3.4 12.3 + - - +
204A ARG* 4.7 8.8 - - - +
390A ILE* 1.3 85.9 + - - +
392A HIS* 1.3 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP* 4.1 7.4 - - - -
203A LYS 3.1 25.7 + - - -
205A SER* 2.9 39.0 + - - -
232A THR* 3.9 18.7 + - + +
390A ILE* 4.5 6.6 + - + +
391A THR* 1.3 79.6 - - - +
393A SER* 1.3 77.1 + - - +
394A TYR* 3.4 22.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TYR* 3.0 34.9 - - - +
201A HIS 3.9 6.3 + - - -
202A ASP* 4.0 13.4 + - - -
392A HIS* 1.3 85.7 - - - +
394A TYR* 1.3 59.7 + - - +
395A PRO* 4.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TYR* 3.5 6.4 - - - -
201A HIS 3.1 19.9 + - - +
203A LYS* 4.1 37.3 + - + -
205A SER* 5.5 0.7 - - - -
232A THR* 6.2 2.2 - - + -
233A THR* 5.0 13.5 - - + +
235A TRP* 4.7 7.6 + - - -
367A TYR* 5.8 0.3 - - - -
392A HIS* 4.0 27.8 - + - +
393A SER* 1.3 76.8 + - - +
395A PRO* 1.3 90.5 - - + +
396A HIS* 2.7 31.4 + - - +
403A PRO* 4.4 7.9 - - + -
404A VAL 2.9 33.1 + - - -
405A ILE* 4.1 13.7 - - + +
406A PHE* 5.8 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TYR* 4.4 14.8 - - + -
198A ILE* 4.0 15.3 - - + -
200A TYR* 3.3 30.7 - - + +
393A SER 4.6 1.3 - - - +
394A TYR* 1.3 114.3 - - + +
396A HIS* 1.3 59.7 + - - +
404A VAL* 3.1 37.6 + - + +
406A PHE* 5.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.5 8.6 - - - +
199A GLU 3.0 37.8 + - - +
201A HIS* 3.5 43.4 + + + +
202A ASP 4.4 2.2 + - - -
203A LYS* 4.2 15.7 - - + +
394A TYR* 2.7 28.8 + - - +
395A PRO* 1.3 76.5 + - - +
397A ASP* 1.3 65.9 + - - +
398A TRP 3.2 0.9 + - - -
401A LYS 3.3 12.8 + - - -
402A LYS 3.1 21.0 - - - +
403A PRO* 3.4 28.6 - - + +
404A VAL* 3.9 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A SER* 2.8 32.2 + - - +
189A SER* 2.8 19.4 + - - -
193A LEU* 4.0 18.7 - - + +
197A GLU 4.2 3.1 - - - -
396A HIS* 1.3 69.8 - - - +
398A TRP* 1.3 59.6 + - - +
399A ARG* 3.0 20.3 + - - +
400A THR* 3.2 23.0 + - - -
401A LYS* 2.6 34.8 + - - -
402A LYS* 2.7 18.2 + - + +
404A VAL* 3.7 2.4 - - + +
----------------------------------------------------------
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