Contacts of the strand formed by residues 299 - 306 (chain X) in PDB entry 2QW0
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 299 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189X VAL 3.9 13.0 - - - +
275X ARG 2.8 15.9 + - - +
276X HIS* 3.6 9.2 + - + +
277X VAL 2.9 24.4 + - - +
298X GLY* 1.3 71.3 - - - -
300X LYS* 1.3 67.7 + - - +
301X VAL* 3.4 21.8 + - - +
316X ARG* 2.7 50.4 + - - +
317X GLN* 3.5 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277X VAL* 3.3 21.5 - - + -
279X PHE* 4.0 14.1 - - + -
292X VAL* 3.4 31.0 + - + -
293X HIS* 3.9 36.1 + - + +
296X LEU* 2.8 33.6 + - - -
297X PRO* 3.3 10.7 + - - +
298X GLY 2.8 21.1 + - - +
299X GLU* 1.3 73.5 - - - +
301X VAL* 1.3 64.0 + - - +
317X GLN* 2.9 42.1 + - - +
318X PRO* 3.4 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 301 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188X GLN 4.7 3.6 - - - +
189X VAL* 4.2 32.3 - - + +
276X HIS* 6.0 0.4 - - + +
277X VAL 2.9 9.6 + - - +
278X THR* 3.3 14.2 - - + +
279X PHE* 3.0 30.7 + - - -
299X GLU* 3.4 28.3 - - + +
300X LYS* 1.3 79.9 - - - +
302X ASN* 1.3 73.8 + - - +
303X ALA* 5.1 1.1 - - + -
314X TYR* 4.1 20.0 - - + -
315X MET 3.5 7.9 - - - +
316X ARG* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 302 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279X PHE* 3.2 13.4 - - + +
281X GLY* 2.9 33.6 + - - -
301X VAL* 1.3 74.4 - - - +
303X ALA* 1.3 60.8 + - - +
314X TYR* 3.2 6.6 - - - +
315X MET* 3.0 33.3 + - + +
318X PRO* 3.8 22.9 - - + +
320X THR 4.2 4.0 + - - -
321X GLY* 2.9 39.1 + - - -
323X GLU 4.9 0.4 + - - -
324X MET* 3.4 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184X PHE* 5.2 4.9 - - + -
189X VAL* 5.8 1.3 - - + -
249X PHE* 4.4 11.2 - - + -
278X THR* 4.5 9.9 - - + -
279X PHE 2.8 13.7 + - - +
280X ALA* 3.2 23.7 - - - +
281X GLY 4.0 2.4 + - - -
282X ALA* 5.3 0.5 + - - +
301X VAL* 5.1 1.8 - - + -
302X ASN* 1.3 77.4 + - - +
304X TYR* 1.3 61.6 + - - +
311X ASN* 4.2 9.0 - - - +
313X LEU 3.6 4.5 - - - +
314X TYR* 4.4 3.4 - - + +
324X MET* 3.8 5.1 - - - +
505X 34Z 3.4 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 304 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280X ALA* 5.5 0.2 - - - -
282X ALA* 4.8 11.9 - - + -
303X ALA* 1.3 75.5 - - - +
305X GLY* 1.3 67.7 + - - +
306X THR* 4.2 11.0 - - + +
311X ASN* 3.0 17.2 - - - +
312X SER* 3.0 26.8 + - - -
313X LEU* 2.9 39.7 + - + -
324X MET* 3.7 14.0 - - + -
353X LEU* 3.5 23.1 - - + +
383X THR* 3.2 28.2 - - + +
385X ASP* 2.7 29.1 + - - -
397X ILE* 3.8 24.0 - - + -
505X 34Z 3.6 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 305 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304X TYR* 1.3 89.6 - - - +
306X THR* 1.3 70.8 + - - +
310X MET 3.1 13.2 - - - -
312X SER* 5.1 0.2 - - - -
505X 34Z 3.2 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208X VAL* 4.3 0.7 - - - +
304X TYR* 4.2 20.0 - - + +
305X GLY* 1.3 80.7 - - - +
307X THR* 1.3 59.0 + - - +
308X GLU* 3.4 13.1 + - - +
309X ALA* 2.8 28.9 + - - +
310X MET* 2.7 33.4 + - - -
312X SER* 5.5 1.8 + - - +
355X VAL* 5.7 0.4 - - + +
381X TYR* 3.9 19.0 - - + +
383X THR* 4.5 8.1 - - + +
385X ASP* 5.5 0.9 - - - +
505X 34Z 3.4 11.5 - - - -
----------------------------------------------------------
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