Contacts of the strand formed by residues 243 - 248 (chain B) in PDB entry 1QZ2
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 LEU 243 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR 3.6 9.0 - - - +
178B TYR* 3.8 11.2 - - + -
183B PHE* 3.5 31.2 - - + -
201B PRO* 4.3 0.7 - - + -
219B VAL 3.8 0.4 - - - +
220B TYR* 3.4 8.7 - - - +
221B LEU* 2.8 40.6 + - + +
226B ALA* 3.3 28.9 - - + -
227B PHE* 4.0 26.0 - - + -
237B ILE* 4.1 9.6 - - + -
241B ALA 4.1 1.8 - - - +
242B GLU* 1.3 87.6 - - - +
244B LYS* 1.3 60.3 + - - +
245B TYR* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLU 3.6 0.2 - - - +
176B GLY* 3.0 4.5 - - - -
177B TYR* 2.7 72.4 + - + +
178B TYR 4.8 2.7 - - - +
180B ASP* 3.8 22.1 + - - +
218B ILE* 3.5 27.8 - - + +
219B VAL 3.7 2.7 - - - -
220B TYR* 3.9 25.1 - - + -
243B LEU* 1.3 74.6 - - - +
245B TYR* 1.3 66.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.1 26.0 - - + -
175B GLU 3.2 4.7 - - - -
176B GLY* 3.3 28.9 - - - -
183B PHE* 3.8 18.1 - + - -
184B ASP* 4.1 13.1 + - + -
199B ASP 4.4 0.7 + - - -
200B LEU* 4.8 0.3 - - - +
201B PRO* 3.4 41.7 - - + +
204B LEU* 4.0 20.6 - - + +
218B ILE* 3.0 8.1 - - - +
219B VAL* 2.6 47.9 + - + +
221B LEU* 3.9 20.4 - - + -
227B PHE* 4.2 3.5 - - - -
243B LEU* 4.2 13.2 - - + -
244B LYS* 1.3 77.7 - - - +
246B GLU* 1.3 60.7 + - - +
247B LEU* 3.8 5.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLN* 5.9 0.2 - - - +
173B ALA 3.2 10.7 - - - +
174B LEU 3.7 0.5 - - - +
175B GLU* 2.8 39.8 + - - +
177B TYR* 4.9 3.0 - - - -
217B SER 3.5 9.2 - - - -
218B ILE* 3.6 13.4 - - - +
245B TYR* 1.3 72.5 - - - +
247B LEU* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 4.0 12.8 - - + -
173B ALA 3.1 13.9 - - - +
174B LEU* 3.3 31.4 - - + -
204B LEU* 3.1 35.4 - - + -
207B ALA* 6.0 0.2 - - + -
208B ILE* 4.0 20.9 - - + -
211B MET* 4.0 17.4 - - - +
216B HIS* 3.3 3.0 - - - +
217B SER* 2.9 37.5 + - - +
218B ILE* 4.7 0.2 - - - +
219B VAL* 5.2 7.6 - - + -
245B TYR* 3.8 14.7 + - + +
246B GLU* 1.3 78.1 - - - +
248B HIS* 1.3 60.9 + - - +
249B LEU 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 3.5 4.8 - - - -
173B ALA* 2.9 47.7 + - + +
214B GLY* 3.5 15.9 + - - -
215B GLU 3.8 2.2 - - - -
216B HIS* 3.1 52.2 + + + +
247B LEU* 1.3 73.3 - - - +
249B LEU* 1.3 63.1 + - - +
250B LYS* 3.1 43.3 + - + +
----------------------------------------------------------
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