Contacts of the strand formed by residues 236 - 242 (chain B) in PDB entry 2Q4E
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 236 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 6.1 5.6 - - - -
212A PRO 4.3 13.5 - - - +
213A GLY 3.9 20.6 - - - +
240A TYR* 2.8 35.0 + - - -
154B LYS 2.6 25.4 + - - +
155B THR* 3.1 15.4 + - - -
228B SER* 6.1 2.0 - - - -
229B LEU 3.3 12.8 - - - +
230B SER* 4.3 8.5 - - - +
231B TRP* 4.3 1.1 - - - -
234B GLY 2.7 14.0 + - - +
235B ARG* 1.3 77.0 - - - +
237B ALA* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 4.6 2.0 - - - -
156B VAL* 3.6 35.9 - - + +
157B GLN 4.5 0.4 - - - +
196B THR* 3.9 15.7 - - + -
200B ASN* 5.0 0.2 - - - +
228B SER* 3.2 2.3 - - - -
229B LEU* 3.0 31.5 + - + -
231B TRP* 4.2 12.7 - - + -
236B THR* 1.3 75.8 - - - +
238B THR* 1.3 74.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLN* 6.0 1.6 - - - +
211A PHE* 4.1 19.3 - - + -
238A THR* 5.4 5.2 + - + -
155B THR* 5.4 0.2 + - - -
157B GLN* 3.1 25.6 - - - +
158B SER 2.6 33.3 + - - +
196B THR* 4.7 0.5 - - - +
211B PHE* 3.5 31.4 - - + -
227B ALA 3.3 7.2 - - - +
228B SER* 3.8 6.7 - - - +
229B LEU* 5.9 0.9 - - - -
237B ALA* 1.3 88.2 - - - +
239B ILE* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER 2.8 4.9 - - - +
185B LEU* 4.8 12.8 - - + -
189B GLY* 5.0 4.7 - - - -
192B ALA* 3.4 42.2 - - + +
193B ILE* 3.7 18.4 - - + +
196B THR* 3.9 11.0 - - + +
211B PHE* 4.5 3.3 - - - -
225B CYS* 4.4 3.6 - - - +
226B GLY* 3.1 30.3 - - - -
227B ALA* 3.2 14.5 + - + +
229B LEU* 5.7 10.7 - - + +
238B THR* 1.3 80.6 - - - +
240B TYR* 1.3 66.5 + - - +
241B CYS* 5.1 0.2 - - - -
346B VAL* 4.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS* 4.7 9.7 + - - +
155A THR* 3.8 29.7 - - + +
157A GLN* 4.6 16.2 - - - +
236A THR* 4.2 13.4 + - + -
254A ILE* 4.0 22.4 - - + -
158B SER 3.0 6.3 + - - -
159B CYS* 3.0 16.6 - - + -
160B PHE* 2.7 31.7 + - - +
161B SER* 4.7 4.3 - - - -
189B GLY* 5.4 0.2 - - - -
192B ALA* 4.6 2.8 - - - +
211B PHE* 5.9 4.0 - + + -
224B SER* 4.2 7.9 + - - -
225B CYS* 3.6 22.4 - - - -
226B GLY* 4.6 3.6 - - - -
239B ILE* 1.3 76.6 - - - +
241B CYS* 1.3 63.6 + - - +
242B SER* 3.6 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE 3.1 5.4 - - - -
184B ALA* 3.4 25.8 - - - +
185B LEU* 4.0 8.5 - - - -
188B ALA* 3.8 4.0 - - + -
189B GLY* 3.4 28.5 - - - +
222B ILE* 5.1 0.2 - - - -
224B SER* 2.9 4.3 - - - -
225B CYS* 2.8 77.4 + - - -
239B ILE* 5.1 1.6 - - - -
240B TYR* 1.3 80.7 - - - +
242B SER* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS* 5.7 0.5 - - - +
160B PHE 3.2 7.5 + - - +
161B SER* 3.3 21.6 - - - -
162B PHE* 3.3 8.8 + - - -
184B ALA* 4.3 4.1 - - - +
188B ALA* 4.8 2.2 - - - +
223B LEU 3.5 1.3 - - - -
224B SER* 3.5 18.6 - - - -
240B TYR* 3.6 20.9 + - - -
241B CYS* 1.3 76.7 - - - +
243B PHE* 1.3 61.9 + - - +
244B LEU* 3.1 18.2 + - - +
245B ALA* 3.2 21.3 + - - +
----------------------------------------------------------
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