Contacts of the strand formed by residues 233 - 240 (chain B) in PDB entry 1UIR
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 ASN 233 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 3.3 45.4 + - + +
197B MET* 3.6 4.5 - - - +
198B ILE* 3.0 41.1 + - + +
224B LYS* 3.8 31.1 + - - +
225B ASN* 3.3 31.8 + - - +
226B HIS* 3.4 9.8 - - - +
232B LEU* 1.3 73.0 - - - +
234B PHE* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 5.0 2.2 - + - -
161B ASP* 5.6 1.3 - - - -
194B GLN* 3.6 43.7 - - + -
196B GLY* 3.8 10.8 - - - -
197B MET* 3.7 28.5 - - + -
198B ILE* 3.8 3.4 - - - -
224B LYS* 3.2 6.8 - - - +
225B ASN 2.9 34.0 + - - +
227B ILE* 4.0 8.1 - - + -
230B PHE* 3.5 34.8 - + - -
232B LEU* 3.6 23.3 + - + -
233B ASN* 1.3 78.7 - - - +
235B GLY* 1.3 59.1 + - - +
236B PHE* 3.5 19.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLN* 3.7 3.5 - - - +
195B THR* 2.7 36.3 + - - -
196B GLY 2.8 17.7 + - - +
198B ILE* 3.5 19.2 - - - +
206B HIS* 3.7 6.5 - - - -
223B TYR 3.6 4.0 - - - -
234B PHE* 1.3 74.9 - - - +
236B PHE* 1.3 62.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 3.9 28.0 - + - -
66B THR* 3.5 24.9 - - + -
67B LEU* 4.1 26.2 - - + -
193B MET 3.1 11.9 - - - +
194B GLN* 3.4 35.4 - - + -
195B THR* 3.4 6.1 - - - -
206B HIS* 3.6 4.7 - - - -
222B SER* 3.3 3.5 - - - -
223B TYR* 2.7 50.9 + + + +
224B LYS* 4.4 1.8 - - - -
225B ASN 4.4 3.8 - - - -
227B ILE* 4.4 7.4 - - + -
234B PHE* 3.5 33.0 - - + -
235B GLY* 1.3 73.7 - - - -
237B LEU* 1.3 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B MET* 4.4 12.8 - - + +
192B GLY* 3.3 3.5 - - - -
193B MET* 3.0 52.5 + - + +
195B THR* 3.2 20.8 - - + +
209B VAL* 4.4 0.2 - - + -
210B HIS* 4.0 29.8 - - + +
213B VAL* 4.0 17.7 - - + -
220B VAL* 3.9 15.5 - - + -
221B ARG 3.3 13.5 - - - +
222B SER* 4.0 6.5 - - - +
223B TYR* 3.7 7.8 - - - -
236B PHE* 1.3 78.1 - - - +
238B LEU* 1.3 68.4 + - - +
239B ALA 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO 4.0 7.6 - - - +
71B ALA* 3.7 19.5 - - + +
74B THR* 3.9 27.6 - - + +
190B VAL* 4.1 11.2 - - + -
191B MET 3.2 1.8 - - - -
192B GLY* 3.8 14.4 - - - -
220B VAL* 3.5 2.6 - - - +
221B ARG 2.9 35.4 + - - +
223B TYR* 3.7 17.0 - - + +
237B LEU* 1.3 83.1 - - - +
239B ALA* 1.3 61.1 + - - +
245B PRO* 3.5 28.9 - - + +
276B PHE* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 3.4 3.4 - - - +
191B MET* 2.7 50.4 + - + +
213B VAL* 3.8 21.8 - - + -
217B PHE* 3.7 27.6 - - + -
219B TYR 3.3 8.1 - - - +
220B VAL* 4.4 1.3 - - + -
237B LEU* 4.6 1.3 - - + -
238B LEU* 1.3 77.1 - - - +
240B SER* 1.3 66.2 + - - +
245B PRO* 4.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLY 2.8 24.0 + - - -
190B VAL* 4.3 5.8 - - - -
217B PHE* 3.7 9.9 - - - -
218B ARG 3.7 1.4 + - - -
219B TYR* 2.9 36.3 + - - +
239B ALA* 1.3 77.7 - - - +
241B ASP* 1.3 64.5 + - - +
242B ALA* 3.2 10.9 + - - +
243B PHE* 3.4 33.8 - - - -
245B PRO* 4.6 3.1 - - - +
----------------------------------------------------------
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