Contacts of the helix formed by residues 174 - 183 (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 THR 174 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.3 6.2 + - - -
170B ARG 3.5 17.3 - - - +
171B LEU* 3.7 7.1 + - + -
172B LEU 3.7 1.0 - - - -
173B TYR* 1.3 79.8 - - - +
175B VAL* 1.3 66.0 + - - +
176B GLU* 3.5 6.7 - - - +
177B PHE* 3.0 22.9 + - - +
178B TYR* 3.2 14.6 + - - -
212B THR* 3.9 3.1 - - - -
293B SER* 3.4 12.6 - - - +
294B THR 3.5 20.2 - - - +
295B ASP* 2.7 29.9 + - - +
298B PRO* 3.8 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR* 1.3 73.5 - - - +
176B GLU* 1.3 62.9 + - - +
178B TYR* 3.3 5.3 + - - +
179B ARG* 2.9 59.8 + - - +
212B THR* 3.4 17.9 - - + +
215B GLU* 3.8 11.9 - - + +
216B ALA* 3.8 15.0 - - + -
292B VAL* 3.1 28.3 - - + -
293B SER 2.8 25.4 + - - +
294B THR* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.4 12.0 + - - +
174B THR* 3.5 0.9 - - - +
175B VAL* 1.3 74.2 + - - +
177B PHE* 1.3 59.9 + - - +
179B ARG* 3.7 22.9 + - + +
180B LEU* 2.9 28.6 + - - +
294B THR* 3.0 18.0 - - - +
295B ASP* 2.5 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 4.4 22.7 - - + -
141B ALA* 4.5 0.9 - - + -
142B ARG* 4.1 29.5 - - + +
145B LEU* 4.5 9.9 - - + -
157B ILE* 3.9 20.0 - - + -
171B LEU 3.6 15.9 - - - +
172B LEU* 3.1 53.8 - - + -
174B THR* 3.0 18.3 + - - +
176B GLU* 1.3 78.5 - - - +
178B TYR* 1.3 68.3 + + - +
180B LEU* 3.1 10.4 + - + +
181B VAL* 2.9 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 4.0 18.4 - - + -
172B LEU 4.0 2.1 + - - -
173B TYR* 3.3 40.5 - - - -
174B THR 3.2 18.9 + - - -
175B VAL* 3.8 5.4 - - - +
177B PHE* 1.3 92.9 - + - +
179B ARG* 1.3 57.3 + - - +
181B VAL* 3.3 6.8 + - - +
182B LYS* 2.8 28.8 + - - +
191B MET* 3.9 15.5 - - + -
193B MET* 3.6 16.6 - - + +
209B VAL* 4.0 4.2 - - - +
212B THR* 3.6 29.4 - - + -
213B VAL* 3.7 27.1 - - + -
216B ALA* 3.8 15.5 - - + -
217B PHE* 3.7 11.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 2.9 38.9 + - - +
176B GLU* 3.7 21.7 + - - +
178B TYR* 1.3 74.2 - - - +
180B LEU* 1.3 60.4 + - - +
182B LYS* 3.2 12.8 + - - +
183B ALA* 2.8 28.6 + - - +
215B GLU* 3.3 32.3 + - - +
216B ALA* 3.7 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.8 36.8 - - + +
145B LEU* 3.7 31.0 - - + -
146B GLU* 3.9 21.1 - - + +
176B GLU 2.9 13.9 + - - +
177B PHE* 3.2 12.3 - - + +
179B ARG* 1.3 77.5 - - - +
181B VAL* 1.3 60.6 + - - +
183B ALA* 3.2 12.1 + - + +
184B HIS* 2.9 46.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 5.8 0.9 - - + -
84B VAL* 5.6 1.3 - - + -
145B LEU* 4.1 17.5 - - + -
155B VAL* 3.7 37.2 - - + +
157B ILE* 4.6 5.8 - - + -
177B PHE* 2.9 46.1 + - + +
178B TYR* 3.5 10.3 - - - +
180B LEU* 1.3 78.0 - - - +
182B LYS* 1.3 64.9 + - - +
184B HIS* 2.9 16.5 + - - +
185B LEU* 3.5 11.2 + - + +
191B MET* 3.7 18.4 - - + -
217B PHE* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR 2.8 17.5 + - - +
179B ARG* 3.6 11.8 - - - +
181B VAL* 1.3 77.1 - - - +
183B ALA* 1.3 61.2 + - - +
184B HIS 3.0 0.2 - - - -
185B LEU* 3.1 25.4 + - + +
216B ALA* 2.7 31.0 + - - -
217B PHE* 3.5 27.3 - - + +
241B ASP* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 3.2 26.2 + - - -
179B ARG 2.8 13.7 + - - +
180B LEU* 3.4 15.9 - - + +
181B VAL 3.1 0.4 - - - -
182B LYS* 1.3 78.4 - - - +
184B HIS* 1.3 64.4 + - + +
185B LEU 3.4 1.6 - - - +
----------------------------------------------------------
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