Contacts of the helix formed by residues 188 - 192 (chain B) in PDB entry 2Q5E
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 PHE 188 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.3 4.7 - - + -
162B PHE* 4.1 0.3 - - - -
163B THR* 3.0 24.4 - - + +
165B SER 3.9 4.3 - - - +
167B ALA* 3.8 26.5 - - + +
170B ALA* 3.6 26.5 - - + -
171B ASP* 3.6 31.2 - - - -
186B ARG* 3.6 33.7 - - + -
187B LEU* 1.3 81.3 - - - +
189B ARG* 1.3 59.5 + - - +
190B GLU* 3.1 26.8 + - - +
191B SER* 2.7 36.5 + - - -
192B CYS* 3.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B THR 3.0 9.0 + - - -
164B ALA* 2.9 35.9 + - - +
165B SER* 3.1 14.0 + - - +
166B LEU* 3.3 52.7 - - + +
188B PHE* 1.3 73.6 - - - +
190B GLU* 1.3 58.4 + - + +
192B CYS* 3.0 27.7 + - - +
199B TYR* 3.4 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 5.2 7.8 - - + +
167B ALA* 4.3 15.4 + - - +
188B PHE* 3.0 32.0 + - - +
189B ARG* 1.3 79.8 + - + +
191B SER* 1.3 61.6 + - - +
192B CYS 3.3 6.7 + - - +
95D THR* 4.5 33.8 - - + +
96D GLU* 6.0 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 4.2 28.3 - - - +
162B PHE* 3.2 25.5 - - - -
187B LEU* 3.7 27.4 - - - +
188B PHE 2.7 22.1 + - - -
190B GLU* 1.3 76.1 + - - +
192B CYS* 1.3 59.2 + - - -
193B VAL 4.1 0.2 + - - -
202B ASP 5.3 1.2 + - - -
205B ARG* 5.0 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PHE* 3.5 22.2 - - - -
163B THR 3.7 17.7 - - - -
164B ALA* 3.9 13.9 - - - -
188B PHE 4.0 0.2 - - - -
189B ARG 3.0 15.9 + - - +
190B GLU 4.0 6.9 - - - +
191B SER* 1.3 81.6 - - - +
193B VAL* 1.3 63.3 + - - +
194B PHE 3.8 1.4 + - - -
199B TYR* 3.8 23.5 - - + -
200B VAL 3.3 10.8 - - - +
201B LYS* 4.0 13.7 - - - -
205B ARG* 6.0 0.4 - - - -
184D ARG* 4.3 4.0 - - - +
----------------------------------------------------------
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