Contacts of the helix formed by residues 167 - 176 (chain B) in PDB entry 2R2N
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 VAL 167 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 4.3 0.2 - - - +
160B ALA* 2.8 26.3 + - + +
161B SER* 3.8 14.4 - - - +
162B ASP* 3.6 25.8 - - + +
166B ILE* 1.3 74.5 - - - +
168B PRO* 1.3 73.1 - - + +
169B ASP* 3.9 23.3 - - + +
170B SER* 3.1 19.1 + - - +
171B LEU 3.2 8.7 + - - -
212B ARG* 3.8 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 3.4 10.1 - - + +
167B VAL* 1.3 85.3 - - + +
169B ASP* 1.3 52.2 + - - +
171B LEU* 3.7 8.7 - - + +
172B ARG* 2.7 44.4 + - - +
212B ARG* 3.6 45.1 - - + +
215B GLU* 3.6 35.0 - - + +
216B ILE* 4.2 9.9 - - + -
219B LEU* 3.9 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B VAL* 3.2 13.5 + - + +
168B PRO* 1.3 76.5 - - - +
170B SER* 1.3 57.8 + - - +
172B ARG* 3.0 22.0 + - - +
173B ASP* 2.9 45.4 + - - +
215B GLU* 5.4 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA* 2.7 48.4 + - - +
167B VAL* 3.1 15.1 + - - +
169B ASP* 1.3 79.6 - - - +
171B LEU* 1.3 57.0 + - - +
173B ASP* 3.5 5.6 + - - +
174B ILE* 3.0 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.8 26.9 - - + -
159B VAL* 3.8 35.3 - - + +
166B ILE* 3.7 22.4 - - + -
167B VAL 3.2 4.9 + - - +
168B PRO* 3.3 7.2 + - + +
170B SER* 1.3 76.9 + - - +
172B ARG* 1.3 65.4 + - - +
174B ILE* 3.2 5.5 + - + +
175B LEU* 3.0 38.1 + - + +
194B LEU* 3.9 17.0 - - + -
216B ILE* 4.1 9.0 - - + -
219B LEU* 4.0 25.4 - - + -
225B PHE* 4.2 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PRO* 2.7 31.2 + - - +
169B ASP* 3.0 32.4 + - - +
171B LEU* 1.3 72.2 - - - +
173B ASP* 1.3 67.2 + - - +
175B LEU* 3.3 6.1 + - - +
176B SER* 3.3 21.0 + - - -
215B GLU* 3.8 23.0 + - - +
218B GLU* 3.0 29.2 + - - -
219B LEU* 3.9 25.6 - - + +
222B LYS* 6.4 0.2 - - - +
223B TYR* 5.0 3.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP* 2.9 30.7 + - - +
170B SER* 3.8 6.5 + - - +
172B ARG* 1.3 80.2 - - - +
174B ILE* 1.3 64.9 + - + +
176B SER* 2.7 24.8 + - - -
177B ARG* 4.3 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.1 14.8 - - + -
157B ILE* 3.6 27.8 - - + -
158B ASN 3.4 25.1 - - - +
159B VAL* 3.9 14.6 - - + -
170B SER* 3.0 37.5 + - - +
171B LEU* 3.2 5.1 + - - +
173B ASP* 1.3 77.4 - - + +
175B LEU* 1.3 65.3 + - + +
176B SER 3.3 0.9 + - - -
177B ARG* 3.2 38.9 + - - +
178B TRP* 4.2 4.0 + - - +
191B PRO* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.2 7.2 - - + -
171B LEU* 3.0 29.9 + - + +
172B ARG* 3.8 4.0 - - - +
173B ASP 3.3 0.2 - - - -
174B ILE* 1.3 73.3 - - + +
176B SER* 1.3 56.5 + - - +
177B ARG 3.1 5.6 - - - -
178B TRP* 3.0 24.3 + - + +
191B PRO* 4.1 29.8 - - + -
219B LEU* 3.9 20.0 - - + -
223B TYR* 3.1 54.8 - - + -
225B PHE* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ARG 3.3 9.6 + - - -
173B ASP* 2.7 26.3 + - - -
175B LEU* 1.3 71.9 - - - +
177B ARG* 1.3 62.8 + - - +
178B TRP 3.0 11.4 + - - +
223B TYR* 4.2 7.6 + - - -
----------------------------------------------------------
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