Contacts of the helix formed by residues 164 - 179 (chain B) in PDB entry 2CNW
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 SER 164 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLY 3.5 3.6 + - - -
163B GLU* 1.3 78.5 - - - +
165B PRO* 1.3 67.2 - - - +
166B GLU* 3.6 13.9 + - - +
167B SER* 3.1 22.2 + - - -
168B ILE* 2.9 27.5 + - - +
170B ARG* 5.0 2.4 + - - -
204B ARG* 4.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU 4.4 2.2 - - - +
164B SER* 1.3 86.7 - - - +
166B GLU* 1.3 57.4 + - - +
168B ILE* 3.7 14.4 - - + +
169B ARG* 3.0 22.2 + - - +
204B ARG* 3.4 45.3 - - + +
205B LEU* 3.8 26.7 - - + +
208B VAL* 3.3 28.8 - - + +
209B LEU* 4.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 3.7 12.5 - - - +
165B PRO* 1.3 78.1 - - - +
167B SER* 1.3 58.0 + - - +
169B ARG* 3.4 25.3 + - - +
170B ARG* 3.0 47.1 + - - +
204B ARG* 2.8 35.0 + - - -
208B VAL* 3.7 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B MET* 5.0 3.1 - - - +
163B GLU* 2.9 28.4 + - - +
164B SER* 3.1 18.8 + - - -
166B GLU* 1.3 77.1 - - - +
168B ILE* 1.3 65.4 + - - +
170B ARG* 3.1 28.2 + - - +
171B ARG* 3.1 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 4.7 6.5 - - + -
134B ALA* 5.3 6.1 - - + -
157B LEU* 5.1 2.7 - - + -
159B VAL* 3.8 44.6 - - + -
163B GLU* 3.6 19.0 + - + +
164B SER 2.9 19.2 + - - +
165B PRO* 3.7 9.4 - - + +
167B SER* 1.3 75.4 - - - +
169B ARG* 1.3 63.1 + - - +
171B ARG* 3.4 3.0 + - - +
172B VAL* 3.0 37.9 + - + +
186B VAL* 6.3 0.7 - - + -
205B LEU* 4.1 21.1 - - + -
209B LEU* 4.4 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 6.3 0.4 - - - +
165B PRO 3.0 18.0 + - - +
166B GLU* 3.5 23.5 + - - +
168B ILE* 1.3 74.5 - - - +
170B ARG* 1.3 66.4 + - - +
172B VAL* 4.0 2.4 - - - +
173B GLU* 2.9 34.0 + - + +
207B GLU 5.3 0.8 + - - -
208B VAL* 3.1 44.2 + - + +
209B LEU* 3.5 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 5.0 1.8 + - - -
166B GLU* 3.0 33.4 + - - +
167B SER* 3.1 38.6 + - - +
169B ARG* 1.3 78.6 - - - +
171B ARG* 1.3 61.0 + - + +
173B GLU* 3.3 5.1 + - - +
174B GLU* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.7 31.1 - - + +
158B GLU 3.0 28.5 + - - +
159B VAL* 3.7 4.0 - - - +
160B MET* 3.8 20.5 - - - +
163B GLU* 2.7 38.4 + - - +
167B SER* 3.1 15.7 + - - +
168B ILE* 4.0 2.6 - - - +
170B ARG* 1.3 77.6 - - + +
172B VAL* 1.3 56.3 + - - +
174B GLU* 3.4 6.9 + - - +
175B LYS* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 4.6 2.2 - - - +
100B LEU* 4.3 10.8 - - + -
130B LEU* 4.3 3.9 - - + +
132B VAL* 4.0 17.7 - - + -
157B LEU* 3.9 27.4 - - + -
168B ILE* 3.0 32.6 + - + +
169B ARG* 4.0 4.7 - - - +
171B ARG* 1.3 73.1 - - - +
173B GLU* 1.3 61.2 + - - +
175B LYS* 4.1 1.0 - - - +
176B ALA* 2.9 35.0 + - - +
184B ILE* 3.6 36.3 - - + -
186B VAL* 6.0 0.7 - - + -
209B LEU* 5.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 4.4 24.1 + - - +
169B ARG* 2.9 23.6 + - + +
170B ARG* 3.5 6.5 - - - +
172B VAL* 1.3 76.7 - - - +
174B GLU* 1.3 57.0 + - - +
176B ALA* 3.9 1.7 - - - +
177B ARG* 2.8 78.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ARG 2.9 15.7 + - - +
171B ARG* 3.6 10.3 - - - +
173B GLU* 1.3 73.1 + - - +
175B LYS* 1.3 58.2 + - - +
177B ARG* 3.0 31.7 + - - +
178B LEU* 2.6 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.8 31.9 - - + -
155B PRO* 4.0 14.0 - - - +
156B VAL 4.8 8.7 - - - -
157B LEU* 4.1 18.4 - - + -
171B ARG 2.9 19.9 + - - +
172B VAL 4.1 1.8 - - - +
174B GLU* 1.3 72.5 - - - +
176B ALA* 1.3 57.8 + - - +
178B LEU* 4.6 4.5 - - - +
179B GLU* 2.6 78.4 + - + +
181B ARG* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 3.8 12.3 - - - +
130B LEU* 4.4 3.7 - - + +
172B VAL 2.9 18.9 + - - +
173B GLU 3.9 0.2 - - - +
175B LYS* 1.3 77.5 - - - +
177B ARG* 1.3 57.6 + - - +
180B ALA* 3.1 9.4 + - - -
181B ARG* 2.8 54.6 + - + +
184B ILE* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 5.3 1.5 - - - +
173B GLU* 2.8 52.2 + - - +
174B GLU* 3.2 31.6 + - - +
176B ALA* 1.3 79.3 - - - +
178B LEU* 1.3 85.8 + - + +
179B GLU 3.2 1.0 + - - -
180B ALA* 3.4 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLU* 2.6 48.0 + - + +
175B LYS* 4.2 3.6 - - - +
177B ARG* 1.3 94.1 - - + +
179B GLU* 1.3 63.7 + - + +
180B ALA 3.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 2.8 31.3 + - - +
155B PRO* 4.1 7.8 - - - +
175B LYS* 2.6 64.0 + - - +
178B LEU* 1.3 83.3 - - + +
180B ALA* 1.3 65.0 + - - +
181B ARG* 3.3 28.2 + - + +
----------------------------------------------------------
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