Contacts of the helix formed by residues 166 - 182 (chain E) in PDB entry 2CEA
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 ALA 166 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E VAL* 4.1 24.0 - - + -
164E GLY 3.4 2.2 - - - +
165E GLY* 1.3 77.6 - - - +
167E GLU* 1.3 66.7 + - - +
168E GLU* 3.3 5.6 - - - -
169E ALA* 3.3 14.9 + - + +
170E ILE* 3.0 31.0 + - + +
205E THR 5.9 1.3 - - - +
210E LEU* 4.5 8.3 - - + -
328E VAL* 5.9 5.4 - - + -
1604E ADP 5.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E GLY* 2.9 16.1 - - - -
166E ALA* 1.3 84.0 + - - +
168E GLU* 1.3 77.7 + - - +
170E ILE* 3.4 7.8 + - + +
171E GLU* 3.1 33.5 + - + +
338E LYS* 6.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E GLY 4.8 1.9 - - - +
166E ALA* 3.9 4.0 - - - -
167E GLU* 1.3 97.1 + - - +
169E ALA* 1.3 62.1 + - - +
171E GLU* 3.4 7.5 + - - +
172E GLU* 3.2 25.6 + - - +
442E ARG* 3.1 30.9 + - - +
593E GLU* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E ALA* 3.3 12.6 + - + +
168E GLU* 1.3 76.1 + - - +
170E ILE* 1.3 66.8 + - - +
172E GLU* 3.1 7.0 + - - +
173E LEU* 2.9 28.0 + - + +
210E LEU* 4.2 23.1 - - + -
326E ILE* 3.7 28.4 - - + +
327E VAL 4.7 5.1 + - - +
328E VAL* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E PHE* 3.8 38.5 - - + +
163E VAL* 4.2 29.6 - - + +
166E ALA* 3.0 28.2 + - - +
167E GLU* 3.8 7.9 - - + +
169E ALA* 1.3 74.8 - - - +
171E GLU* 1.3 68.0 + - - +
173E LEU* 2.8 17.9 + - - +
174E LYS* 2.9 40.6 + - - +
210E LEU* 3.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E GLU* 3.1 27.3 + - + +
168E GLU* 3.7 6.5 - - - +
169E ALA 3.3 0.2 - - - -
170E ILE* 1.3 79.5 - - - +
172E GLU* 1.3 63.5 + - + +
174E LYS* 3.4 44.5 + - - +
175E GLU* 4.4 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D ARG* 5.7 4.8 + - - -
168E GLU 3.2 17.3 + - - +
169E ALA* 3.1 10.9 + - - +
170E ILE 3.1 0.6 - - - -
171E GLU* 1.3 79.8 - - - +
173E LEU* 1.3 61.8 + - - +
174E LYS 3.3 0.9 + - - -
175E GLU* 3.6 18.2 + - - +
176E VAL* 4.4 4.2 + - - +
324E LYS* 3.1 37.0 + - - -
325E LYS 6.0 0.7 - - - -
326E ILE* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E PHE* 4.5 5.4 - - + -
169E ALA* 2.9 18.4 + - + +
170E ILE* 2.8 5.8 + - - +
172E GLU* 1.3 72.3 - - - +
174E LYS* 1.3 65.8 + - - +
175E GLU 3.1 3.1 - - - -
176E VAL* 2.9 21.2 + - + +
177E VAL* 3.0 13.8 + - - +
197E ILE* 4.5 13.2 - - + -
199E LEU* 5.3 2.9 - - + -
210E LEU* 3.6 41.5 - - + -
214E VAL* 3.9 24.9 - - + +
303E MET* 4.1 22.7 - - + -
326E ILE* 3.4 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D ARG* 5.8 2.5 - - - -
160E PHE* 4.2 21.5 - - + +
170E ILE* 2.9 27.2 + - + +
171E GLU* 3.4 43.7 + - - +
172E GLU 3.2 1.4 - - - -
173E LEU* 1.3 77.8 - - - +
175E GLU* 1.3 60.5 + - - +
177E VAL* 3.3 11.6 + - + +
178E GLU* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D GLU* 5.1 2.3 - - - +
379D LEU* 3.2 34.1 - - + +
383D ARG* 2.2 52.7 + - + +
400D ARG* 4.7 6.2 + - - -
171E GLU 4.4 2.3 + - - +
172E GLU* 3.6 13.2 + - - +
173E LEU 3.1 0.2 - - - -
174E LYS* 1.3 75.4 - - - +
176E VAL* 1.3 67.0 + - + +
178E GLU* 3.3 8.7 + - - +
179E PHE* 3.0 21.7 + - - +
186E PHE* 4.0 7.0 - - + -
193E MET* 3.8 16.3 - - + +
324E LYS* 5.7 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E GLU 4.6 3.4 - - - +
173E LEU* 2.9 22.5 + - + +
175E GLU* 1.3 77.3 - - + +
177E VAL* 1.3 62.8 + - - +
179E PHE* 3.3 2.6 + - - +
180E LEU* 3.0 29.9 + - + +
193E MET* 3.4 20.9 - - + -
194E PRO* 5.7 1.1 - - + -
197E ILE* 3.6 26.7 - - + -
214E VAL* 4.1 19.3 - - + -
301E ILE* 4.0 26.5 - - + -
303E MET* 5.6 1.3 - - - -
324E LYS* 6.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E PHE* 4.0 20.2 - - + -
173E LEU 3.0 16.7 + - - +
174E LYS* 3.4 10.5 - - + +
175E GLU 3.2 0.2 - - - -
176E VAL* 1.3 73.9 - - - +
178E GLU* 1.3 72.9 + - - +
180E LEU* 3.1 4.4 + - - +
181E LYS* 2.9 30.6 + - + +
214E VAL* 4.1 15.5 - - + +
217E GLU* 3.9 44.9 - - + +
218E ALA* 3.9 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D ALA 5.6 0.2 - - - +
383D ARG* 4.1 34.5 - - + +
174E LYS* 3.0 19.9 + - + +
175E GLU* 3.3 8.5 + - - +
177E VAL* 1.3 81.4 - - - +
179E PHE* 1.3 67.4 + - - +
181E LYS* 3.2 26.9 + - - +
182E ASP* 3.2 9.0 + - - +
185E LYS* 6.0 0.3 - - - +
186E PHE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E GLU 3.0 12.5 + - - +
176E VAL 3.4 8.3 - - - +
178E GLU* 1.3 78.4 - - - +
180E LEU* 1.3 63.1 + - + +
182E ASP 3.0 0.3 + - - -
183E PRO* 2.9 50.1 - - + +
186E PHE* 3.4 42.5 - + + -
187E ASN* 4.4 4.7 - - - -
191E ALA 5.3 1.6 - - - -
193E MET* 3.6 36.1 - - + -
296E SER* 3.3 36.3 - - - -
297E LYS* 4.6 1.8 - - - -
299E GLY* 3.9 17.0 - - - -
300E ILE 4.8 0.4 - - - -
301E ILE* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E VAL* 3.0 21.6 + - + +
179E PHE* 1.3 82.4 - - + +
181E LYS* 1.3 62.5 + - - +
182E ASP 3.4 0.2 + - - -
183E PRO* 3.9 4.2 - - - +
214E VAL* 3.6 31.2 - - + -
218E ALA* 3.7 21.3 - - + -
220E VAL* 3.9 16.3 - - + +
254E PRO* 3.9 20.3 - - + +
255E CYS 4.0 15.7 - - - +
256E ILE* 3.7 17.7 - - + -
299E GLY 3.3 27.1 - - - +
301E ILE* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E VAL* 2.9 26.5 + - + +
178E GLU* 3.5 25.3 + - - +
180E LEU* 1.3 77.0 - - - +
182E ASP* 1.3 64.8 + - + +
183E PRO* 4.2 0.9 - - - +
217E GLU 4.6 6.5 - - - +
218E ALA* 4.0 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 182 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E GLU 3.2 4.7 + - - +
179E PHE 3.0 5.9 + - - +
181E LYS* 1.3 84.4 - - + +
183E PRO* 1.3 69.9 - - - +
184E SER* 2.6 33.0 + - - -
185E LYS* 3.0 41.3 + - + +
186E PHE* 3.9 4.0 - - - -
188E ARG* 5.4 0.3 + - - -
----------------------------------------------------------
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