Contacts of the helix formed by residues 182 - 188 (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 ASP 182 (chain E).
----------------------------------------------------------
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
Residues in contact with PRO 183 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E PHE* 2.9 36.8 - - + +
180E LEU 3.9 6.3 - - - +
181E LYS 4.2 1.1 - - - +
182E ASP* 1.3 85.5 - - - +
184E SER* 1.3 56.8 + - - +
185E LYS 3.2 0.2 - - - -
186E PHE* 3.1 6.9 + - - +
187E ASN* 2.9 31.9 + - - +
254E PRO* 3.9 18.2 - - + -
297E LYS 3.8 17.7 - - - +
298E GLU 4.6 0.9 - - - +
299E GLY* 3.8 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E ASP* 2.6 28.6 + - - -
183E PRO* 1.3 76.0 - - - +
185E LYS* 1.3 64.9 + - - +
186E PHE 3.0 2.0 - - - -
187E ASN* 3.7 12.3 - - - +
188E ARG* 3.0 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D ALA* 3.9 17.3 - - - +
385D GLY* 3.2 37.8 + - - -
386D ARG 5.1 1.4 - - - +
178E GLU 6.0 0.2 - - - +
182E ASP* 3.0 37.4 + - + +
184E SER* 1.3 78.5 + - - +
186E PHE* 1.3 68.9 + - + +
188E ARG* 3.3 48.8 + - - +
189E ILE* 3.9 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D LEU* 3.9 19.1 - - + -
382D ALA* 3.7 32.1 - - + -
383D ARG* 4.4 7.4 - - - -
175E GLU* 4.0 8.7 - - + -
178E GLU* 3.8 17.5 - - + -
179E PHE* 3.4 61.0 - + + -
182E ASP 3.9 6.7 - - - -
183E PRO 3.4 6.5 - - - +
184E SER 3.0 0.6 - - - -
185E LYS* 1.3 85.5 - - + +
187E ASN* 1.3 65.8 + - - +
188E ARG 3.0 2.8 + - - -
189E ILE* 3.1 4.9 + - - +
190E GLY 3.1 16.6 + - - -
191E ALA* 3.1 30.1 + - + +
193E MET* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 187 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E PHE* 4.4 6.8 - - - -
183E PRO* 2.9 25.1 + - - +
184E SER* 3.7 8.9 - - - +
186E PHE* 1.3 76.5 - - - +
188E ARG* 1.3 62.3 + - - +
189E ILE 3.2 0.9 + - - -
190E GLY* 3.3 12.1 + - - +
191E ALA 5.1 3.0 - - - +
297E LYS* 3.3 57.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 188 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D PRO* 4.5 5.9 - - - +
385D GLY 4.0 6.5 + - - -
386D ARG 4.5 2.6 + - - -
387D ASP* 4.0 29.6 + - - +
182E ASP* 5.4 0.2 + - - -
184E SER* 3.0 25.7 + - - +
185E LYS* 3.3 55.9 + - - +
186E PHE 3.0 0.4 - - - -
187E ASN* 1.3 78.2 - - - +
189E ILE* 1.3 64.9 + - + +
190E GLY 3.6 0.2 - - - -
----------------------------------------------------------
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