Contacts of the strand formed by residues 300 - 306 (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 ILE 300 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E PHE* 5.0 0.3 - - - -
194E PRO 5.0 0.2 - - - +
195E LYS* 4.4 3.1 - - - +
246E PHE* 5.7 1.8 - - + -
249E ALA* 4.1 10.3 - - + +
250E LYS* 4.0 37.7 - - + -
253E ALA* 3.6 21.5 - - + -
255E CYS* 3.7 15.7 - - - -
257E VAL* 4.5 9.2 - - + -
294E PHE* 3.3 52.7 - - + -
295E ASP 4.7 0.4 - - - +
296E SER* 3.8 10.5 + - - +
298E GLU* 4.3 14.1 - - + -
299E GLY* 1.3 77.9 - - - +
301E ILE* 1.3 67.1 + - - +
302E VAL* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E VAL* 4.0 29.8 - - + -
179E PHE* 4.2 12.3 - - + -
180E LEU* 4.2 19.1 - - + -
193E MET* 4.4 12.3 - - + -
194E PRO* 3.2 26.7 - - + +
195E LYS 4.0 1.8 - - - +
197E ILE* 4.2 15.9 - - + -
255E CYS 3.2 7.4 + - - +
256E ILE* 3.3 11.6 - - + +
257E VAL* 3.0 23.7 + - - +
296E SER* 6.1 0.2 - - - +
299E GLY 3.9 0.2 + - - -
300E ILE* 1.3 78.2 - - - +
302E VAL* 1.3 64.6 + - - +
303E MET* 3.8 22.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E LYS 3.0 13.5 + - - +
196E GLY* 3.1 3.8 - - - -
197E ILE 2.9 24.1 + - - -
246E PHE* 4.2 7.9 - - + -
257E VAL* 3.3 22.7 - - + +
259E ILE* 4.1 18.2 - - + -
291E MET* 3.1 33.4 - - + -
294E PHE* 3.9 12.6 - - + -
300E ILE* 4.4 4.0 - - + -
301E ILE* 1.3 76.1 - - - +
303E MET* 1.3 64.1 + - - +
322E PHE* 3.7 23.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 303 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E LEU* 4.1 23.6 - - + -
176E VAL* 5.6 0.4 - - - -
197E ILE* 3.5 16.4 - - + +
199E LEU* 3.5 39.3 - - + -
211E ALA* 4.1 22.7 - - + +
214E VAL* 4.7 9.0 - - + -
256E ILE* 4.5 15.5 - - + -
257E VAL 2.8 8.0 + - - +
258E PHE* 3.3 16.6 - - + -
259E ILE* 2.8 25.8 + - - +
301E ILE* 3.8 21.1 - - + -
302E VAL* 1.3 79.5 - - - +
304E ALA* 1.3 63.2 + - - +
322E PHE* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 304 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E ILE 2.9 6.0 + - - +
198E LEU* 3.6 10.3 - - + +
199E LEU* 2.7 36.7 + - - +
258E PHE* 4.5 2.5 - - - -
259E ILE* 3.3 13.0 - - + +
262E ILE* 4.0 19.7 - - + -
303E MET* 1.3 77.7 - - - +
305E ALA* 1.3 58.1 + - - +
322E PHE* 3.4 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E LEU* 3.3 4.9 - - + -
207E LYS* 3.9 26.2 - - + -
258E PHE* 3.8 16.6 - - + -
259E ILE 3.1 5.9 + - - -
260E ASP* 3.7 21.8 - - - +
261E GLU 3.1 7.1 + - - -
262E ILE* 3.0 26.6 + - - +
304E ALA* 1.3 76.7 - - - +
306E THR* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E LEU* 4.2 20.6 - - + -
199E LEU 3.1 8.6 + - - +
200E VAL* 3.4 2.6 - - + -
201E GLY 3.2 22.8 + - - +
207E LYS* 3.8 4.9 - - - +
261E GLU* 5.0 1.3 - - - +
262E ILE* 4.2 7.6 - - + -
263E ASP* 2.9 26.1 + - - +
305E ALA* 1.3 76.8 - - - +
307E ASN* 1.3 57.3 + - - +
308E ARG* 2.7 30.1 + - - +
309E PRO* 4.0 24.0 - - + -
312E LEU* 4.2 5.4 - - + -
----------------------------------------------------------
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