Contacts of the helix formed by residues 233 - 247 (chain E) in PDB entry 3KDO
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 233 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E ALA* 1.3 78.3 - - - +
234E LEU* 1.3 67.6 + - - +
235E LEU 3.4 0.7 - - - +
236E GLU* 3.1 22.0 + - - +
237E MET* 2.9 19.3 + - - +
99I ALA 3.2 24.9 - - - +
100I ASN* 4.0 3.4 + - - -
101I LEU* 4.5 3.0 + - - +
102I PRO* 3.7 19.7 - - - +
261I TRP 4.1 5.2 - - - +
262I GLY 3.9 4.2 - - - +
265I ARG* 3.8 37.3 + - + +
266I TYR 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ASP* 1.3 71.5 - - - +
235E LEU* 1.3 68.1 + - + +
237E MET* 2.9 20.8 + - + +
238E GLU* 2.9 23.7 + - - +
263E ALA* 4.1 12.6 - - + -
266E TYR* 4.0 17.9 - - + -
267E ILE* 4.0 24.9 - - + -
234I LEU* 3.5 25.8 - - + -
262I GLY 2.9 19.2 + - - +
263I ALA* 4.4 3.6 - - + -
265I ARG* 6.2 0.4 - - - +
266I TYR* 3.5 45.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ASP* 3.4 1.2 - - - +
234E LEU* 1.3 84.4 - - + +
236E GLU* 1.3 70.4 + - - +
238E GLU* 3.1 25.1 + - - +
239E GLN* 3.0 32.4 + - + +
266I TYR* 3.9 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E ALA* 3.8 16.8 - - + -
233E ASP* 3.1 30.3 + - - +
235E LEU* 1.3 82.6 - - - +
237E MET* 1.3 58.5 + - - +
239E GLN* 3.4 19.4 + - - +
240E ARG* 3.1 55.8 + - - +
97I GLU* 4.8 2.5 - - - +
99I ALA 5.3 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ILE* 3.1 43.6 - - + +
231E THR* 4.3 4.3 - - - -
232E ALA 3.1 31.6 - - - +
233E ASP 2.9 7.8 + - - +
234E LEU* 2.9 17.9 + - + +
236E GLU* 1.3 74.8 - - - +
238E GLU* 1.3 58.9 + - - +
240E ARG* 3.5 2.5 + - - +
241E LEU* 3.0 35.9 + - - +
254E VAL* 5.0 2.5 - - - -
259E THR* 4.1 26.7 - - + +
263E ALA* 5.7 0.4 - - + -
267E ILE* 4.3 20.2 - - + -
262I GLY* 3.7 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E LEU* 2.9 25.1 + - + +
235E LEU* 3.1 26.2 + - - +
237E MET* 1.3 75.7 - - - +
239E GLN* 1.3 65.8 + - + +
241E LEU* 3.4 4.0 + - - +
242E GLU* 3.0 22.6 + - - +
266E TYR* 2.6 40.0 + - + -
267E ILE* 5.0 2.2 - - + -
270E LEU* 3.7 26.2 - - + +
274E TYR* 4.9 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E LEU* 3.0 16.8 + - + +
236E GLU* 3.4 35.5 + - - +
237E MET 3.4 0.2 - - - -
238E GLU* 1.3 76.3 - - + +
240E ARG* 1.3 61.7 + - + +
242E GLU* 3.2 15.2 + - - +
243E VAL* 2.9 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E THR* 4.3 3.6 - - - +
196E SER* 3.5 22.9 + - - +
202E PHE* 3.4 41.7 - - + +
203E GLU* 6.0 0.9 - - - +
229E ASN 5.2 0.8 + - - -
230E ILE* 3.9 25.3 + - + +
231E THR 4.1 5.5 + - - -
232E ALA* 3.8 14.3 - - - +
236E GLU* 3.1 44.4 + - - +
237E MET 3.9 3.4 - - - +
239E GLN* 1.3 79.4 - - + +
241E LEU* 1.3 63.2 + - - +
243E VAL* 3.5 3.7 + - + -
244E LEU* 3.2 27.8 + - - +
97I GLU* 2.5 42.2 + - - -
100I ASN* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ILE* 3.8 17.7 - - + +
237E MET 3.0 21.2 + - - +
238E GLU 3.6 4.7 - - - +
239E GLN 3.3 0.2 - - - -
240E ARG* 1.3 75.6 - - - +
242E GLU* 1.3 63.6 + - - +
244E LEU* 3.2 8.0 + - + +
245E ALA* 3.1 22.5 + - - +
252E ALA* 3.6 31.0 - - + -
267E ILE* 4.1 21.3 - - + +
270E LEU* 3.9 32.8 - - + -
271E ALA* 4.2 11.9 - - + +
274E TYR* 4.0 12.8 - - + -
276E LEU* 3.8 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E GLU 3.0 14.0 + - - +
239E GLN* 3.2 16.7 + - - +
241E LEU* 1.3 76.6 - - - +
243E VAL* 1.3 61.0 + - + +
245E ALA* 3.3 2.1 + - - +
246E ASP* 3.0 42.3 + - - +
274E TYR* 3.9 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E PHE* 4.2 11.0 - - + -
203E GLU* 4.5 20.2 - - + -
206E ALA* 3.9 27.4 - - + -
207E GLU* 6.1 0.2 - - + -
239E GLN* 2.9 19.8 + - + +
240E ARG* 3.7 10.5 - - + +
241E LEU 3.3 0.2 - - - -
242E GLU* 1.3 76.1 - - + +
244E LEU* 1.3 65.5 + - - +
246E ASP* 3.4 6.6 + - - +
247E LEU* 3.1 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E PHE* 3.6 26.9 - - + -
206E ALA* 4.5 1.3 - - + -
226E TRP* 3.8 2.5 - - + -
228E ALA* 3.8 12.8 - - + -
230E ILE* 4.1 6.7 - - + -
240E ARG 3.2 15.2 + - - +
241E LEU* 3.2 8.2 + - - +
243E VAL* 1.3 77.0 - - - +
245E ALA* 1.3 63.5 + - - +
247E LEU 3.2 2.3 + - - -
248E GLY 3.1 3.6 + - - -
249E LEU* 3.0 58.1 + - + +
251E HIS 3.4 20.9 - - - +
252E ALA* 3.8 20.9 - - + -
276E LEU* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E LEU 3.1 7.8 + - - +
242E GLU 3.7 7.0 - - - +
244E LEU* 1.3 75.5 - - - +
246E ASP* 1.3 61.5 + - - +
248E GLY* 2.9 20.1 + - - -
249E LEU 5.1 0.4 - - - -
274E TYR* 3.4 50.5 - - + +
276E LEU* 4.3 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E GLU* 3.0 38.7 + - - +
243E VAL* 3.8 5.9 - - - +
245E ALA* 1.3 79.0 - - - +
247E LEU* 1.3 64.0 + - + +
248E GLY* 3.4 0.9 + - - -
274E TYR* 5.8 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E ALA* 3.5 21.5 - - + +
207E GLU* 3.5 47.8 - - + +
210E ALA* 4.1 23.8 - - + +
243E VAL* 3.1 24.7 + - + +
244E LEU 3.2 3.8 + - - +
245E ALA 3.2 0.2 - - - -
246E ASP* 1.3 79.4 - - + +
248E GLY* 1.3 60.6 + - - +
249E LEU* 3.2 8.0 + - + +
----------------------------------------------------------
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