Contacts of the helix formed by residues 233 - 248 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 1.3 77.9 - - - +
234A LEU* 1.3 67.8 + - - +
235A LEU 3.4 0.7 - - - -
236A GLU* 3.0 23.7 + - - +
237A MET* 2.9 18.8 + - - +
99H ALA 3.3 23.4 - - - +
100H ASN* 4.1 5.6 + - - -
101H LEU* 4.5 2.9 + - - +
102H PRO* 3.8 17.9 - - - +
261H TRP 4.2 6.1 - - - +
262H GLY 3.6 4.8 - - - +
265H ARG* 3.9 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASP* 1.3 71.2 - - - +
235A LEU* 1.3 69.4 + - + +
237A MET* 2.9 20.8 + - + +
238A GLU* 3.0 25.9 + - + +
263A ALA* 4.2 13.2 - - + -
266A TYR* 3.9 24.7 - - + -
267A ILE* 4.1 16.6 - - + -
234H LEU* 3.3 29.6 - - + -
262H GLY 2.9 15.8 + - - +
263H ALA* 4.2 3.6 - - + -
266H TYR* 3.5 43.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASP* 3.4 1.0 - - - +
234A LEU* 1.3 85.8 - - + +
236A GLU* 1.3 72.6 + - - +
238A GLU* 3.3 22.5 + - - +
239A GLN* 3.1 33.5 + - - +
266H TYR* 3.8 37.4 - - + +
269H ASP* 6.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 3.8 15.7 - - + -
233A ASP* 3.0 34.3 + - - +
235A LEU* 1.3 82.6 - - - +
237A MET* 1.3 65.8 + - - +
239A GLN* 3.4 19.2 + - - +
240A ARG* 3.2 47.5 + - - +
97H GLU* 5.1 2.9 - - - +
99H ALA 5.4 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 3.3 40.7 - - + +
231A THR* 4.3 5.8 - - - -
232A ALA 3.3 35.4 - - - +
233A ASP 2.9 5.3 + - - +
234A LEU* 2.9 24.9 + - + +
236A GLU* 1.3 73.6 - - - +
238A GLU* 1.3 65.3 + - - +
240A ARG* 3.3 2.6 + - - +
241A LEU* 3.0 29.5 + - - +
254A VAL* 5.0 3.1 - - - -
259A THR* 4.3 20.9 - - + -
263A ALA* 5.5 0.9 - - + -
267A ILE* 4.0 26.2 - - + -
262H GLY* 4.0 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 3.0 23.2 + - + +
235A LEU* 3.4 24.3 - - - +
236A GLU 3.3 0.2 - - - -
237A MET* 1.3 74.7 - - - +
239A GLN* 1.3 66.8 + - + +
241A LEU* 3.2 4.6 + - - +
242A GLU* 3.0 22.2 + - - +
266A TYR* 2.5 45.6 + - + -
267A ILE* 5.5 1.3 - - + -
270A LEU* 4.2 19.3 - - + +
274A TYR* 4.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 3.1 20.6 + - - +
236A GLU* 3.7 23.7 + - - +
238A GLU* 1.3 79.8 - - + +
240A ARG* 1.3 62.1 + - + +
242A GLU* 3.2 15.5 + - - +
243A VAL* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A THR* 4.2 6.3 - - - -
196A SER* 3.6 19.8 + - - +
202A PHE* 3.5 41.9 - - + +
229A ASN 5.1 0.6 + - - -
230A ILE* 3.8 24.2 + - + +
231A THR 3.8 6.9 + - - -
232A ALA* 3.6 22.4 - - - +
236A GLU* 3.2 31.3 + - - +
237A MET 3.8 3.6 - - - +
238A GLU 3.2 0.2 - - - -
239A GLN* 1.3 80.9 + - + +
241A LEU* 1.3 66.1 + - - +
243A VAL* 3.3 7.2 + - + +
244A LEU* 3.1 27.2 + - - +
97H GLU* 2.8 40.4 + - - -
100H ASN* 4.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 3.6 20.6 - - + -
237A MET 3.0 21.6 + - - +
238A GLU* 3.5 5.8 - - - +
240A ARG* 1.3 75.1 - - - +
242A GLU* 1.3 64.3 + - - +
244A LEU* 3.2 8.0 + - - +
245A ALA* 3.0 22.7 + - - +
252A ALA* 3.6 31.0 - - + -
267A ILE* 4.3 18.8 - - + +
270A LEU* 3.6 31.9 - - + -
271A ALA* 4.3 10.8 - - + -
274A TYR* 3.9 14.1 - - + -
276A LEU* 4.0 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLU 3.0 12.3 + - - +
239A GLN* 3.3 16.7 - - - +
241A LEU* 1.3 75.1 - - - +
243A VAL* 1.3 64.7 + - + +
245A ALA* 3.4 0.9 + - - +
246A ASP* 2.9 46.7 + - - +
274A TYR* 3.8 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 4.0 13.0 - - + -
203A GLU* 4.7 15.3 - - + -
206A ALA* 3.8 28.7 - - + -
239A GLN* 2.9 20.6 + - + +
240A ARG* 3.4 13.7 - - + +
241A LEU 3.3 0.2 - - - -
242A GLU* 1.3 76.4 - - - +
244A LEU* 1.3 64.1 + - - +
246A ASP* 3.5 6.6 + - - +
247A LEU* 3.1 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PHE* 3.9 10.5 - - + -
206A ALA* 4.8 0.9 - - + -
226A TRP* 3.9 2.2 - - + -
228A ALA* 3.7 23.1 - - + -
230A ILE* 4.2 12.6 - - + -
240A ARG 3.1 15.7 + - - +
241A LEU* 3.2 7.8 + - - +
243A VAL* 1.3 75.5 - - - +
245A ALA* 1.3 66.1 + - - +
247A LEU* 3.0 12.3 + - - +
248A GLY 3.1 7.8 + - - -
249A LEU* 3.1 39.4 + - + -
251A HIS 3.4 22.2 - - - +
252A ALA* 3.7 22.9 - - + -
276A LEU* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU 3.0 4.1 + - - +
242A GLU 3.7 6.5 - - - +
244A LEU* 1.3 76.5 - - - +
246A ASP* 1.3 59.1 + - - +
248A GLY* 2.7 26.2 + - - -
249A LEU 5.0 1.1 - - - +
274A TYR* 3.2 50.7 - - + +
276A LEU* 4.4 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU* 2.9 40.9 + - - +
243A VAL* 3.7 7.1 - - - +
245A ALA* 1.3 77.1 - - - +
247A LEU* 1.3 62.5 + - + +
248A GLY* 3.3 1.0 + - - -
274A TYR* 5.9 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA* 3.4 41.5 - - + +
207A GLU* 2.9 32.1 - - - +
210A ALA* 4.2 21.1 - - + +
243A VAL* 3.1 22.0 + - + +
244A LEU 3.0 6.2 + - - +
246A ASP* 1.3 78.7 - - + +
248A GLY* 1.3 63.0 + - - +
249A LEU* 3.3 11.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ALA 2.7 16.8 + - - -
246A ASP 3.1 2.0 + - - -
247A LEU* 1.3 78.2 - - - +
249A LEU* 1.3 65.0 + - - +
250A LYS* 4.4 7.6 - - - +
----------------------------------------------------------
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