Contacts of the helix formed by residues 229 - 241 (chain A) in PDB entry 1UKI
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 229 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 6.2 0.7 - - - -
227A GLY 3.2 2.3 - - - -
228A THR* 1.3 109.0 + - - +
230A HIS* 1.3 67.1 + - + +
231A ILE* 2.9 15.0 - - + +
232A ASP* 3.2 6.4 + - + +
233A GLN* 2.7 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 5.2 16.2 - - + +
197A ILE* 3.8 32.1 - - + +
198A LEU* 5.8 0.2 - - - +
229A ASP* 1.3 82.8 + - - +
231A ILE* 1.3 83.8 + - + +
233A GLN* 3.5 12.3 - - - +
234A TRP* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASP* 2.9 8.4 - - + +
230A HIS* 1.3 105.4 - - + +
232A ASP* 1.3 61.7 + - - +
233A GLN 2.7 9.3 + - - -
234A TRP* 2.9 6.5 + - - +
235A ASN* 2.9 21.1 + - - +
259A TYR* 3.4 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLY* 3.0 10.3 - - - -
228A THR* 3.1 29.0 + - - +
229A ASP* 3.2 8.7 + - + +
231A ILE* 1.3 80.5 - - - +
233A GLN* 1.3 57.4 + - - +
235A ASN* 3.8 12.7 - - - +
236A LYS* 2.9 60.9 + - - +
259A TYR* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 2.9 33.3 + - + +
190A TYR* 3.0 20.9 + - + +
192A ARG 5.2 1.6 + - - -
197A ILE* 4.0 25.7 - - + +
225A PHE* 2.9 30.0 - - - +
226A PRO 3.2 15.7 - - - +
227A GLY 5.3 0.4 - - - +
229A ASP 2.7 18.7 + - - +
230A HIS* 3.5 11.0 - - - +
231A ILE 2.7 0.6 - - - -
232A ASP* 1.3 75.6 - - - +
234A TRP* 1.3 65.0 + - - +
235A ASN 3.1 1.3 - - - -
236A LYS* 3.4 3.7 + - - +
237A VAL* 2.8 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PRO* 3.8 20.2 - - + -
197A ILE* 4.4 11.0 - - + -
198A LEU* 3.8 38.4 - - + -
230A HIS 3.3 10.6 + - - +
231A ILE* 2.9 7.9 + - - +
233A GLN* 1.3 80.7 - - - +
235A ASN* 1.3 66.6 + - - +
237A VAL* 3.3 10.7 + - + +
238A ILE* 3.1 58.2 + - + +
244A PRO* 3.8 14.1 - - + -
248A PHE* 4.5 4.0 - + - -
252A LEU* 4.8 2.0 - - + -
256A VAL* 5.8 0.4 - - + -
259A TYR* 4.1 23.1 - + + -
260A VAL* 3.3 33.0 - - + +
263A ARG* 5.6 1.5 - - - +
304A ILE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ILE 2.9 15.0 + - - +
232A ASP* 3.7 17.3 - - - +
234A TRP* 1.3 82.6 - - - +
236A LYS* 1.3 56.8 + - + +
237A VAL 3.2 0.2 + - - -
238A ILE* 3.7 2.9 - - - +
239A GLU* 2.9 34.3 + - - +
259A TYR* 3.8 8.8 + - - +
263A ARG* 2.9 48.9 + - - +
266A TYR* 3.8 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 4.1 5.9 - - - -
226A PRO* 4.1 22.9 - - + -
227A GLY* 3.3 25.6 - - - +
228A THR* 6.0 0.4 - - - -
232A ASP* 2.9 47.6 + - - +
233A GLN* 3.4 4.7 + - - +
235A ASN* 1.3 76.7 - - + +
237A VAL* 1.3 58.2 + - + +
239A GLU* 3.7 18.5 + - - +
240A GLN* 3.1 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PRO* 5.3 5.2 - - + -
209A TRP* 3.8 28.7 - - + +
225A PHE* 3.8 32.5 - - + -
233A GLN* 2.8 33.0 - - + +
234A TRP* 3.6 13.5 - - + +
235A ASN 3.2 0.6 - - - -
236A LYS* 1.3 76.3 - - - +
238A ILE* 1.3 56.5 + - - +
241A LEU* 2.8 43.4 + - + +
304A ILE* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TRP* 3.1 62.0 + - + +
235A ASN* 3.7 7.0 - - - +
237A VAL* 1.3 73.2 - - - +
239A GLU* 1.3 71.4 + - - +
242A GLY* 2.7 27.3 + - - +
243A THR* 3.4 35.7 - - + -
244A PRO* 3.3 18.8 - - + -
260A VAL* 5.5 3.1 - - + -
266A TYR* 3.7 14.5 - - + +
304A ILE* 3.5 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASN* 2.9 16.9 + - - +
236A LYS* 3.7 24.0 + - - +
238A ILE* 1.3 84.3 - - - +
240A GLN* 1.3 68.4 + - + +
266A TYR* 3.8 36.7 + - + +
268A GLY* 3.1 18.2 + - - -
269A TYR* 3.7 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LYS* 3.9 19.9 + - - +
224A LEU* 3.7 24.4 + - - +
225A PHE* 4.0 17.3 - - + -
236A LYS* 3.1 23.4 + - + +
237A VAL 4.0 1.8 - - - +
239A GLU* 1.3 85.3 - - + +
241A LEU* 1.3 58.8 + - + +
268A GLY* 3.1 18.7 - - - -
269A TYR* 3.1 27.9 + - + +
274A LEU* 3.4 32.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
209A TRP* 3.1 39.3 - - + -
225A PHE* 4.2 15.7 - - + -
237A VAL* 2.8 20.8 + - + +
240A GLN* 1.3 77.9 - - + +
242A GLY* 1.3 58.7 + - - +
267A ALA 3.9 2.4 - - - +
268A GLY* 3.2 7.8 - - - -
269A TYR 3.7 10.0 + - - +
271A PHE* 4.0 20.9 - - + -
274A LEU* 4.4 13.2 - - + -
302A LEU* 3.5 28.9 - - + +
304A ILE* 3.7 16.6 - - + -
----------------------------------------------------------
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