Contacts of the helix formed by residues 228 - 240 (chain B) in PDB entry 1ASZ
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 LEU 228 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASN* 1.3 70.1 + - - +
229B ASP* 1.3 57.4 + - - +
231B ARG* 4.0 19.9 - - - +
232B LEU* 2.8 54.3 - - + +
235B ARG* 5.3 1.1 - - - +
541B ASN* 3.1 40.2 - - + +
543B ARG* 4.5 7.6 - - + +
544B ARG* 3.2 45.5 - - - +
669S C 4.7 13.2 - - - +
670S G 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASN* 2.7 9.5 + - + +
228B LEU* 1.3 75.0 - - - +
230B THR* 1.3 58.3 + - - +
232B LEU* 3.3 7.3 + - - +
233B ASP* 2.6 40.9 + - - +
554B ARG* 4.6 11.8 + - - -
667S C 5.1 0.9 + - - -
668S G 3.6 51.1 + - - +
669S C 3.9 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 4.2 4.9 - - - +
226B VAL* 3.4 23.6 - - + +
227B ASN* 2.7 27.0 + - + +
229B ASP* 1.3 73.0 - - - +
231B ARG* 1.3 66.6 + - - +
232B LEU 3.1 1.1 - - - -
233B ASP* 3.1 7.4 + - - -
234B TYR* 3.1 42.4 + - - +
611S U 4.3 11.3 + - - +
612S U 3.2 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 5.0 1.6 - - - -
210B ASP 4.3 3.6 + - - -
211B ALA* 3.1 36.0 + - - +
213B ARG 5.2 3.4 + - - -
225B VAL* 3.9 17.4 + - - +
226B VAL* 4.0 12.6 - - + -
227B ASN* 2.8 30.0 + - - +
228B LEU* 4.0 27.6 - - - +
230B THR* 1.3 76.7 - - - +
232B LEU* 1.3 69.5 + - + +
234B TYR 3.0 5.2 - - - +
235B ARG* 3.0 22.3 + - - +
238B ASP* 2.6 54.9 + - - +
244B ASN* 5.5 0.4 - - - +
383B GLN* 4.4 6.7 + - - -
384B TYR* 4.5 13.7 + - - -
544B ARG* 5.2 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 2.8 37.0 - - + +
229B ASP* 3.3 6.2 + - - +
230B THR 3.1 0.6 - - - -
231B ARG* 1.3 82.2 - - + +
233B ASP* 1.3 61.5 + - - +
235B ARG* 3.1 53.4 - - - +
543B ARG* 3.8 35.2 - - + +
549B PRO* 4.1 13.0 - - + -
554B ARG* 3.1 33.0 - - - +
557B PRO* 3.2 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ASP* 5.6 1.7 - - - +
229B ASP* 2.6 39.6 + - - +
230B THR* 3.1 8.7 + - - +
232B LEU* 1.3 75.8 - - - +
234B TYR* 1.3 77.8 + - + +
235B ARG 3.5 0.8 + - - -
554B ARG* 2.9 28.9 + - - +
557B PRO* 4.5 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A TYR* 4.1 20.6 - + - -
205B PRO* 3.6 35.8 - - + +
206B ILE* 3.3 35.1 - - + +
230B THR* 3.1 25.4 + - - +
231B ARG 3.0 5.5 - - - +
233B ASP* 1.3 91.7 - - + +
235B ARG* 1.3 58.2 + - - +
236B VAL* 3.4 4.3 - - - -
237B ILE* 3.2 14.2 + - + +
238B ASP* 2.9 22.7 + - - +
610S G 5.8 0.2 + - - -
611S U 5.0 9.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 5.3 1.6 - - - +
231B ARG* 3.0 6.8 + - - +
232B LEU* 3.1 47.5 + - - +
233B ASP 3.5 1.0 - - - -
234B TYR* 1.3 72.9 - - - +
236B VAL* 1.3 67.6 + - + +
237B ILE 3.1 1.6 - - - -
238B ASP* 3.4 23.5 + - - +
239B LEU* 2.9 54.2 + - + +
244B ASN* 4.8 6.3 + - - -
248B PHE* 3.5 15.2 - - - -
543B ARG 3.8 1.0 + - - -
544B ARG* 2.8 26.2 + - - +
546B SER 2.8 25.0 + - - -
547B LEU 2.9 18.6 + - - +
548B PHE* 5.1 5.8 - - + -
549B PRO* 4.6 3.0 - - + +
557B PRO* 3.9 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN* 3.7 29.8 - - + +
311A VAL* 4.0 23.6 - - + -
312A ALA* 3.3 32.2 - - - +
510A ASP 5.5 2.2 - - - +
514A GLY* 4.5 6.5 - - - +
517A TYR* 3.4 34.3 - - + -
234B TYR* 4.8 2.5 - - - +
235B ARG* 1.3 77.3 - - + +
237B ILE* 1.3 64.4 + - + +
239B LEU* 3.8 3.1 - - - +
240B ARG* 3.6 5.3 - - - -
548B PHE* 4.8 12.8 - - + -
557B PRO* 5.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A TYR* 3.0 55.9 - - + -
204B LEU* 4.2 14.8 - - + -
205B PRO* 3.8 24.9 - - + +
206B ILE* 4.0 19.7 - - + +
208B LEU* 4.0 22.9 - - + +
234B TYR* 3.2 12.0 + - + +
235B ARG 3.1 0.2 - - - -
236B VAL* 1.3 79.5 - - + +
238B ASP* 1.3 67.1 + - - +
239B LEU 3.1 1.8 - - - -
240B ARG* 3.0 34.2 + - - +
241B THR 4.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 4.1 8.9 - - + +
211B ALA* 3.6 9.9 - - - +
231B ARG* 2.6 62.0 + - + +
234B TYR 2.9 16.7 + - - +
235B ARG* 3.4 24.4 + - - +
237B ILE* 1.3 76.2 - - - +
239B LEU* 1.3 54.1 + - - +
241B THR* 2.8 21.6 - - - +
244B ASN* 2.4 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA* 3.9 14.1 - - + +
314A PHE* 3.8 16.6 - - + -
235B ARG* 2.9 61.0 + - + +
236B VAL* 3.8 6.7 - - - +
237B ILE 3.1 0.2 - - - -
238B ASP* 1.3 78.6 - - - +
240B ARG* 1.3 61.2 + - - +
241B THR 3.1 3.5 + - - +
244B ASN* 3.2 32.1 - - + +
245B GLN* 3.6 10.2 + - - -
248B PHE* 3.1 39.3 - - + -
547B LEU* 4.1 7.0 - - + +
548B PHE* 4.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 2.9 32.4 + - - +
312A ALA 3.7 6.0 + - - +
313A ASP* 3.3 29.6 - - + +
517A TYR* 2.7 48.2 + - - +
518A GLY 3.7 2.0 + - - -
114B ARG* 3.4 9.8 - - - +
131B ARG* 3.8 27.7 + - - +
133B GLN* 4.5 0.7 - - - +
163B GLU* 2.7 41.5 + - - +
204B LEU* 3.9 4.4 - - - +
208B LEU* 4.1 8.1 - - + -
236B VAL 3.6 15.7 + - - -
237B ILE* 3.0 23.5 + - - +
239B LEU* 1.3 75.8 - - - +
241B THR* 1.3 65.1 + - - +
242B VAL 3.6 0.3 + - - -
245B GLN* 4.1 9.3 + - - +
----------------------------------------------------------
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