Contacts of the helix formed by residues 272 - 286 (chain B) in PDB entry 4IXU
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 THR 272 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 4.0 10.8 - - - +
255B PHE* 3.5 4.8 - - - -
256B ASP* 5.6 0.7 - - + -
259B LEU* 3.7 6.3 - - - -
270B GLY 4.7 0.9 - - - +
271B LEU* 1.3 78.0 - - - +
273B TYR* 1.3 66.7 + - - +
274B ARG* 3.6 8.9 + - - +
275B GLU* 3.0 37.2 + - - +
276B GLY 3.0 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 4.1 5.4 - - - -
259B LEU* 3.3 27.5 - - + +
272B THR* 1.3 73.7 - - - +
274B ARG* 1.3 65.8 + - + +
276B GLY* 3.2 2.9 + - - -
277B MET* 2.9 50.5 + - + +
314B LEU* 3.6 27.6 - - + -
317B ASP* 2.6 34.1 + - - -
327B ARG* 5.4 6.5 - - - -
268C VAL* 3.4 30.4 - - + +
269C GLY* 3.6 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B THR* 3.2 8.3 + - - +
273B TYR* 1.3 83.9 - - + +
275B GLU* 1.3 57.9 + - + +
277B MET* 3.4 3.1 + - - +
278B TYR* 2.9 28.8 + - - +
327B ARG* 3.8 15.5 - - - +
219C MET* 3.3 12.9 - - + +
222C ILE* 3.5 18.4 + - - +
223C ASP* 2.8 41.5 + - - +
269C GLY* 3.7 33.9 - - - +
270C GLY 3.1 18.9 + - - -
272C THR* 4.0 11.1 - - - +
275C GLU* 2.8 42.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG* 2.8 46.3 + - - -
222B ILE* 3.4 14.6 - - - +
227B ILE* 4.0 24.2 + - + +
271B LEU* 3.5 16.9 - - + +
272B THR* 3.0 32.9 + - - +
274B ARG* 1.3 76.7 - - + +
276B GLY* 1.3 57.7 + - - +
278B TYR* 3.1 7.6 + - - +
279B ILE* 2.9 34.8 + - - +
223C ASP* 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE* 4.6 6.5 - - - -
255B PHE* 3.6 26.9 - - - -
271B LEU* 4.5 4.6 - - - +
272B THR 3.0 11.1 + - - -
273B TYR 3.2 0.2 + - - -
275B GLU* 1.3 75.1 - - - +
277B MET* 1.3 69.3 + - - +
279B ILE* 3.4 14.3 + - - +
280B ALA* 3.1 22.3 + - - +
318B VAL* 5.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 4.2 5.6 - - + -
273B TYR* 2.9 53.7 + - + +
274B ARG 3.7 4.9 - - - +
276B GLY* 1.3 77.2 - - - +
278B TYR* 1.3 58.3 + - - +
280B ALA* 3.3 1.0 + - - -
281B GLU* 2.8 38.0 + - - +
314B LEU* 4.4 1.1 - - + -
317B ASP* 3.8 31.4 - - + +
318B VAL* 3.8 38.4 - - + +
321B SER* 3.5 10.4 + - - +
327B ARG* 4.1 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ILE* 3.8 24.9 - - + -
228B GLN* 3.5 29.8 + - + +
231B MET* 3.9 9.9 - - + -
232B GLU* 6.0 0.2 - - - +
274B ARG 2.9 18.6 + - - +
275B GLU 3.1 5.1 + - - +
277B MET* 1.3 76.8 - - - +
279B ILE* 1.3 63.7 + - - +
281B GLU* 3.3 10.9 + - - +
282B GLU* 2.9 47.0 + - + +
327B ARG* 4.0 8.0 - - - +
220C ARG* 3.4 25.4 - - + -
223C ASP* 4.3 11.0 - - + +
224C ARG* 2.7 50.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 5.3 0.2 - - + -
142B VAL* 4.2 25.4 - - + -
196B ILE* 4.0 21.5 - - + -
227B ILE* 3.7 20.0 - - + -
231B MET* 3.9 26.9 - - + +
248B LEU* 5.0 1.6 - - + -
250B PHE* 4.5 8.3 - - + -
271B LEU* 3.8 30.3 - - + -
275B GLU 2.9 17.8 + - - +
276B GLY* 3.5 8.5 - - - +
278B TYR* 1.3 75.2 - - - +
280B ALA* 1.3 64.7 + - - +
282B GLU* 3.2 4.0 + - - +
283B ILE* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU* 5.3 1.3 - - + -
250B PHE* 5.6 0.9 - - + -
276B GLY 3.1 12.9 + - - +
277B MET* 3.7 1.1 - - - +
279B ILE* 1.3 82.0 - - - +
281B GLU* 1.3 57.8 + - - +
283B ILE* 3.3 8.2 + - - +
284B HIS 2.9 23.6 + - - -
318B VAL* 3.6 13.7 - - + +
321B SER* 3.5 32.2 - - - +
322B SER* 3.4 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B MET* 2.8 17.1 + - - +
278B TYR* 3.3 5.5 + - - +
280B ALA* 1.3 76.7 - - - +
282B GLU* 1.3 56.6 + - - +
284B HIS* 3.2 5.3 + - - +
285B ASN* 2.8 36.0 + - - +
321B SER* 3.1 25.3 + - - +
325B GLN 4.1 9.8 - - - +
326B THR* 5.1 3.1 - - + -
327B ARG* 2.8 59.1 + - - +
220C ARG* 3.1 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B MET* 3.9 13.2 - - + +
232B GLU* 6.1 1.0 - - - +
235B PHE* 3.6 22.7 - - + -
278B TYR* 2.9 48.4 + - + +
279B ILE 3.7 3.4 - - - +
281B GLU* 1.3 72.7 - - - +
283B ILE* 1.3 66.5 + - - +
285B ASN* 3.2 24.8 + - - +
286B THR* 3.2 18.0 + - - +
220C ARG* 2.6 39.7 + - - -
224C ARG* 5.0 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 4.2 15.0 - - + -
231B MET* 4.7 1.1 - - + -
235B PHE* 4.0 22.9 - - + -
246B ILE* 4.0 22.7 - - + -
248B LEU* 4.1 29.2 - - + -
279B ILE* 3.0 23.6 + - + +
280B ALA* 3.3 8.9 + - - +
282B GLU* 1.3 75.7 - - - +
284B HIS* 1.3 60.9 + - - +
286B THR* 2.7 26.5 + - - +
287B GLY 4.0 0.3 + - - -
289B LEU* 3.8 43.7 + - + +
322B SER* 4.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ALA 2.9 7.3 + - - -
281B GLU* 3.4 7.6 - - - +
283B ILE* 1.3 77.4 - - - +
285B ASN* 1.3 75.1 + - - +
287B GLY* 3.0 22.0 + - - -
289B LEU* 5.4 2.5 - - - -
321B SER 3.5 13.5 - - - +
322B SER 3.4 18.5 + - - +
323B PHE* 3.5 9.1 - - - -
324B GLY* 3.4 36.4 + - - -
326B THR* 6.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLU* 2.8 19.5 + - - +
282B GLU* 3.2 33.8 + - - +
284B HIS* 1.3 91.4 - - - +
286B THR* 1.3 61.5 + - - +
287B GLY* 3.1 0.8 + - - -
220C ARG* 3.6 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE* 3.6 36.8 - - + -
239B ILE* 4.2 7.9 - - + -
243B GLN* 4.6 4.5 + - - +
246B ILE* 3.4 18.2 - - + +
282B GLU 3.2 15.9 + - - +
283B ILE 2.7 16.5 + - - +
285B ASN* 1.3 77.3 - - - +
287B GLY* 1.3 59.6 + - - +
288B LEU* 3.0 30.9 + - - +
289B LEU 4.0 0.2 + - - -
----------------------------------------------------------
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