Contacts of the helix formed by residues 218 - 234 (chain B) in PDB entry 1TE6
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 GLU 218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.5 6.3 - - - +
216B ILE* 4.7 1.2 - - - +
217B LEU* 1.3 90.7 + - + +
219B ASN* 1.3 62.5 + - - +
220B SER* 3.9 15.8 + - - +
221B GLU* 3.0 43.4 + - + +
222B ALA 3.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.4 17.7 - - - +
163B ALA* 3.8 8.4 - - - +
164B MET* 3.0 68.5 - - - +
167B PHE* 3.7 4.8 - - + -
217B LEU 4.1 5.0 - - - +
218B GLU* 1.3 75.6 + - - +
220B SER* 1.3 61.8 + - - +
222B ALA* 3.3 5.5 + - - +
223B LEU* 3.3 24.1 + - - +
258B LEU* 4.4 13.2 - - - +
278B LEU* 5.0 1.8 - - + +
282B PHE* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLU* 3.9 15.8 + - - +
219B ASN* 1.3 76.9 - - - +
221B GLU* 1.3 60.6 + - - +
223B LEU* 3.4 6.9 + - - +
224B GLU* 2.9 28.2 + - - +
282B PHE* 4.1 23.3 - - - -
286B TYR* 3.4 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS* 4.7 12.0 + - - +
199B TYR* 2.7 31.9 + - - +
216B ILE* 2.9 24.9 - - + +
217B LEU 5.3 0.7 + - - -
218B GLU* 3.0 30.8 + - + +
220B SER* 1.3 80.2 + - - +
222B ALA* 1.3 64.6 + - - +
224B GLU* 3.2 7.8 + - + +
225B LEU* 3.0 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 4.0 13.6 - - + +
162B LEU* 4.1 11.2 - - + -
167B PHE* 3.7 33.7 - - + -
216B ILE* 5.2 4.4 - - + +
218B GLU 3.4 1.8 + - - -
219B ASN 3.3 10.2 + - - +
221B GLU* 1.3 80.0 - - - +
223B LEU* 1.3 62.2 + - - +
225B LEU* 3.2 13.5 + - - +
226B VAL* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 3.7 22.9 - - + -
219B ASN 3.3 13.3 + - - +
220B SER* 3.7 6.7 - - - +
221B GLU 3.3 0.2 - - - -
222B ALA* 1.3 79.3 - - - +
224B GLU* 1.3 57.9 + - - +
226B VAL* 3.4 4.9 + - + +
227B LYS* 2.9 30.3 + - - +
241B ILE* 3.9 27.4 - - + +
243B MET* 4.1 6.3 - - - -
282B PHE* 3.6 43.3 - - + -
286B TYR* 3.6 33.5 - - + +
288B VAL* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS* 5.8 6.1 - - - +
220B SER 2.9 17.9 + - - +
221B GLU* 3.5 11.7 - - + +
222B ALA 3.2 0.2 - - - -
223B LEU* 1.3 77.5 - - - +
225B LEU* 1.3 55.3 + - + +
227B LYS* 3.4 25.4 + - - +
228B GLU* 3.0 34.1 + - - +
286B TYR* 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 5.1 5.6 - - + -
191B LEU* 4.2 8.7 - - + +
194B VAL* 3.9 20.5 - - + +
195B ILE* 3.3 36.3 - - + -
198B LYS* 4.3 12.8 - - + +
199B TYR* 3.6 32.5 - - + +
214B PRO* 4.3 11.2 - - + -
216B ILE* 5.0 3.1 - - + -
221B GLU* 3.0 20.6 + - + +
222B ALA* 3.5 13.2 - - - +
224B GLU* 1.3 74.6 - - + +
226B VAL* 1.3 66.3 + - + +
228B GLU* 3.4 9.3 + - - +
229B ALA* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.2 12.3 - - + -
152B ILE* 3.9 23.3 - - + -
167B PHE* 4.4 13.5 - - + +
168B MET 5.0 1.1 - - - +
169B ILE* 3.4 17.9 - - + -
187B VAL* 5.8 0.7 - - + -
191B LEU* 5.0 2.9 - - + -
222B ALA 3.1 15.8 + - - +
223B LEU* 3.7 8.1 - - - +
225B LEU* 1.3 73.6 - - - +
227B LYS* 1.3 66.2 + - - +
229B ALA* 3.2 6.9 + - + +
230B ILE* 2.9 23.3 + - + +
241B ILE* 3.1 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU 2.9 17.9 + - - +
224B GLU* 3.5 35.4 + - - +
225B LEU 3.3 0.2 - - - -
226B VAL* 1.3 77.8 - - - +
228B GLU* 1.3 65.5 + - - +
230B ILE* 3.2 7.4 + - - +
231B ASP* 2.9 49.6 + - - +
241B ILE* 5.4 3.5 - - + +
285B ASP 4.8 4.5 - - - +
286B TYR* 3.9 20.4 - - + -
287B PRO* 4.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 3.5 34.9 - - + +
198B LYS* 5.7 4.9 + - - +
224B GLU* 3.0 23.7 + - - +
225B LEU* 3.7 9.7 - - - +
226B VAL 3.3 0.2 - - - -
227B LYS* 1.3 82.9 - - - +
229B ALA* 1.3 52.0 + - - +
231B ASP* 3.3 7.2 + - + +
232B LYS* 2.7 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 4.1 12.2 - - + +
190B THR* 3.7 12.3 - - - +
191B LEU* 3.7 40.6 - - + +
194B VAL* 4.7 4.7 - - + +
225B LEU 3.1 17.0 + - - +
226B VAL* 3.2 5.8 + - - +
228B GLU* 1.3 73.3 - - - +
230B ILE* 1.3 66.8 + - - +
232B LYS* 4.4 0.4 - - - -
233B ALA* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 3.7 12.3 - - + -
187B VAL* 3.2 34.1 - - + -
226B VAL* 2.9 21.9 + - + +
227B LYS* 3.5 8.5 - - - +
229B ALA* 1.3 75.2 - - - +
231B ASP* 1.3 67.1 + - - +
233B ALA* 3.3 3.1 + - - +
234B GLY 3.2 4.0 + - - -
235B TYR* 3.1 47.5 + - - +
236B THR* 3.6 12.3 - - - -
239B ILE* 3.2 41.3 - - + +
241B ILE* 4.6 5.4 - - + -
287B PRO* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LYS* 2.9 43.7 + - - +
228B GLU* 3.7 6.3 - - + +
230B ILE* 1.3 79.8 - - - +
232B LYS* 1.3 57.1 + - - +
234B GLY* 2.9 20.4 + - - -
236B THR* 2.4 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 3.6 26.1 + - + +
193B GLY* 5.2 2.2 - - - -
194B VAL* 3.9 25.5 - - + +
197B ASP* 4.6 12.9 + - - -
228B GLU* 2.7 28.3 + - + +
231B ASP* 1.3 74.0 - - - +
233B ALA* 1.3 59.7 + - - +
234B GLY 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 4.5 4.3 - - + +
187B VAL* 3.8 16.2 - - + +
190B THR* 3.9 17.9 - - - +
229B ALA 3.0 17.4 + - - +
230B ILE 3.7 4.5 - - - +
231B ASP 3.1 0.4 - - - -
232B LYS* 1.3 76.9 - - - +
234B GLY* 1.3 61.4 + - - +
235B TYR* 3.5 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE 3.2 0.2 + - - -
231B ASP 2.9 15.7 + - - -
232B LYS 3.2 1.2 - - - -
233B ALA* 1.3 79.5 - - - +
235B TYR* 1.3 68.7 + - - +
236B THR* 3.6 3.3 + - - -
237B GLU* 5.5 2.9 - - - +
----------------------------------------------------------
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