Contacts of the helix formed by residues 220 - 237 (chain B) in PDB entry 2QKW
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 220 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B HIS* 3.2 57.4 + - + +
161B ILE* 3.6 22.0 - - + +
193B ASP* 2.8 36.7 - - - +
194B GLN 5.9 0.2 - - - -
195B THR* 4.1 8.1 + - - +
219B THR* 1.3 73.0 - - - +
221B LYS* 1.3 78.2 + - + +
222B SER 3.1 0.4 - - - -
223B ASP* 3.1 16.2 + - - +
224B VAL* 3.8 1.3 + - - +
302B SER* 4.7 10.4 - - - -
303B MET 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 3.0 13.0 - - - +
220B GLU* 1.3 87.4 - - + +
222B SER* 1.3 63.1 + - - +
223B ASP 3.1 2.2 - - - -
224B VAL* 3.1 24.5 + - + +
225B TYR 3.3 6.4 + - - -
297B SER* 3.6 29.1 + - - +
298B GLU* 4.2 7.3 + - - +
300B ARG* 3.2 40.4 + - + +
301B PRO 3.6 15.7 - - - +
302B SER* 3.8 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ARG* 6.0 0.9 - - - -
209B ASP* 2.7 40.5 + - - +
212B TYR* 3.9 8.1 - - - +
217B ARG 4.5 0.3 + - - -
218B LEU* 3.7 19.6 - - - +
219B THR* 2.8 30.9 + - - -
221B LYS* 1.3 79.5 - - - +
223B ASP* 1.3 61.8 + - - +
225B TYR 3.8 1.1 + - - -
226B SER* 3.2 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 4.9 6.0 - - + +
155B LEU* 5.4 0.2 - - - +
156B HIS* 3.0 26.2 + - + +
161B ILE* 3.4 11.5 - - - +
162B HIS* 2.7 32.4 + - - +
163B ARG* 2.7 30.0 + - - -
165B VAL* 4.3 11.2 - - + +
220B GLU 3.1 8.8 + - - +
221B LYS 3.1 0.2 - - - -
222B SER* 1.3 77.0 - - - +
224B VAL* 1.3 55.6 + - - +
226B SER* 3.2 8.4 + - - -
227B PHE* 2.7 35.2 + - - +
303B MET* 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B HIS* 4.7 0.9 - - + -
220B GLU* 4.2 3.4 - - - +
221B LYS* 3.1 25.9 + - + +
223B ASP* 1.3 74.6 - - - +
225B TYR* 1.3 54.3 + - - +
227B PHE* 3.2 2.9 + - - +
228B GLY* 2.7 32.6 + - - -
292B CYS* 3.5 32.2 - - + +
300B ARG* 4.0 9.4 - - + -
301B PRO* 3.4 27.6 - - + +
302B SER* 4.6 0.2 - - - -
303B MET* 3.8 37.5 - - + +
306B VAL* 4.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY 4.6 3.4 - - - -
207B TYR 3.7 17.5 - - - -
208B ILE 3.5 18.4 - - - -
209B ASP* 3.9 2.9 - - + -
210B PRO* 3.4 26.2 - - + +
221B LYS 3.3 3.4 + - - -
222B SER 3.9 6.7 - - - +
224B VAL* 1.3 77.2 - - - +
226B SER* 1.3 63.5 + - - +
228B GLY 3.0 9.4 + - - -
229B VAL* 3.1 19.7 + - + +
251B ASN* 4.9 2.8 + - - -
253B ALA* 3.8 17.1 + - + +
292B CYS 3.4 11.1 + - - -
293B LEU* 3.3 53.2 - - + +
295B LEU* 5.5 1.9 - - + +
300B ARG* 3.4 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ARG* 5.0 6.6 + - - -
165B VAL* 3.8 30.9 + - - -
207B TYR* 2.7 34.7 + - - +
208B ILE* 4.9 0.2 - - - -
209B ASP 4.7 1.0 + - - -
222B SER 3.2 12.6 + - - -
223B ASP* 3.2 11.4 + - - -
224B VAL 3.2 0.6 - - - -
225B TYR* 1.3 77.3 - - - +
227B PHE* 1.3 61.7 + - - +
229B VAL* 3.2 14.7 + - - +
230B VAL* 3.3 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B CYS* 3.3 26.7 - - - -
148B ALA* 3.7 24.9 - - + -
149B ALA* 3.9 9.2 - - + -
152B LEU* 3.5 23.1 - - + -
165B VAL* 3.8 11.4 - - + +
170B ILE* 5.1 5.2 - - + -
223B ASP 2.7 20.2 + - - +
224B VAL 3.6 4.3 - - - +
226B SER* 1.3 70.6 - - - +
228B GLY* 1.3 59.3 + - - +
230B VAL* 3.0 13.6 + - + +
231B LEU* 2.9 58.2 + - + +
292B CYS* 5.1 1.3 - - - -
303B MET* 3.9 12.6 - - + -
306B VAL* 3.7 26.2 - - + -
310B LEU* 3.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL 2.7 14.6 + - - -
225B TYR 3.0 6.7 + - - -
227B PHE* 1.3 77.3 - - - +
229B VAL* 1.3 60.7 + - - +
231B LEU* 3.4 21.3 - - - +
232B PHE* 3.4 15.9 + - - -
289B ALA* 4.1 1.1 - - - +
292B CYS* 3.5 22.0 - - - +
293B LEU* 3.9 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY 3.9 13.2 - - - +
207B TYR* 3.6 15.7 - - + -
225B TYR* 3.1 18.8 + - + +
226B SER 3.5 7.6 - - - +
227B PHE 3.1 0.4 - - - -
228B GLY* 1.3 75.4 - - - +
230B VAL* 1.3 60.8 + - - +
232B PHE* 3.0 5.9 + - - +
233B GLU* 2.8 26.5 + - - +
241B ILE* 3.0 36.6 - - + -
252B LEU* 3.8 12.0 - - + +
253B ALA* 3.5 27.1 - - + -
293B LEU* 3.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.0 18.2 - - + -
145B CYS* 5.8 1.8 - - - -
165B VAL* 4.0 11.4 - - + -
166B LYS* 3.8 30.5 - - - -
167B SER* 4.0 7.4 - - - +
170B ILE* 3.9 22.0 - - + -
207B TYR* 4.2 3.8 - - + -
226B SER 3.5 14.6 - - - +
227B PHE* 3.0 16.9 + - + +
229B VAL* 1.3 75.0 - - - +
231B LEU* 1.3 56.7 + - + +
233B GLU* 3.1 11.0 + - + +
234B VAL* 2.8 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B CYS* 4.1 9.0 - - - -
227B PHE* 2.9 49.5 + - + +
228B GLY* 3.4 13.2 - - - +
229B VAL 3.1 0.2 - - - -
230B VAL* 1.3 76.5 - - - +
232B PHE* 1.3 57.9 + - - +
234B VAL* 3.3 4.3 + - - +
235B LEU 3.1 14.4 + - - -
285B PHE* 3.1 48.1 - - + +
288B THR* 4.6 8.5 - - + -
289B ALA* 3.7 34.1 - - + +
292B CYS* 4.1 9.0 - - - -
306B VAL* 4.8 0.4 - - + -
310B LEU* 3.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B GLY 3.4 10.0 + - - -
229B VAL* 3.0 3.2 + - - +
231B LEU* 1.3 77.3 - - - +
233B GLU* 1.3 61.7 + - - +
235B LEU* 4.0 24.9 - - + -
236B CYS* 2.9 37.3 + - - +
252B LEU* 3.6 22.9 - - + -
256B ALA* 3.5 34.5 - - + -
257B VAL* 4.7 1.6 - - + -
260B HIS* 4.8 6.3 - + + -
269B VAL* 6.0 1.3 - - + -
285B PHE* 5.5 0.4 - + - -
286B GLY* 3.8 10.3 - - - -
289B ALA* 3.3 37.0 - - + -
290B VAL* 3.6 26.0 - - + -
293B LEU* 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 3.7 0.2 + - - -
126B LEU* 3.9 8.1 - - + +
167B SER* 2.9 34.1 + - - -
207B TYR* 2.9 32.8 + - - -
229B VAL 2.8 12.2 + - - +
230B VAL* 3.3 12.5 - - + +
232B PHE* 1.3 79.0 - - - +
234B VAL* 1.3 60.0 - - - +
237B ALA* 3.1 25.0 + - - +
238B ARG 3.7 8.3 - - - +
239B SER* 2.9 45.9 + - - +
241B ILE* 4.2 8.6 - - + +
252B LEU* 4.0 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.7 28.9 - - + -
126B LEU* 3.7 16.4 - - + +
136B MET* 5.4 1.1 - - + -
138B TRP* 5.1 2.0 - - + -
141B ARG* 3.4 53.1 + - + +
145B CYS* 3.7 30.3 - - - -
230B VAL* 2.8 21.6 + - + +
231B LEU 3.5 7.6 - - - +
233B GLU* 1.3 76.4 - - - +
235B LEU* 1.3 63.3 + - - +
237B ALA* 3.9 2.3 + - - -
285B PHE* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TRP* 3.8 34.1 - - + -
231B LEU 3.1 13.6 + - - +
232B PHE* 3.2 30.9 + - + +
234B VAL* 1.3 81.1 - - - +
236B CYS* 1.3 69.4 + - - +
260B HIS* 5.5 4.3 - - + -
266B GLU 5.5 0.7 - - - +
269B VAL* 4.2 13.9 - - + -
270B ASP* 3.1 23.7 - - + +
271B PRO* 3.6 4.9 - - - +
273B LEU* 3.7 8.0 - - - +
277B ILE* 4.4 5.2 - - + -
282B LEU* 3.9 28.0 - - + +
285B PHE* 3.7 16.4 - - + -
286B GLY* 5.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 2.9 27.6 + - - +
235B LEU* 1.3 82.0 - - - +
237B ALA* 1.3 60.3 + - - +
238B ARG* 2.8 30.4 + - + +
252B LEU* 4.3 13.9 - - + -
256B ALA* 5.1 2.7 - - - -
269B VAL* 3.3 48.6 - - - +
270B ASP* 3.7 3.1 - - - +
271B PRO* 3.3 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.5 18.4 - - + +
127B TYR* 3.1 38.7 - - + +
141B ARG* 4.9 4.5 - - - +
233B GLU 3.1 15.6 + - - -
234B VAL 3.9 2.7 + - - +
235B LEU 3.3 3.4 - - - +
236B CYS* 1.3 77.1 - - - +
238B ARG* 1.3 51.0 + - - +
239B SER 2.4 19.8 + - - -
271B PRO* 3.4 25.8 - - + -
----------------------------------------------------------
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