Contacts of the helix formed by residues 232 - 253 (chain B) in PDB entry 1QK0
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 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B CYS 3.9 21.1 - - - +
177B ALA* 4.3 12.6 + - - +
229B ASN* 2.8 23.9 + - - +
230B LEU 3.7 1.5 - - - +
231B GLY* 1.3 78.5 - - - +
233B PRO* 1.3 72.5 - - + +
234B LYS* 4.0 7.0 - - + +
235B CYS* 2.8 21.6 + - - +
236B ALA 3.1 9.5 + - - -
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Residues in contact with PRO 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU 5.2 0.2 - - - +
231B GLY 3.5 8.9 - - - +
232B THR* 1.3 86.4 - - + +
234B LYS* 1.3 57.4 + - - +
236B ALA* 3.2 6.7 + - + -
237B ASN* 2.8 45.7 + - - +
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 4.2 36.2 - - + +
174B ARG 4.2 10.5 + - - -
175B ASP 4.5 4.2 + - - -
176B CYS* 3.4 33.8 - - + +
178B ALA 5.2 6.7 + - - +
180B ALA 6.1 0.2 - - - -
181B SER* 4.6 9.9 - - - +
232B THR* 3.1 5.5 + - + +
233B PRO* 1.3 78.8 - - - +
235B CYS* 1.3 58.3 + - - +
237B ASN* 4.0 5.8 - - - +
238B ALA* 3.2 28.1 + - - +
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Residues in contact with CYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B CYS* 2.0 50.9 - - - -
177B ALA* 3.3 26.0 - - - -
225B ASN* 3.9 10.1 - - + +
226B LEU* 4.1 6.9 - - + +
229B ASN 3.3 27.4 - - - +
230B LEU* 4.4 4.0 - - + -
232B THR* 2.8 4.9 + - - +
234B LYS* 1.3 77.6 - - - +
236B ALA* 1.3 67.4 + - - +
238B ALA* 3.1 2.6 + - - +
239B GLN* 3.0 22.9 + - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 3.5 35.6 + - + +
232B THR 3.1 6.5 + - - +
233B PRO* 3.7 10.3 - - + +
235B CYS* 1.3 77.1 - - - +
237B ASN* 1.3 69.1 + - - +
238B ALA 3.3 0.7 + - - -
239B GLN* 3.4 17.9 + - - +
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Residues in contact with ASN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ASP* 6.0 1.8 - - - +
187B ILE* 4.5 7.6 - - - +
233B PRO* 2.8 27.9 + - - +
234B LYS* 4.1 5.2 - - - +
236B ALA* 1.3 82.4 - - - +
238B ALA* 1.3 59.0 + - - +
239B GLN 3.5 0.2 - - - -
240B SER* 5.0 4.4 + - - -
241B ALA* 5.4 1.2 + - - +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 4.2 7.6 - - + +
176B CYS* 4.7 0.7 - - + -
187B ILE* 3.5 25.4 - - + -
234B LYS 3.2 17.9 + - - +
235B CYS* 3.1 6.7 + - - +
237B ASN* 1.3 77.6 - - - +
239B GLN* 1.3 65.9 + - - +
240B SER 3.4 2.5 - - - -
241B ALA* 3.2 3.6 + - - +
242B TYR* 2.8 45.7 + - + -
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LEU* 3.9 26.7 - - + +
230B LEU* 3.9 29.8 - - + +
235B CYS 3.0 9.8 + - - +
236B ALA* 3.4 15.5 + - - +
237B ASN 3.5 0.2 - - - -
238B ALA* 1.3 77.2 - - - +
240B SER* 1.3 65.1 + - - +
242B TYR* 3.2 2.6 + - - +
243B LEU* 2.9 47.3 + - + +
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Residues in contact with SER 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ALA 5.0 0.4 + - - -
237B ASN 5.0 3.7 + - - -
238B ALA 3.4 0.6 - - - -
239B GLN* 1.3 79.7 - - - +
241B ALA* 1.3 57.3 + - - +
243B LEU* 3.4 7.2 + - - +
244B GLU* 2.8 33.8 + - - +
501B NAG 4.2 3.0 + - - -
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B PRO* 4.4 5.2 - - + -
187B ILE* 3.4 37.5 - - + -
192B VAL* 3.7 25.1 - - + -
237B ASN 5.4 0.8 + - - +
238B ALA* 3.2 3.4 + - - +
240B SER* 1.3 78.1 - - - +
242B TYR* 1.3 58.4 + - + +
244B GLU* 4.5 4.5 - - - -
245B CYS* 2.8 37.6 + - - +
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Residues in contact with TYR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 4.3 20.4 - - + -
172B PRO* 3.4 26.5 - - + -
173B ASP 2.6 21.2 + - - -
174B ARG* 4.7 0.9 - - - -
175B ASP 3.4 7.3 + - - -
176B CYS* 3.1 38.6 + - + +
221B ASP 4.8 0.2 - - - -
222B SER* 3.7 42.8 - - - -
223B LEU 4.7 0.2 - - - -
226B LEU* 4.0 22.9 - - + -
238B ALA* 2.8 24.8 + - + +
239B GLN 3.4 8.1 - - - +
241B ALA* 1.3 77.8 - - + +
243B LEU* 1.3 57.3 + - - +
245B CYS* 3.9 0.5 - - - +
246B ILE* 2.9 42.2 + - + +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 4.0 14.1 - - + -
226B LEU* 3.8 20.2 - - + -
239B GLN* 2.9 39.7 + - + +
240B SER* 3.8 4.3 - - - +
242B TYR* 1.3 74.8 - - - +
244B GLU* 1.3 62.6 + - - +
246B ILE* 4.2 3.4 - - + +
247B ASN* 3.1 24.9 + - - +
282B LEU* 4.1 17.5 - - + -
286B VAL* 4.7 5.2 - - + -
501B NAG 3.3 47.0 + - + +
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Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B VAL* 3.8 20.3 - - + +
196B LYS* 2.8 33.1 + - - +
240B SER* 2.8 22.6 + - - +
241B ALA* 3.8 5.4 - - - +
243B LEU* 1.3 73.1 - - - +
245B CYS* 1.3 63.2 + - - +
247B ASN* 3.4 4.9 + - - +
248B TYR* 3.1 20.8 + - - +
501B NAG 3.5 32.2 + - - +
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Residues in contact with CYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 3.4 13.7 - - + -
172B PRO* 3.7 24.5 - - - -
192B VAL* 4.0 22.0 - - - -
195B TYR* 3.3 43.2 - - + -
196B LYS* 5.4 2.2 - - - +
241B ALA 2.8 24.1 + - - +
244B GLU* 1.3 72.4 - - - +
246B ILE* 1.3 61.5 + - - +
248B TYR* 3.1 8.1 + - - +
249B ALA 2.9 23.9 + - - -
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 4.2 19.3 - - + -
195B TYR* 5.2 0.7 - - - -
218B ILE* 4.7 3.8 - - + -
219B GLU* 4.7 8.7 - - + -
222B SER* 3.7 15.9 - - - +
223B LEU* 3.2 40.4 - - + -
242B TYR* 2.9 31.3 + - + +
243B LEU* 4.2 4.5 - - - +
245B CYS* 1.3 71.4 - - - +
247B ASN* 1.3 61.7 + - - +
249B ALA* 3.5 5.8 + - - +
250B VAL* 3.0 27.7 + - + +
262B LEU* 4.0 22.0 - - + -
286B VAL* 4.1 19.7 - - + -
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Residues in contact with ASN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LEU 3.1 20.2 + - - +
244B GLU* 3.6 5.6 - - - +
246B ILE* 1.3 77.1 - - - +
248B TYR* 1.3 67.0 + - - +
250B VAL* 4.0 3.8 - - - +
251B THR* 3.0 33.1 + - - +
286B VAL* 5.1 5.9 + - + +
289B ASN* 3.3 28.4 + - - +
290B ALA* 3.7 16.6 - - - +
501B NAG 3.3 39.9 + - - +
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Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B TYR* 5.4 0.4 - + + -
196B LYS* 3.3 64.0 - - + +
199B ILE* 3.8 17.0 - - + -
200B ASP* 2.5 28.0 + - - -
244B GLU 3.1 12.6 + - - +
245B CYS* 3.1 12.7 + - - +
247B ASN* 1.3 81.1 + - - +
249B ALA* 1.3 56.5 + - - +
251B THR* 3.0 6.6 + - - -
252B GLN* 2.9 64.4 + - + +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 5.1 1.6 - - + -
195B TYR* 3.9 9.2 - - - +
199B ILE* 3.5 35.0 - - + -
218B ILE* 4.8 12.6 - - + -
245B CYS 2.9 14.9 + - - +
246B ILE* 3.8 6.7 - - - +
248B TYR* 1.3 77.3 - - - +
250B VAL* 1.3 58.0 + - - +
253B LEU* 2.9 41.7 + - + +
260B MET* 4.8 1.3 - - - -
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE* 4.7 12.3 - - + -
246B ILE* 3.0 30.8 + - + +
247B ASN* 4.1 3.6 - - - +
249B ALA* 1.3 75.9 - - - +
251B THR* 1.3 60.2 + - - +
254B ASN* 3.4 8.7 - - - +
260B MET* 3.4 30.1 - - + +
262B LEU* 4.9 2.9 - - + -
286B VAL* 4.8 6.5 - - + -
290B ALA* 4.2 9.0 - - + -
293B PRO* 3.4 29.3 - - + +
296B LEU* 3.7 31.2 - - + -
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ARG* 4.8 1.9 + - - -
247B ASN* 3.0 27.7 + - - +
248B TYR* 3.0 10.2 + - - -
250B VAL* 1.3 77.2 - - - +
252B GLN* 1.3 75.7 + - - +
253B LEU 3.3 0.4 - - - -
254B ASN* 3.2 22.4 + - - +
290B ALA* 3.5 36.1 - - + +
293B PRO* 5.2 1.1 - - - -
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Residues in contact with GLN 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ILE* 3.7 16.8 - - + -
200B ASP* 4.4 2.9 - - - +
203B ARG* 2.6 62.1 + - - +
248B TYR* 2.9 61.7 + - + +
251B THR* 1.3 84.9 + - - +
253B LEU* 1.3 61.1 + - - +
254B ASN 3.2 0.7 - - - -
255B LEU* 4.3 1.4 - - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 4.2 17.3 - - + -
199B ILE* 4.2 18.2 - - + +
202B ILE* 3.8 16.6 - - + -
203B ARG* 3.8 35.2 - - + +
206B VAL* 4.9 7.2 - - + -
216B LEU* 3.7 25.6 - - + -
218B ILE* 4.4 7.4 - - + -
249B ALA* 2.9 23.5 + - + +
252B GLN* 1.3 77.7 - - - +
254B ASN* 1.3 54.0 + - - +
255B LEU* 2.8 19.9 + - + -
258B VAL* 3.4 23.5 - - + +
260B MET* 3.8 13.2 - - - -
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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
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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) + - + + + + + -
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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