Contacts of the helix formed by residues 224 - 242 (chain Q) in PDB entry 5L4K
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 ASP 224 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218Q HIS* 3.0 43.7 - - + +
221Q GLU* 3.5 29.5 + - - +
222Q GLU 3.4 1.8 - - - -
223Q LYS* 1.3 88.7 - - - +
225Q TRP* 1.3 55.7 + - - +
226Q LYS* 3.1 6.3 - - - +
227Q THR* 2.7 39.6 + - - +
228Q ALA* 3.4 4.4 + - - +
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Residues in contact with TRP 225 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Q ALA* 3.7 31.2 + - + +
221Q GLU 4.4 3.3 + - - -
222Q GLU* 3.3 39.9 - - + -
223Q LYS 3.6 2.4 - - - -
224Q ASP* 1.3 76.8 - - - +
226Q LYS* 1.3 61.6 + - - +
227Q THR 3.0 0.9 + - - -
228Q ALA* 3.5 12.9 + - + +
229Q TYR* 3.5 12.5 + - - +
257Q CYS* 3.6 29.0 - - - +
260Q MET* 3.4 60.4 - - + +
261Q LEU* 3.6 26.1 - - + +
322Q HIS* 4.2 8.6 + + - -
325Q LYS* 3.7 32.1 - - + -
329Q ASN* 5.2 4.0 - - - -
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Residues in contact with LYS 226 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223Q LYS 4.1 15.3 - - - +
224Q ASP* 4.3 5.8 - - - +
225Q TRP* 1.3 78.0 - - - +
227Q THR* 1.3 63.9 + - - +
229Q TYR* 4.5 8.3 - - - +
230Q SER* 4.1 5.0 + - - -
261Q LEU* 3.7 23.8 - - + +
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Residues in contact with THR 227 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218Q HIS* 3.9 14.8 - - + +
224Q ASP* 2.7 25.1 + - - +
226Q LYS* 1.3 74.6 - - - +
228Q ALA* 1.3 55.1 + - - +
229Q TYR 3.1 2.0 - - - -
230Q SER* 2.4 46.8 + - - +
231Q TYR* 3.6 27.0 + - + +
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Residues in contact with ALA 228 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215Q GLY* 4.3 11.4 - - - +
218Q HIS* 5.0 4.8 - - + +
219Q ALA* 4.5 9.0 - - + +
224Q ASP 3.4 3.5 + - - +
225Q TRP* 3.5 14.3 + - + +
227Q THR* 1.3 79.8 - - - +
229Q TYR* 1.3 54.6 + - - +
230Q SER 2.8 10.2 + - - -
231Q TYR* 3.0 10.2 + - - +
232Q PHE* 3.0 40.6 + - + -
257Q CYS* 4.0 21.5 - - - -
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Residues in contact with TYR 229 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225Q TRP 3.5 12.4 + - - +
226Q LYS* 4.5 7.9 - - - +
227Q THR 2.9 0.2 + - - -
228Q ALA* 1.3 77.8 - - - +
230Q SER* 1.3 57.2 + - - +
232Q PHE* 4.9 4.3 - - - +
233Q TYR* 3.2 37.7 + + - +
254Q MET* 3.6 37.7 - - + -
257Q CYS* 4.8 10.0 - - + +
258Q LYS* 3.6 47.6 - - + +
261Q LEU* 5.5 2.2 - - + -
266Q ASP* 4.1 3.0 + - - -
270Q LEU* 3.2 31.4 - - + +
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Residues in contact with SER 230 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226Q LYS 4.1 4.0 + - - -
227Q THR* 2.4 40.6 + - - +
229Q TYR* 1.3 70.6 - - - +
231Q TYR* 1.3 72.3 + - - -
233Q TYR* 2.9 16.5 + - - +
234Q GLU* 2.9 20.3 + - - +
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Residues in contact with TYR 231 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194Q ARG* 3.7 21.1 + - - -
210Q LEU* 6.2 1.1 - - + -
211Q ASP* 3.5 25.0 - - - +
214Q SER* 3.7 25.8 - - - -
215Q GLY* 3.9 11.7 - - - +
218Q HIS* 3.4 34.3 - + - -
227Q THR* 3.6 23.9 - - + +
228Q ALA* 3.0 5.0 + - - +
230Q SER* 1.3 81.8 - - - +
232Q PHE* 1.3 65.1 + - - +
234Q GLU* 2.9 25.9 + - - +
235Q ALA* 2.8 23.1 + - - +
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Residues in contact with PHE 232 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Q MET* 3.7 31.9 - - + -
215Q GLY* 3.5 33.9 - - - -
216Q ILE* 3.5 10.1 - - + -
219Q ALA* 4.8 4.0 - - + -
228Q ALA* 3.0 35.2 + - + +
229Q TYR* 4.8 0.7 - - - -
231Q TYR* 1.3 76.6 - - - +
233Q TYR* 1.3 56.8 + - - +
235Q ALA* 3.7 5.6 - - + +
236Q PHE* 2.9 28.1 + - - +
250Q SER* 4.7 9.4 - - - +
253Q TYR* 3.7 47.1 - + + -
254Q MET* 4.1 23.6 - - + +
257Q CYS* 4.5 13.0 - - - -
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Residues in contact with TYR 233 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229Q TYR* 3.2 41.1 + + - +
230Q SER* 2.9 11.9 + - - +
232Q PHE* 1.3 75.7 - - - +
234Q GLU* 1.3 67.2 + - + +
236Q PHE* 3.0 12.4 + + - +
237Q GLU* 3.0 51.8 + - + +
254Q MET* 3.3 32.4 - - + -
270Q LEU* 4.2 9.7 - - + +
275Q LEU* 5.7 4.3 - - - +
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Residues in contact with GLU 234 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211Q ASP* 3.7 24.1 - - - +
230Q SER* 2.9 18.7 + - - +
231Q TYR* 2.9 30.7 + - - +
233Q TYR* 1.3 77.1 - - + +
235Q ALA* 1.3 56.7 + - - +
237Q GLU* 3.5 12.1 + - - +
238Q GLY* 2.9 27.0 + - - -
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Residues in contact with ALA 235 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208Q ALA* 3.8 11.7 - - - +
211Q ASP* 3.9 7.7 - - + +
212Q MET* 3.8 35.2 - - + +
231Q TYR 2.8 17.7 + - - +
232Q PHE* 3.7 6.7 - - - +
234Q GLU* 1.3 72.9 - - - +
236Q PHE* 1.3 57.8 + - - +
238Q GLY 4.5 0.2 - - - +
239Q TYR* 2.9 38.9 + - + +
250Q SER* 4.2 8.7 - - - +
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Residues in contact with PHE 236 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232Q PHE 2.9 17.7 + - - +
233Q TYR* 3.0 16.7 + + - +
235Q ALA* 1.3 73.0 - - - +
237Q GLU* 1.3 75.1 + - + +
239Q TYR* 4.2 1.0 - - - +
240Q ASP* 2.9 47.1 + - + +
247Q ALA* 4.6 12.6 - - + -
250Q SER* 4.5 10.0 - - - -
251Q LEU* 3.8 47.6 - - + +
254Q MET* 4.6 12.6 - - + -
275Q LEU* 3.8 25.1 - - + -
276Q ALA* 5.3 0.2 - - - -
278Q ARG* 4.0 9.0 - - - -
279Q TYR* 4.6 12.6 - + + -
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Residues in contact with GLU 237 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233Q TYR* 3.0 40.7 + - + +
234Q GLU* 3.8 11.9 - - - +
236Q PHE* 1.3 83.3 - - + +
238Q GLY* 1.3 68.1 + - - +
240Q ASP* 3.1 7.3 + - - +
241Q SER* 3.1 16.8 + - - -
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Residues in contact with GLY 238 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Q PRO* 5.3 8.5 - - - +
208Q ALA* 4.3 12.1 - - - -
234Q GLU 2.9 18.1 + - - -
235Q ALA 3.6 1.1 - - - -
236Q PHE 3.1 0.2 - - - -
237Q GLU* 1.3 73.5 - - - +
239Q TYR* 1.3 64.1 + - - +
241Q SER* 2.7 24.3 + - - -
242Q ILE* 3.8 6.0 + - - +
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Residues in contact with TYR 239 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205Q LYS* 4.7 12.6 - - + -
208Q ALA* 3.7 23.5 - - + +
209Q THR* 3.1 41.4 + - - +
212Q MET* 4.1 15.7 - - + +
235Q ALA 2.9 20.6 + - - +
236Q PHE* 4.2 1.6 - - - +
238Q GLY* 1.3 69.5 - - - -
240Q ASP* 1.3 61.8 + - - +
241Q SER 3.2 0.5 + - - -
242Q ILE* 3.2 25.3 + - + +
243Q ASP 3.6 6.1 + - - -
244Q SER* 3.3 27.4 + - - +
246Q LYS* 3.5 43.2 - - + +
247Q ALA* 4.1 14.8 - - - +
250Q SER* 3.5 25.1 - - - -
279Q TYR* 4.8 0.2 + - - -
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Residues in contact with ASP 240 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236Q PHE* 2.9 31.4 + - + +
237Q GLU* 3.2 9.9 - - - +
238Q GLY 2.9 0.4 + - - -
239Q TYR* 1.3 78.5 - - - +
241Q SER* 1.3 61.9 + - - +
242Q ILE 3.3 0.9 + - - -
243Q ASP* 3.5 15.6 + - - +
247Q ALA* 4.6 1.3 - - - +
278Q ARG* 3.2 40.7 + - - -
279Q TYR* 3.0 38.7 + - + -
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Residues in contact with SER 241 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Q PRO* 6.0 2.8 - - - +
237Q GLU 3.1 8.2 + - - -
238Q GLY* 2.7 19.2 + - - -
240Q ASP* 1.3 72.9 - - - +
242Q ILE* 1.3 65.4 + - - +
243Q ASP* 3.4 7.3 + - - +
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Residues in contact with ILE 242 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Q PRO* 4.2 24.7 - - + +
205Q LYS* 3.7 47.1 - - + +
238Q GLY 4.3 3.1 - - - +
239Q TYR* 3.2 25.8 + - + +
241Q SER* 1.3 86.4 - - - +
243Q ASP* 1.3 71.9 + - - +
244Q SER* 4.3 6.9 - - - +
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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