Contacts of the helix formed by residues 246 - 262 (chain Q) in PDB entry 5GJQ
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 LYS 246 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212Q MET* 5.5 0.2 - - + -
239Q TYR* 3.0 44.2 - - + +
245Q PRO* 1.3 80.7 - - + +
247Q ALA* 1.3 55.7 + - - +
248Q ILE 3.0 2.7 - - - -
249Q THR* 2.6 44.3 + - + +
250Q SER 3.4 2.6 + - - -
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Residues in contact with ALA 247 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236Q PHE* 3.3 29.9 - - + +
239Q TYR* 2.8 46.8 - - + +
240Q ASP* 3.4 20.6 - - - +
244Q SER* 4.3 7.4 - - - +
245Q PRO 3.4 0.8 - - - -
246Q LYS* 1.3 75.2 - - - +
248Q ILE* 1.3 64.0 + - + +
249Q THR 3.1 0.9 + - - -
250Q SER 3.2 10.5 + - - +
251Q LEU* 3.3 2.1 + - - +
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Residues in contact with ILE 248 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236Q PHE* 5.5 0.4 - - - -
244Q SER 4.2 15.9 - - - +
245Q PRO 4.2 9.9 - - - +
246Q LYS 3.0 0.4 - - - -
247Q ALA* 1.3 77.7 - - + +
249Q THR* 1.3 60.7 + - - +
251Q LEU* 4.3 6.6 + - - +
252Q LYS 4.3 6.2 + - - -
278Q ARG 5.8 0.2 - - - +
279Q TYR* 4.0 33.9 - - + +
283Q GLN* 2.3 54.4 - - + +
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Residues in contact with THR 249 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212Q MET* 3.3 18.2 - - + -
245Q PRO 4.9 0.4 + - - -
246Q LYS* 2.6 25.5 + - + +
248Q ILE* 1.3 74.1 - - - +
250Q SER* 1.3 59.9 + - - +
252Q LYS* 3.1 22.7 + - - +
253Q TYR* 2.6 51.5 + - + +
283Q GLN* 5.6 0.4 - - - -
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Residues in contact with SER 250 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212Q MET* 3.0 29.8 - - - +
232Q PHE* 2.9 34.1 + - - +
235Q ALA 4.5 0.4 - - - -
236Q PHE* 3.6 16.6 + - - -
246Q LYS 3.4 1.7 + - - -
247Q ALA 3.2 5.1 + - - -
249Q THR* 1.3 75.0 - - - +
251Q LEU* 1.3 66.8 + - - +
252Q LYS 3.0 1.8 - - - -
253Q TYR* 3.0 13.4 + - - -
254Q MET* 2.8 22.3 + - - +
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Residues in contact with LEU 251 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236Q PHE* 2.9 28.5 - - + -
247Q ALA 3.3 7.9 + - - +
248Q ILE* 4.3 7.4 - - - +
250Q SER* 1.3 77.2 - - - +
252Q LYS* 1.3 63.8 + - - +
254Q MET* 3.3 31.1 + - + +
255Q LEU* 3.0 32.9 + - + +
270Q LEU* 4.8 19.7 - - + +
276Q ALA* 3.1 34.8 - - + -
279Q TYR* 5.1 9.0 - - + -
283Q GLN* 6.3 1.8 - - + -
284Q THR* 4.9 15.3 - - + -
287Q LEU* 4.6 1.1 - - - -
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Residues in contact with LYS 252 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248Q ILE 4.3 1.9 + - - -
249Q THR* 3.1 27.6 + - - +
250Q SER 3.0 0.2 - - - -
251Q LEU* 1.3 77.3 - - - +
253Q TYR* 1.3 72.0 + - + +
255Q LEU 3.1 2.8 + - - -
256Q LEU* 2.9 28.9 + - + +
283Q GLN* 3.8 32.0 - - + +
287Q LEU* 3.1 35.1 - - + +
312Q GLU* 3.6 32.7 + - - +
313Q LEU* 6.0 1.8 - - + -
315Q ASP 5.4 1.8 + - - -
316Q ASP* 3.8 17.4 + - - -
319Q ILE* 4.2 15.0 - - + +
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Residues in contact with TYR 253 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212Q MET* 4.4 3.4 - - + -
216Q ILE* 5.3 14.1 - - + -
232Q PHE* 3.1 38.8 - + + -
249Q THR* 2.6 59.9 + - + +
250Q SER* 3.0 14.8 + - - -
252Q LYS* 1.3 83.2 + - + +
254Q MET* 1.3 66.4 + - - +
256Q LEU* 2.8 34.2 + - + +
257Q CYS* 3.1 19.7 + - - -
316Q ASP* 4.6 17.2 + - - -
318Q ILE* 5.2 16.4 - - + -
319Q ILE* 5.1 8.1 - - + -
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Residues in contact with MET 254 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229Q TYR* 3.5 31.9 - - + +
232Q PHE* 3.8 17.0 - - + +
233Q TYR* 3.5 44.0 - - + -
236Q PHE* 3.5 37.0 - - + -
250Q SER 2.8 10.1 + - - +
251Q LEU* 3.4 35.4 - - + +
253Q TYR* 1.3 77.7 - - - +
255Q LEU* 1.3 57.5 + - - +
257Q CYS* 3.9 3.7 + - - -
258Q LYS* 3.8 9.4 + - - +
270Q LEU* 4.6 13.9 - - + -
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Residues in contact with LEU 255 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251Q LEU* 3.0 20.6 + - + +
252Q LYS 3.4 7.4 - - - +
253Q TYR 3.0 0.2 - - - -
254Q MET* 1.3 74.8 - - - +
256Q LEU* 1.3 67.7 + - - +
257Q CYS 3.3 0.2 - - - -
258Q LYS* 2.9 6.1 + - + +
259Q ILE* 2.8 29.4 + - + +
267Q VAL* 4.0 27.4 - - + +
270Q LEU* 3.1 44.4 - - + -
271Q VAL* 5.7 3.6 - - + -
283Q GLN 5.1 2.2 - - - +
284Q THR* 5.2 8.7 - - + +
287Q LEU* 3.4 42.8 - - + -
288Q LYS* 4.9 3.1 - - + +
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Residues in contact with LEU 256 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225Q TRP* 4.4 0.2 - - - -
252Q LYS* 2.9 30.0 + - + +
253Q TYR* 2.8 27.0 + - + +
255Q LEU* 1.3 75.4 - - - +
257Q CYS* 1.3 63.4 + - - +
259Q ILE* 3.0 13.0 + - + +
260Q MET* 2.9 27.6 + - - +
287Q LEU* 3.8 20.4 - - + -
318Q ILE* 5.2 2.0 - - + -
319Q ILE* 4.8 20.2 - - + -
322Q HIS* 3.1 53.6 - - + +
326Q LEU* 4.8 5.1 - - + +
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Residues in contact with CYS 257 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225Q TRP* 3.3 40.1 - - + +
229Q TYR* 3.8 22.2 - - + -
232Q PHE* 3.5 32.1 - - - -
253Q TYR 3.1 17.7 + - - -
254Q MET* 3.9 6.5 - - - +
256Q LEU* 1.3 77.1 - - - +
258Q LYS* 1.3 57.4 + - - +
260Q MET* 3.5 1.2 + - - +
261Q LEU* 2.8 37.9 + - + +
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Residues in contact with LYS 258 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229Q TYR* 2.7 53.0 + - + -
254Q MET 3.8 3.9 + - - +
255Q LEU* 2.9 13.4 + - - +
257Q CYS* 1.3 77.4 - - - +
259Q ILE* 1.3 59.2 + - - +
261Q LEU* 3.7 11.9 - - + +
262Q ASN 3.0 24.4 + - - -
263Q THR* 3.1 29.0 + - - +
266Q ASP* 2.4 65.0 + - + +
267Q VAL* 3.8 12.6 - - + -
270Q LEU* 4.8 6.5 - - + -
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Residues in contact with ILE 259 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255Q LEU* 2.8 22.6 + - + +
256Q LEU* 3.4 9.4 - - + +
258Q LYS* 1.3 76.3 - - - +
260Q MET* 1.3 60.0 + - - +
262Q ASN* 3.5 16.2 + - - +
263Q THR 5.2 1.1 - - - +
267Q VAL* 4.8 5.2 - - + -
287Q LEU* 3.8 41.1 - - + +
290Q VAL* 4.2 21.1 - - + +
291Q ALA* 4.6 16.6 - - + +
294Q SER* 5.2 13.3 + - - -
326Q LEU* 3.1 38.2 - - + +
329Q ASN* 4.8 2.3 + - - +
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Residues in contact with MET 260 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225Q TRP* 3.4 36.3 - - + +
256Q LEU 2.9 18.9 + - - +
257Q CYS 3.8 3.6 - - - +
259Q ILE* 1.3 73.9 - - - +
261Q LEU* 1.3 61.6 + - - +
262Q ASN* 3.1 19.2 + - - +
321Q THR 4.8 0.2 - - - -
322Q HIS* 3.0 40.6 - - + -
325Q LYS* 3.0 48.2 - - + -
326Q LEU* 3.6 15.3 - - + -
329Q ASN* 3.7 14.5 + - - +
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Residues in contact with LEU 261 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225Q TRP* 4.4 16.2 - - + -
226Q LYS* 4.7 18.6 - - + +
229Q TYR* 5.5 4.9 - - + -
257Q CYS* 2.8 37.6 + - + +
258Q LYS* 3.3 19.5 + - + +
260Q MET* 1.3 73.6 - - + +
262Q ASN* 1.3 73.0 + - - +
263Q THR* 4.1 12.4 + - - +
266Q ASP* 5.7 1.3 - - - +
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Residues in contact with ASN 262 (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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258Q LYS 3.0 5.7 + - - -
259Q ILE 3.5 11.5 + - - +
260Q MET 3.1 14.3 + - - +
261Q LEU* 1.3 83.4 + - - +
263Q THR* 1.3 61.4 + - - +
264Q PRO 4.0 1.5 - - - -
294Q SER* 5.4 3.1 + - - -
329Q ASN* 3.8 21.9 + - - +
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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
------------------------------------------------------------
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