Contacts of the helix formed by residues 318 - 339 (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 ILE 318 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178Q HIS* 3.8 20.0 - - + +
216Q ILE* 3.2 50.0 - - + +
219Q ALA* 4.7 8.3 - - + -
220Q ALA* 5.2 6.5 - - + -
253Q TYR* 5.2 14.4 - - + -
256Q LEU* 5.2 4.5 - - + -
316Q ASP* 4.1 6.6 + - - +
317Q PRO* 1.3 81.2 - - + +
319Q ILE* 1.3 66.4 + - - +
320Q SER 3.0 3.5 + - - -
321Q THR* 3.1 23.0 + - - -
322Q HIS* 3.5 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252Q LYS* 4.2 19.7 - - + +
253Q TYR* 5.1 8.1 - - + -
256Q LEU* 4.8 17.5 - - + -
312Q GLU 5.0 0.4 - - - +
313Q LEU* 3.7 41.3 - - + +
316Q ASP* 1.6 51.8 - - + +
317Q PRO 3.5 0.2 - - - -
318Q ILE* 1.3 79.0 - - - +
320Q SER* 1.3 62.8 + - - +
322Q HIS* 3.1 10.8 + - + -
323Q LEU* 3.0 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 320 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313Q LEU 5.4 0.8 + - - -
316Q ASP 4.2 9.6 + - - -
317Q PRO 3.7 16.1 + - - -
318Q ILE 3.0 0.4 + - - -
319Q ILE* 1.3 77.3 - - - +
321Q THR* 1.3 61.2 + - - +
323Q LEU* 3.5 12.5 + - - +
324Q ALA* 3.4 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 321 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219Q ALA 5.1 2.2 + - - -
220Q ALA* 6.0 3.1 - - - -
222Q GLU* 3.0 24.6 + - - -
225Q TRP* 6.0 0.9 - - - -
260Q MET* 4.8 0.4 - - - +
317Q PRO 4.6 1.5 + - - -
318Q ILE* 3.1 13.4 + - - -
320Q SER* 1.3 74.2 - - - +
322Q HIS* 1.3 69.7 + - - +
324Q ALA* 2.8 23.0 + - - +
325Q LYS* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 322 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219Q ALA* 3.6 27.4 - - + +
225Q TRP* 2.5 40.5 + + - -
256Q LEU* 3.1 43.4 - - + +
260Q MET* 3.0 29.6 - - + -
318Q ILE* 3.5 20.1 + - + +
319Q ILE* 3.1 8.8 + - + +
321Q THR* 1.3 83.8 - - - +
323Q LEU* 1.3 58.0 + - + +
326Q LEU* 2.9 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290Q VAL* 6.1 2.5 - - + -
302Q PHE* 4.0 14.9 - - + -
306Q LEU* 3.6 34.3 - - + +
313Q LEU* 4.4 26.0 - - + +
319Q ILE* 3.0 39.6 + - + +
320Q SER* 3.8 10.1 - - - +
321Q THR 3.1 0.2 - - - -
322Q HIS* 1.3 77.8 - - + +
324Q ALA* 1.3 61.1 + - - +
326Q LEU* 4.3 8.5 - - + -
327Q TYR* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320Q SER 3.4 8.8 + - - +
321Q THR* 2.8 12.1 + - - +
323Q LEU* 1.3 75.7 - - - +
325Q LYS* 1.3 73.7 + - + +
327Q TYR* 3.4 9.9 + - - +
328Q ASP* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222Q GLU* 2.5 43.2 + - - +
225Q TRP* 4.8 10.2 - - + -
260Q MET* 3.0 43.3 - - + -
321Q THR* 2.9 21.9 + - - +
324Q ALA* 1.3 83.0 - - + +
326Q LEU* 1.3 60.7 + - - +
328Q ASP* 3.0 16.1 + - - +
329Q ASN* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 326 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256Q LEU* 5.4 4.9 - - + -
259Q ILE* 3.1 48.9 - - + +
260Q MET* 3.6 27.8 - - + -
287Q LEU* 6.2 0.4 - - + -
290Q VAL* 4.1 15.5 - - + -
302Q PHE* 3.4 22.4 - - + -
322Q HIS* 2.9 30.8 + - + +
323Q LEU* 4.1 7.6 - - + +
325Q LYS* 1.3 76.0 - - - +
327Q TYR* 1.3 63.8 + - - +
329Q ASN* 3.4 6.3 + - + +
330Q LEU* 2.9 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 327 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299Q LEU* 3.4 31.6 - - + -
302Q PHE* 3.5 21.5 - + + -
303Q GLU* 5.8 4.3 - - + -
306Q LEU* 5.4 6.3 - - + -
323Q LEU 2.9 22.1 + - - +
324Q ALA* 3.6 9.0 - - - +
326Q LEU* 1.3 76.4 - - - +
328Q ASP* 1.3 77.6 + - - +
330Q LEU* 3.2 4.2 + - - +
331Q LEU* 3.0 43.6 + - + +
356Q LEU* 4.9 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324Q ALA 3.0 13.5 + - - +
325Q LYS* 3.0 11.7 + - - +
327Q TYR* 1.3 89.2 - - - +
329Q ASN* 1.3 66.2 + - - +
331Q LEU* 3.0 17.1 + - - +
332Q GLU* 3.0 20.5 + - - +
364Q LYS* 4.2 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 329 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259Q ILE 4.8 2.6 + - - +
260Q MET* 3.7 31.7 + - - +
262Q ASN* 3.8 19.4 + - - +
294Q SER* 5.3 4.3 + - - +
325Q LYS* 3.0 20.3 + - - +
326Q LEU* 3.9 6.0 - - - +
328Q ASP* 1.3 78.6 - - - +
330Q LEU* 1.3 61.4 + - - +
332Q GLU* 3.9 9.7 - - - +
333Q GLN* 3.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294Q SER* 3.1 51.1 - - - +
297Q ARG* 3.4 8.9 - - - +
298Q SER 3.3 17.9 - - - +
299Q LEU* 4.2 9.1 - - + +
302Q PHE* 2.5 64.2 - - + -
326Q LEU* 2.9 13.4 + - + +
327Q TYR 3.3 9.6 - - - +
328Q ASP 3.0 0.4 + - - -
329Q ASN* 1.3 75.3 - - - +
331Q LEU* 1.3 66.2 + - - +
333Q GLN* 3.4 1.9 + - - +
334Q ASN* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299Q LEU* 3.4 30.2 - - + +
327Q TYR* 3.0 40.9 + - + +
328Q ASP* 3.0 11.2 + - - +
330Q LEU* 1.3 72.8 - - - +
332Q GLU* 1.3 66.0 + - - +
334Q ASN* 3.4 1.4 + - - +
335Q LEU* 3.1 43.6 + - + +
354Q ILE* 5.5 2.0 - - + -
356Q LEU* 4.2 20.4 - - + -
360Q ASP 6.0 0.2 - - - +
361Q VAL* 6.4 0.9 - - - -
364Q LYS* 3.2 42.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328Q ASP* 3.0 22.9 + - - +
329Q ASN* 3.9 10.8 - - - +
331Q LEU* 1.3 78.6 - - - +
333Q GLN* 1.3 63.5 + - - +
335Q LEU* 3.4 4.1 + - - +
336Q ILE* 3.0 32.7 + - + +
364Q LYS* 2.3 48.2 + - - +
368Q MET* 2.6 40.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 333 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294Q SER* 4.4 5.2 - - - +
295Q LYS* 3.6 11.6 + - - +
297Q ARG* 1.6 55.1 + - + +
329Q ASN 3.3 16.4 + - - +
330Q LEU* 3.7 2.2 - - + +
331Q LEU 3.3 0.4 - - - -
332Q GLU* 1.3 76.2 - - - +
334Q ASN* 1.3 66.7 + - - +
336Q ILE* 2.7 30.3 + - + +
337Q ARG* 2.9 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 334 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297Q ARG* 2.7 27.9 + - - +
298Q SER* 4.4 7.2 - - - -
299Q LEU* 4.3 4.3 + - - +
330Q LEU 3.0 9.9 + - - +
331Q LEU* 3.7 4.6 + - - +
333Q GLN* 1.3 71.8 - - - +
335Q LEU* 1.3 60.0 + - - +
337Q ARG* 3.2 7.4 + - - +
338Q VAL* 2.6 42.4 + - - +
353Q LEU 5.8 0.3 - - - -
354Q ILE* 1.8 59.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331Q LEU* 3.1 41.1 + - + +
332Q GLU 3.4 8.5 - - - +
333Q GLN 2.8 1.6 + - - -
334Q ASN* 1.3 82.6 - - - +
336Q ILE* 1.3 55.6 + - - +
337Q ARG 2.9 3.6 - - - -
338Q VAL* 2.7 26.1 + - + +
339Q ILE* 3.1 16.7 + - + +
350Q ILE* 3.5 31.0 - - + -
354Q ILE* 4.9 5.4 - - + -
361Q VAL* 4.5 13.7 - - + -
364Q LYS* 4.0 15.9 - - + -
365Q LEU* 4.4 16.8 - - + -
368Q MET* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332Q GLU* 3.0 27.1 + - + +
333Q GLN* 2.7 23.1 + - + +
335Q LEU* 1.3 71.0 - - - +
337Q ARG* 1.3 55.5 + - + -
339Q ILE* 3.7 12.3 - - + +
340Q GLU* 3.0 26.1 + - + +
368Q MET* 3.7 19.7 - - + -
373Q LYS* 5.6 6.5 - - + -
374Q PHE* 5.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P SER* 5.9 2.6 - - - -
395P ASN* 6.3 0.8 - - - +
398P VAL* 3.2 37.4 - - + +
295Q LYS 4.0 3.4 + - - -
296Q ASN* 2.6 51.8 + - - +
297Q ARG* 4.5 5.5 - - + +
333Q GLN* 2.9 11.3 + - - +
334Q ASN* 3.5 12.6 - - - +
336Q ILE* 1.3 76.7 - - + +
338Q VAL* 1.3 64.1 + - - +
339Q ILE 3.3 0.4 - - - -
340Q GLU* 3.5 18.9 - - + +
341Q PRO* 3.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334Q ASN* 2.6 46.9 - - - +
335Q LEU* 2.7 20.7 + - + +
337Q ARG* 1.3 74.2 - - - +
339Q ILE* 1.3 58.3 + - - +
341Q PRO* 4.4 4.4 - - - +
342Q PHE* 4.2 10.9 - - - +
345Q VAL* 5.0 6.1 - - + +
349Q HIS* 5.9 2.0 - - + -
350Q ILE* 3.7 39.0 - - + -
353Q LEU* 4.5 17.5 - - + -
354Q ILE* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335Q LEU* 3.3 18.4 - - + +
336Q ILE* 3.7 13.2 - - + +
338Q VAL* 1.3 78.1 - - + +
340Q GLU* 1.3 71.2 + - - +
341Q PRO 3.5 1.7 - - - -
342Q PHE* 3.7 14.2 + - - +
345Q VAL* 4.2 5.4 - - + -
350Q ILE* 4.2 16.2 - - + -
365Q LEU* 4.4 7.9 - - + -
368Q MET* 4.9 0.7 - - + -
374Q PHE* 3.6 50.0 - - + -
385Q LEU* 3.2 28.0 - - + -
387Q ILE* 2.7 33.6 - - + +
----------------------------------------------------------
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