Contacts of the helix formed by residues 279 - 307 (chain A) in PDB entry 1GQE
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 SER 279 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASP* 2.7 14.1 + - - +
278A ARG* 1.3 82.5 - - - +
280A GLN* 1.3 63.3 + - - +
281A HIS* 2.9 35.6 + - - -
282A LYS* 3.3 18.6 + - - +
283A ASN* 3.1 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 3.3 37.1 - - + +
259A SER* 3.4 29.9 + - - +
261A VAL* 3.5 19.1 - - + +
278A ARG 3.7 3.6 + - - -
279A SER* 1.3 72.7 + - - +
281A HIS* 1.3 65.3 + - - +
283A ASN 3.1 2.3 + - - -
284A LYS* 2.9 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A SER* 2.9 19.7 + - - -
280A GLN* 1.3 80.8 - - - +
282A LYS* 1.3 77.2 + - + +
284A LYS* 3.5 10.4 + - + +
285A ASP* 3.1 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASP* 3.0 42.0 + - + +
279A SER* 3.2 17.9 + - - +
280A GLN 3.1 0.6 - - - -
281A HIS* 1.3 98.4 - - + +
283A ASN* 1.3 66.5 + - - +
285A ASP* 3.4 7.8 + - - +
286A GLN* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A SER 2.9 28.5 + - - +
260A ALA* 4.0 1.6 - - - +
261A VAL* 3.9 5.8 - - + -
274A CYS* 3.3 42.8 + - - +
275A GLN* 4.2 3.2 - - - +
276A ASN 3.6 0.7 + - - -
277A ASP* 2.9 47.3 + - - +
279A SER 3.1 11.9 + - - -
280A GLN 3.1 7.7 + - - +
282A LYS* 1.3 73.8 - - - +
284A LYS* 1.3 61.2 + - - +
287A ALA* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ILE* 3.8 27.1 - - + +
261A VAL* 3.7 26.6 - - + +
263A ILE* 4.1 5.4 - - + +
280A GLN* 2.9 13.7 + - + +
281A HIS* 3.6 14.4 - - + +
283A ASN* 1.3 75.5 - - - +
285A ASP* 1.3 64.8 + - - +
287A ALA* 3.2 1.7 + - - +
288A MSE 2.8 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A HIS* 3.1 30.2 + - - +
282A LYS* 3.6 10.1 - - - +
283A ASN 3.4 0.2 - - - -
284A LYS* 1.3 85.6 + - - +
286A GLN* 1.3 58.9 + - - +
288A MSE 3.3 8.4 + - - +
289A LYS* 3.0 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 2.8 37.1 + - - -
166A ILE* 4.5 11.6 - - + +
182A LYS* 4.6 6.6 - - - +
274A CYS* 3.5 22.7 - - - -
276A ASN* 5.0 1.8 - - - +
282A LYS 3.1 14.1 + - - +
285A ASP* 1.3 75.3 - - - +
287A ALA* 1.3 66.4 + - - +
288A MSE 3.0 1.6 - - - -
289A LYS* 3.1 23.9 + - - +
290A GLN* 3.0 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 4.0 17.3 - - + +
263A ILE* 3.6 24.0 - - + -
272A THR* 2.9 24.8 + - - +
273A GLN 4.4 1.6 - - - -
274A CYS* 4.0 8.0 - - + +
283A ASN 2.8 21.0 + - - +
284A LYS* 3.7 2.9 - - - +
286A GLN* 1.3 73.9 - - - +
288A MSE 1.3 61.9 + - - +
290A GLN* 3.3 13.0 + - - +
291A MSE 3.1 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 5.2 7.0 - - - +
239A LEU* 3.9 29.4 - - + -
241A ILE* 4.4 11.4 - - + -
263A ILE* 3.6 12.3 - - + +
284A LYS* 2.8 47.6 + - - +
285A ASP* 3.3 9.4 - - - +
287A ALA* 1.3 75.2 - - - +
289A LYS* 1.3 65.6 + - + +
291A MSE 3.1 8.6 + - - +
292A LYS* 3.1 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 5.2 11.1 + - - +
129A TYR* 4.4 2.5 - - - +
225A GLU* 3.9 30.4 - - - +
227A ASP* 3.9 29.7 + - + +
228A ASP* 5.2 1.7 + - - -
285A ASP* 3.0 27.0 + - - +
286A GLN* 3.1 25.4 + - - +
288A MSE 1.3 76.2 - - - +
290A GLN* 1.3 62.7 + - - +
292A LYS* 3.4 12.8 + - - +
293A ALA* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 3.8 22.9 - - + -
166A ILE* 3.2 22.7 - - - +
180A THR* 4.2 10.1 + - - +
223A TYR* 3.8 11.2 + - + +
272A THR* 3.7 11.9 - - + +
273A GLN 3.0 34.3 + - - +
274A CYS* 4.1 0.2 - - - +
286A GLN* 3.0 44.0 + - - +
287A ALA* 3.5 9.0 - - - +
289A LYS* 1.3 75.5 - - - +
291A MSE 1.3 60.5 + - - +
293A ALA* 3.2 7.0 + - - +
294A LYS* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 4.7 4.7 - - + -
239A LEU* 4.5 14.8 - - + -
263A ILE* 3.2 41.7 - - + +
265A HIS* 3.9 8.7 - - + +
270A ILE* 3.5 41.5 - - - +
271A VAL* 4.1 0.4 - - - -
272A THR* 3.5 22.4 - - + +
287A ALA 3.1 12.7 + - - +
288A MSE 3.1 13.2 + - - +
290A GLN* 1.3 74.9 - - - +
292A LYS* 1.3 65.3 + - + +
294A LYS* 3.2 1.6 + - - -
295A LEU* 2.9 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A VAL* 4.3 10.5 - - + +
227A ASP* 3.3 29.2 + - + +
230A ILE* 5.2 5.8 + - + +
232A ILE 4.6 12.6 - - - +
233A GLU* 3.2 40.6 + - - +
234A ILE* 4.4 21.1 - - + +
288A MSE 3.1 35.4 + - + +
289A LYS* 3.7 7.8 - - - +
291A MSE 1.3 76.0 - - - +
293A ALA* 1.3 57.9 + - - +
295A LEU* 3.5 5.3 + - - +
296A TYR* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 4.7 2.2 - - + -
223A TYR* 3.8 15.1 - - + +
224A PRO* 2.9 31.2 - - - +
225A GLU* 4.5 8.1 - - - +
226A VAL* 4.0 10.3 - - + +
289A LYS 3.1 14.1 + - - +
290A GLN* 3.5 10.3 - - - +
291A MSE 3.1 0.2 - - - -
292A LYS* 1.3 75.4 - - - +
294A LYS* 1.3 59.1 + - - +
296A TYR* 3.4 2.1 + - - +
297A GLU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP* 2.6 29.9 + - - -
221A PHE* 4.1 14.9 - - + -
223A TYR* 3.4 32.3 - - + -
270A ILE* 3.2 38.2 - - + +
271A VAL* 3.0 23.5 + - - +
272A THR* 3.8 11.3 - - + +
290A GLN 2.9 18.8 + - - +
291A MSE 3.8 5.6 - - - +
293A ALA* 1.3 76.3 - - - +
295A LEU* 1.3 60.1 + - - +
297A GLU* 3.3 8.6 + - - +
298A VAL* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 3.4 35.9 - - + -
265A HIS* 3.7 44.4 - - + +
268A THR* 4.3 6.3 - - + +
270A ILE* 3.9 18.4 - - + -
291A MSE 2.9 27.6 + - + +
292A LYS* 3.9 4.0 - - - +
294A LYS* 1.3 74.5 - - - +
296A TYR* 1.3 61.7 + - - +
298A VAL* 3.4 9.9 + - + +
299A GLU* 2.9 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 5.0 3.5 + - - +
123A TYR* 3.3 32.0 + + - -
224A PRO* 5.3 3.8 - - + -
226A VAL* 4.0 14.8 - - + -
230A ILE* 3.3 38.1 - - + -
232A ILE* 5.8 5.4 - - + -
292A LYS 3.0 18.5 + - - +
293A ALA 3.7 3.8 - - - +
294A LYS 3.3 0.2 - - - -
295A LEU* 1.3 74.7 - - - +
297A GLU* 1.3 57.6 + - - +
299A GLU* 3.0 11.8 + - + +
300A MSE 2.7 69.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A TYR* 3.2 23.6 + - - -
221A PHE* 3.2 35.9 - - + -
222A VAL 3.7 9.1 - - - +
223A TYR* 4.0 9.4 - - + -
224A PRO* 3.8 9.5 - - + +
293A ALA 2.9 18.2 + - - +
294A LYS 3.3 6.5 - - - +
296A TYR* 1.3 79.5 - - - +
298A VAL* 1.3 61.2 + - - +
300A MSE 3.3 8.5 + - - +
301A GLN* 3.0 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 5.4 4.9 - - + -
268A THR* 5.7 10.5 - - + -
270A ILE* 6.3 3.6 - - + -
294A LYS* 2.9 22.2 + - + +
295A LEU* 3.6 12.6 - - + +
296A TYR 3.1 0.2 - - - -
297A GLU* 1.3 77.3 - - + +
299A GLU* 1.3 67.7 + - - +
301A GLN* 3.0 29.2 + - - +
302A LYS* 3.1 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 2.9 21.2 + - + +
296A TYR* 3.6 13.9 - - + +
298A VAL* 1.3 78.5 - - - +
300A MSE 1.3 57.8 + - - +
302A LYS* 3.4 28.4 + - - +
303A LYS* 2.8 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 4.1 23.3 - - - +
296A TYR* 2.7 51.6 + - + +
297A GLU* 3.5 10.3 - - - +
299A GLU* 1.3 71.5 - - - +
301A GLN* 1.3 61.7 + - + +
303A LYS* 3.3 31.0 - - + +
304A ASN* 2.9 70.6 + - - +
307A LYS* 4.4 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 6.0 0.2 - - - +
221A PHE* 4.8 3.4 - - - -
297A GLU* 3.0 41.1 + - - +
298A VAL* 3.0 24.2 + - - +
300A MSE 1.3 74.7 - - - +
302A LYS* 1.3 62.4 + - + +
304A ASN* 3.0 8.8 + - - +
305A ALA* 2.8 27.4 + - - +
316A ASP* 5.0 5.8 - - - +
317A ILE 5.2 10.4 + - - +
319A TRP* 3.9 38.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 3.1 32.3 + - + +
299A GLU* 3.8 28.0 - - - +
301A GLN* 1.3 78.2 - - + +
303A LYS* 1.3 62.9 + - - +
305A ALA* 3.0 23.5 + - - +
306A GLU* 3.2 16.0 + - + +
316A ASP* 5.1 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLU* 2.8 21.1 + - + +
300A MSE 3.3 30.7 - - + +
302A LYS* 1.3 79.4 - - - +
304A ASN* 1.3 60.2 + - - +
305A ALA 3.4 0.3 + - - -
306A GLU* 3.4 24.8 + - - +
307A LYS* 3.4 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MSE 2.9 51.7 + - - +
301A GLN* 3.0 6.6 + - - +
303A LYS* 1.3 74.7 - - - +
305A ALA* 1.3 61.9 + - - +
306A GLU 3.3 0.2 - - - -
307A LYS* 3.6 20.8 + - + +
308A GLN* 2.9 43.6 + - - +
317A ILE* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN 2.8 11.4 + - - +
302A LYS* 3.0 16.7 + - - +
304A ASN* 1.3 78.7 - - - +
306A GLU* 1.3 59.8 + - + +
308A GLN* 3.5 7.2 - - - +
309A ALA* 3.3 21.8 + - - +
316A ASP* 3.3 26.7 - - - +
317A ILE* 5.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LYS 3.2 13.4 + - - +
303A LYS* 3.4 21.2 + - - +
305A ALA* 1.3 76.3 - - + +
307A LYS* 1.3 61.4 + - + +
308A GLN 3.0 6.0 + - - -
309A ALA* 3.4 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 5.9 1.6 + - - -
300A MSE 4.4 7.9 - - - +
303A LYS* 3.4 21.2 + - - +
304A ASN* 3.9 32.3 - - - +
305A ALA 3.4 0.4 - - - -
306A GLU* 1.3 77.1 - - + +
308A GLN* 1.3 64.2 + - + +
309A ALA 3.6 0.7 - - - -
----------------------------------------------------------
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