Contacts of the helix formed by residues 281 - 305 (chain A) in PDB entry 1EQB
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 GLU 281 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LYS* 3.7 14.0 + - - +
278A GLU* 3.2 18.7 + - + +
279A ALA 4.4 1.0 - - - +
280A MET* 1.3 81.7 - - - +
282A PRO* 1.3 71.1 - - - +
283A GLU* 3.3 25.4 - - + +
284A PHE* 3.0 26.2 + - + +
285A LYS* 3.5 4.7 + - - +
11B TYR* 2.8 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A MET 4.1 4.0 - - - +
281A GLU* 1.3 90.5 - - + +
283A GLU* 1.3 77.6 + - - +
285A LYS* 3.0 20.0 + - + +
286A THR* 3.3 17.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 3.3 27.7 - - + +
282A PRO* 1.3 95.7 - - - +
284A PHE* 1.3 55.8 + - - +
286A THR* 3.1 12.0 + - - +
287A TYR* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY 3.9 14.6 - - - -
209A ALA* 3.9 8.3 - - + -
210A ALA* 4.6 5.8 - - + -
230A THR 4.0 8.3 - - - -
231A LEU* 4.0 22.2 - - + -
232A ALA* 4.8 3.8 - - + -
278A GLU* 3.5 15.9 - - + +
279A ALA* 3.0 44.4 - - + +
281A GLU* 3.0 16.7 + - + +
283A GLU* 1.3 78.6 - - - +
285A LYS* 1.3 61.0 + - - +
287A TYR* 3.4 16.1 - + - +
288A GLN* 3.0 54.3 + - + +
371A ARG* 5.1 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA* 3.1 44.6 - - + +
211A GLY* 5.3 0.9 - - - -
212A VAL* 6.2 0.2 - - - +
281A GLU 3.5 4.1 + - - +
282A PRO* 3.0 15.3 + - + +
284A PHE* 1.3 78.2 - - - +
286A THR* 1.3 65.8 + - + +
287A TYR 3.1 0.2 - - - -
288A GLN 3.6 1.2 + - - -
289A GLN* 3.1 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO 3.3 9.8 + - - +
283A GLU* 3.1 20.5 + - - -
285A LYS* 1.3 76.7 - - + +
287A TYR* 1.3 64.3 + - - +
289A GLN* 3.4 23.9 + - - +
290A GLN* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 3.3 19.7 + - - -
230A THR* 4.5 4.4 - - - -
232A ALA* 5.1 1.6 - - + -
283A GLU 3.0 18.5 + - - +
284A PHE* 3.4 19.5 - + - +
285A LYS 3.1 0.4 - - - -
286A THR* 1.3 75.9 + - - +
288A GLN* 1.3 98.9 + - - +
290A GLN* 3.1 9.1 + - - +
291A VAL* 3.0 35.8 + - + +
367A PRO* 2.8 24.8 + - - +
370A THR* 3.8 10.5 - - + -
371A ARG* 3.3 50.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY 3.5 15.7 - - - +
207A LEU* 3.0 31.2 + - + +
210A ALA* 3.4 28.5 - - + -
212A VAL* 4.2 6.2 - - + +
230A THR* 3.2 15.5 + - - +
284A PHE* 3.0 41.0 + - + +
286A THR 3.4 0.2 - - - -
287A TYR* 1.3 103.1 - - - +
289A GLN* 1.3 63.0 + - - +
291A VAL* 3.1 10.1 + - - +
292A ALA* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A VAL* 4.0 19.1 - - + +
285A LYS* 3.1 39.9 + - - +
286A THR* 3.4 27.5 + - - +
287A TYR 3.1 0.4 - - - -
288A GLN* 1.3 77.9 - - - +
290A GLN* 1.3 56.1 + - - +
292A ALA* 3.6 4.3 + - - +
293A LYS* 3.0 47.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
286A THR 3.1 13.3 + - - +
287A TYR* 3.1 7.5 + - - +
289A GLN* 1.3 74.6 - - - +
291A VAL* 1.3 56.6 + - - +
293A LYS* 3.4 11.9 - - - +
294A ASN* 2.6 69.1 + - - +
370A THR* 3.4 17.7 - - + -
374A PHE 3.9 0.8 - - - +
375A LYS* 3.5 30.7 - - + +
376A GLU* 3.3 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.6 6.1 - - + -
287A TYR* 3.0 34.5 + - + +
288A GLN* 3.2 18.4 - - - +
290A GLN* 1.3 77.9 - - - +
292A ALA* 1.3 64.5 + - - +
294A ASN 3.3 0.2 + - - -
295A ALA* 3.0 12.0 + - - +
317A HIS* 3.6 25.8 - - + -
366A THR* 2.7 33.3 + - - +
367A PRO* 3.9 12.3 - - + -
370A THR* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 5.1 3.1 - - + -
212A VAL* 4.2 20.4 - - + -
288A GLN 3.0 10.8 + - - +
289A GLN 4.0 3.1 - - - +
291A VAL* 1.3 79.1 - - - +
293A LYS* 1.3 63.2 + - - +
295A ALA* 3.2 4.2 + - - +
296A LYS* 3.1 31.7 + - - +
315A ASP 5.4 3.1 - - - +
316A ASN* 3.7 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 3.0 36.0 + - - +
290A GLN* 3.4 16.3 - - - +
291A VAL 3.2 0.2 - - - -
292A ALA* 1.3 76.5 - - - +
294A ASN* 1.3 62.0 + - - +
296A LYS* 3.2 20.2 + - + +
297A ALA* 3.2 12.1 + - - +
376A GLU* 3.2 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN* 2.6 28.8 + - - +
291A VAL 3.7 3.8 - - - +
293A LYS* 1.3 70.8 - - - +
295A ALA* 1.3 66.6 + - - +
297A ALA* 3.2 7.7 + - - +
298A MET* 3.1 26.7 + - - +
366A THR* 3.8 11.9 - - + -
369A ILE* 5.0 2.3 - - + +
370A THR* 2.9 25.4 + - - +
374A PHE* 3.2 24.7 + - - +
375A LYS 3.0 5.0 - - - -
376A GLU* 3.0 30.4 + - - +
379A ALA* 4.1 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL 3.0 12.7 + - - +
292A ALA 3.2 10.3 + - - +
294A ASN* 1.3 77.4 - - - +
296A LYS* 1.3 61.3 + - - +
298A MET* 3.3 3.7 + - - +
299A VAL* 3.2 25.5 + - - +
314A THR* 3.9 11.2 - - + -
316A ASN 3.4 20.4 - - - +
317A HIS 3.9 9.0 - - - +
318A LEU 4.7 0.2 - - - +
319A PHE* 4.0 6.1 - - + -
366A THR* 3.4 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA* 3.1 21.4 + - - +
293A LYS* 3.2 13.6 + - + +
295A ALA* 1.3 78.6 - - - +
297A ALA* 1.3 60.4 + - - +
299A VAL* 3.2 5.5 + - - +
300A GLU* 3.1 31.8 + - - +
314A THR* 2.7 41.2 + - + +
315A ASP* 3.9 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LYS 3.2 8.7 + - - +
294A ASN* 3.2 10.6 + - - +
296A LYS* 1.3 80.1 - - - +
298A MET* 1.3 59.8 + - - +
300A GLU* 3.6 13.9 + - - +
301A VAL* 3.5 24.8 + - - +
376A GLU* 4.2 21.5 - - + +
379A ALA* 4.6 2.7 - - + -
380A LYS* 3.8 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.1 14.8 - - + -
294A ASN 3.1 13.1 + - - +
295A ALA 3.8 2.2 - - - +
296A LYS 3.3 0.4 - - - -
297A ALA* 1.3 75.0 - - - +
299A VAL* 1.3 65.1 + - - +
301A VAL* 3.5 3.5 + - - +
302A PHE* 3.1 31.3 + - + -
319A PHE* 3.8 17.0 - - + -
364A VAL* 4.4 9.0 - - + -
366A THR* 4.0 20.6 - - - -
369A ILE* 4.3 7.6 - - - -
379A ALA* 3.5 18.6 - - + +
382A LEU* 3.8 23.8 - - + -
383A ALA* 3.7 35.7 - - + +
386A MET* 3.9 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA 3.2 9.0 + - - +
296A LYS* 3.2 9.8 + - - +
298A MET* 1.3 74.7 - - - +
300A GLU* 1.3 69.6 + - + +
302A PHE* 3.1 7.6 + - - +
303A LEU* 3.0 41.2 + - + +
309A VAL* 4.4 9.0 - - + -
312A GLY 4.4 0.2 - - - +
313A GLY* 4.1 18.2 - - - -
314A THR* 3.7 16.2 - - + +
319A PHE* 3.4 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LYS* 3.1 22.4 + - + +
297A ALA* 3.7 16.4 - - - +
299A VAL* 1.3 77.1 - - + +
301A VAL* 1.3 64.8 + - + +
303A LEU* 3.0 10.5 + - - +
304A GLU* 2.9 40.8 + - - +
380A LYS* 4.0 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA 3.5 15.3 - - - +
298A MET 3.5 6.5 + - - +
299A VAL 3.3 0.6 - - - -
300A GLU* 1.3 76.0 - - + +
302A PHE* 1.3 64.3 + - - +
304A GLU* 3.2 12.8 + - + +
305A ARG* 2.9 40.1 + - + +
380A LYS* 3.7 32.1 - - + +
383A ALA* 3.8 7.0 - - + +
384A GLY* 3.9 29.6 - - - +
387A CYS* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A MET* 3.1 29.3 + - + +
299A VAL* 3.1 8.0 + - - +
301A VAL* 1.3 76.0 - - - +
303A LEU* 1.3 59.8 + - - +
305A ARG* 3.3 6.2 + - - +
306A GLY 3.4 0.5 + - - -
307A TYR* 2.9 44.8 + - + +
309A VAL* 4.0 13.7 - - + -
319A PHE* 4.2 16.2 - + - -
321A VAL* 3.7 30.3 - - + -
362A ILE* 5.1 2.2 - - + -
364A VAL* 5.1 1.3 - - + -
383A ALA* 3.7 26.9 - - + -
386A MET* 4.0 36.3 - - + -
387A CYS* 4.1 17.7 - - - -
390A LEU* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.0 26.2 + - + +
300A GLU* 3.5 8.3 - - - +
302A PHE* 1.3 70.8 - - - +
304A GLU* 1.3 64.3 + - + +
305A ARG 3.0 4.5 - - - -
306A GLY* 3.0 14.2 + - - -
307A TYR 3.3 20.4 - - - +
308A LYS* 5.0 0.2 - - - -
309A VAL* 3.8 23.8 - - + +
312A GLY* 3.8 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 2.9 36.7 + - - +
301A VAL* 3.2 10.7 + - + +
303A LEU* 1.3 75.9 - - + +
305A ARG* 1.3 62.6 + - + +
306A GLY 3.3 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 2.9 25.3 + - + +
302A PHE 3.8 2.9 - - - +
303A LEU 3.0 0.6 - - - -
304A GLU* 1.3 83.6 - - + +
306A GLY* 1.3 58.9 + - - +
307A TYR* 3.6 12.8 - - + -
326A LYS* 4.7 2.9 + - - -
384A GLY* 3.5 24.5 + - - -
387A CYS* 3.3 26.3 - - - +
388A ASP* 2.7 35.1 + - - +
391A ASP* 2.8 31.3 + - - +
----------------------------------------------------------
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