Contacts of the helix formed by residues 284 - 305 (chain A) in PDB entry 2OIB
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 284 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PRO 3.7 3.0 + - - -
283A LEU* 1.3 73.4 - - - +
285A TRP* 1.3 59.3 + - - +
286A HIS* 3.7 5.8 + - - +
287A MET* 3.2 25.2 + - - +
288A ARG* 2.9 31.7 + - - +
418A MET* 4.7 4.0 - - - +
419A ASN* 6.1 0.2 - - - -
420A ASP* 3.5 18.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER* 1.3 68.1 - - - +
286A HIS* 1.3 67.5 + - - +
288A ARG* 3.2 7.7 + - + +
289A CYS* 3.0 45.6 + - - -
380A ILE* 4.5 7.0 - - + -
381A ILE* 4.3 21.3 - - + -
418A MET* 3.8 27.4 - - + -
420A ASP* 2.8 40.0 + - - +
421A ALA* 3.7 12.1 - - - -
422A ASP* 4.0 3.4 - - - -
425A SER* 2.7 29.6 + - - -
426A VAL* 3.6 42.1 - - + +
429A MET* 3.6 34.5 - - + -
457A MET* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER* 4.0 5.7 + - - +
285A TRP* 1.3 80.9 - - - +
287A MET* 1.3 65.9 + - - +
289A CYS* 3.3 6.8 + - + +
290A LYS* 3.1 56.8 + - + +
420A ASP* 3.1 15.2 + - - +
420B ASP* 6.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.2 14.1 - - + -
284A SER* 3.2 24.7 + - - +
286A HIS* 1.3 81.5 - - - +
288A ARG* 1.3 57.8 + - - +
290A LYS* 3.1 41.9 + - + +
291A ILE* 2.9 44.1 + - + +
322A ALA 4.4 3.6 - - - +
323A PHE* 3.5 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 6.1 0.7 - - + -
274A LEU* 3.7 19.3 + - + +
282A PRO* 4.8 1.0 - - - +
283A LEU* 2.9 48.3 + - + +
284A SER 2.9 21.2 + - - +
285A TRP* 3.5 11.7 - - + +
287A MET* 1.3 75.9 - - - +
289A CYS* 1.3 55.9 + - - +
291A ILE* 3.4 9.8 + - - +
292A ALA* 2.9 29.6 + - - +
380A ILE* 2.7 61.0 + - + +
383A GLY 4.2 0.6 - - - +
415A ASP* 2.8 37.4 + - - +
417A LYS* 3.8 8.7 + - - +
418A MET* 3.4 29.6 - - - +
429A MET* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A TRP* 3.0 56.4 + - - -
286A HIS* 3.7 9.6 - - + +
288A ARG* 1.3 75.6 - - - +
290A LYS* 1.3 58.0 + - + +
292A ALA* 3.4 2.3 + - - +
293A GLN* 2.9 36.9 + - - +
425A SER* 5.1 0.9 - - - -
429A MET* 4.0 8.7 - - - -
457A MET* 3.9 24.0 - - + +
458A THR* 4.3 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A HIS* 3.1 45.2 + - + +
287A MET* 3.1 39.3 + - + +
289A CYS* 1.3 77.5 - - + +
291A ILE* 1.3 55.4 + - - +
293A GLN* 3.4 16.7 + - - +
294A GLY* 2.9 25.8 + - - -
322A ALA 4.9 5.9 + - - -
325A ALA* 5.4 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.2 27.8 - - + -
283A LEU* 4.1 25.8 - - + -
287A MET* 2.9 39.8 + - + +
288A ARG* 3.7 7.0 - - - +
290A LYS* 1.3 72.6 - - - +
292A ALA* 1.3 57.2 + - - +
294A GLY 3.3 0.3 + - - -
295A ALA* 2.8 34.2 + - + +
317A ILE* 4.5 3.4 - - + -
319A LEU* 3.9 24.0 - - + -
323A PHE* 3.5 21.8 - - + +
325A ALA* 3.4 18.8 - - + +
380A ILE* 5.0 2.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
288A ARG 2.9 18.0 + - - +
289A CYS 3.6 4.9 - - - +
290A LYS 3.4 0.2 - - - -
291A ILE* 1.3 77.3 - - - +
293A GLN* 1.3 56.8 + - - +
295A ALA* 3.5 3.8 + - - -
296A ALA* 3.0 27.9 + - - +
373A PHE* 3.5 9.3 - - - -
377A LEU* 3.9 25.1 - - + -
380A ILE* 4.0 11.0 - - + +
429A MET* 4.0 14.6 - - + -
454A LEU* 3.7 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A CYS* 2.9 20.9 + - - +
290A LYS* 3.6 19.5 - - - +
292A ALA* 1.3 71.5 - - - +
294A GLY* 1.3 60.0 + - - +
296A ALA* 3.4 2.9 + - - +
297A ASN* 2.9 41.7 + - - +
454A LEU* 3.3 32.4 + - + +
455A GLN* 4.1 22.8 + - - +
457A MET* 4.8 1.8 - - + +
458A THR* 2.6 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASN* 3.2 34.1 - - - +
290A LYS 2.9 15.3 + - - -
291A ILE 3.6 3.1 - - - -
293A GLN* 1.3 75.9 - - - +
295A ALA* 1.3 60.8 + - - +
297A ASN* 3.1 4.8 + - - -
298A GLY 3.0 19.4 + - - -
325A ALA* 3.9 6.1 - - - -
----------------------------------------------------------
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 ILE* 2.8 21.0 + - + +
292A ALA* 3.7 2.2 - - - +
294A GLY* 1.3 70.9 - - - +
296A ALA* 1.3 58.4 + - - +
298A GLY* 3.1 3.3 + - - -
299A ILE* 2.9 34.6 + - - +
317A ILE* 4.2 21.1 - - + -
325A ALA* 3.5 11.0 - - + +
327A ILE* 3.8 14.6 - - + +
373A PHE* 3.6 22.7 - - + -
376A VAL* 5.9 0.2 - - + -
380A ILE* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA 3.0 17.4 + - - +
293A GLN* 3.6 5.2 - - - +
295A ALA* 1.3 75.7 - - - +
297A ASN* 1.3 60.0 + - - +
299A ILE* 3.4 1.5 + - - -
300A ASN* 2.8 31.1 + - - +
373A PHE* 4.0 11.3 - - + -
447A ILE* 3.6 19.8 - - + +
450A VAL* 4.5 3.6 - - + -
451A GLN* 4.5 12.7 - - + -
454A LEU* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A HIS* 3.9 12.3 + - + +
244A ASN* 3.4 19.4 + - - +
293A GLN* 2.9 27.3 + - - +
294A GLY* 3.1 4.4 + - - +
296A ALA* 1.3 75.7 - - - +
298A GLY* 1.3 62.5 + - - +
300A ASN* 3.4 4.0 + - - +
301A PHE* 3.1 22.3 + - - +
451A GLN* 2.5 41.9 + - - +
455A GLN* 5.3 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A HIS* 4.2 3.6 - - - -
244A ASN* 3.6 21.9 - - - +
245A LEU* 3.5 28.3 - - - +
294A GLY 3.0 10.9 + - - -
295A ALA 3.1 3.8 + - - -
297A ASN* 1.3 73.0 - - - +
299A ILE* 1.3 62.7 + - - +
301A PHE* 3.3 3.8 + - - +
302A LEU* 3.2 16.8 + - - +
327A ILE* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA 2.9 19.0 + - - +
298A GLY* 1.3 71.9 - - - +
300A ASN* 1.3 65.5 + - - +
302A LEU* 3.1 11.9 + - + +
303A HIS* 2.9 52.6 + - + +
309A HIS* 6.4 0.2 - - + -
312A ILE* 4.0 24.2 - - + -
327A ILE* 4.0 15.7 - - + +
369A ASP* 4.6 8.7 - - + +
370A ILE* 5.0 1.1 - - + -
373A PHE* 3.6 42.4 - - + -
447A ILE* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA 2.8 18.9 + - - +
297A ASN 3.4 6.2 + - - +
299A ILE* 1.3 76.6 - - - +
301A PHE* 1.3 57.4 + - - +
303A HIS* 3.3 0.5 + - - +
304A GLU* 2.9 55.9 + - - +
447A ILE* 3.4 27.6 - - + +
448A LYS* 3.2 26.9 + - - +
451A GLN* 3.0 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LYS 4.2 5.4 - - - -
240A CYS* 3.5 31.9 - - + -
241A GLN 3.5 26.7 - - - -
242A HIS* 3.6 32.1 - + + +
245A LEU* 3.8 16.6 - - + -
297A ASN 3.1 9.6 + - - +
298A GLY 3.3 8.5 + - - +
300A ASN* 1.3 74.7 - - - +
302A LEU* 1.3 65.2 + - - +
304A GLU* 4.2 11.4 - - - -
305A ASN* 2.9 57.2 + - - +
321C GLU* 3.6 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 5.3 0.9 - - + -
240A CYS* 4.0 19.7 - - - -
245A LEU* 3.9 22.2 - - + -
298A GLY 3.2 14.3 + - - +
299A ILE* 3.1 16.0 + - + +
301A PHE* 1.3 77.5 - - - +
303A HIS* 1.3 61.2 + - + +
305A ASN* 3.2 5.0 + - - +
306A HIS 3.0 9.0 + - - -
307A HIS* 2.8 44.0 + - + +
309A HIS* 4.3 18.8 - - + +
327A ILE* 4.3 11.9 - - + -
330A PHE* 3.8 35.4 - - + -
369A ASP* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 2.9 33.7 + - + +
302A LEU* 1.3 79.9 - - + +
304A GLU* 1.3 57.1 + - - +
306A HIS* 2.9 26.9 + - - -
307A HIS 3.1 21.8 - - - +
366A PRO* 3.3 41.4 - - + +
369A ASP* 2.9 27.4 + - + +
370A ILE* 4.1 10.4 - - + +
447A ILE* 3.6 28.1 + - + +
----------------------------------------------------------
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 ASN* 2.9 50.2 + - - +
301A PHE* 3.7 14.3 - - - +
303A HIS* 1.3 72.8 - - - +
305A ASN* 1.3 66.1 + - - +
306A HIS* 3.6 18.4 + - - -
448A LYS* 4.0 11.4 + - + +
321C GLU* 5.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LYS* 2.8 46.4 + - - +
240A CYS* 4.9 2.2 - - - -
301A PHE* 2.9 64.3 + - + +
302A LEU* 3.3 4.5 - - - +
303A HIS 3.1 0.2 - - - -
304A GLU* 1.3 83.9 + - - +
306A HIS* 1.3 64.5 + - - +
307A HIS* 3.0 15.8 + - - +
----------------------------------------------------------
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