Contacts of the helix formed by residues 282 - 299 (chain A) in PDB entry 2XAR
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 HIS 282 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 3.5 20.4 + - - +
279A GLU* 3.1 34.6 + - + +
280A ASP 4.6 2.9 - - - -
281A GLY* 1.3 78.1 + - - +
283A ARG* 1.3 63.9 + - - +
284A THR 3.3 2.2 - - - -
285A GLU* 2.9 36.1 + - + +
286A CYS* 3.3 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLU* 2.7 44.4 + - - +
270A ASP* 5.2 1.9 - - - +
272A LEU* 3.6 36.7 - - + +
273A LYS* 3.3 28.8 - - - +
274A GLY 4.3 1.2 - - - +
276A ILE* 3.7 32.7 + - + +
278A SER* 3.9 18.7 + - - +
279A GLU 4.1 0.4 + - - +
280A ASP* 2.6 47.7 + - - +
281A GLY 3.4 1.0 - - - -
282A HIS* 1.3 78.0 - - - +
284A THR* 1.3 57.8 + - - +
286A CYS 3.5 0.5 + - - -
287A PHE* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 3.9 35.6 + - + +
265A GLY 4.6 1.7 + - - -
268A PHE* 3.7 21.3 - - + -
269A GLU* 2.7 30.7 + - - +
272A LEU* 4.2 7.8 - - - +
281A GLY 4.9 2.9 - - - -
282A HIS 3.3 0.4 - - - -
283A ARG* 1.3 75.3 - - - +
285A GLU* 1.3 57.1 + - - +
287A PHE* 3.2 3.9 + - - +
288A LEU* 2.9 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 5.8 0.7 - - - +
230A LYS* 6.4 2.0 - - - -
281A GLY 5.2 1.8 + - - +
282A HIS* 2.9 45.9 + - + +
284A THR* 1.3 78.6 - - - +
286A CYS* 1.3 63.5 + - + +
288A LEU* 3.4 13.3 + - + +
289A GLN* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 4.0 17.5 - - + -
278A SER* 5.2 4.0 - - - -
282A HIS* 3.3 19.2 + - - +
283A ARG 4.0 2.7 - - - +
284A THR 3.3 0.4 - - - -
285A GLU* 1.3 80.7 - - - +
287A PHE* 1.3 58.7 + - - +
289A GLN* 3.2 8.7 + - - +
290A LEU* 2.9 27.2 + - - +
392A LEU* 4.2 12.6 - - + +
394A PRO* 4.0 28.5 - - - -
395A THR* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 3.5 27.1 - - + -
165A VAL* 3.4 26.5 - - + -
240A PHE* 4.6 5.2 - + - -
242A VAL* 3.8 18.8 - - + -
268A PHE* 3.7 23.6 - + - -
272A LEU* 3.8 12.8 - - + -
276A ILE* 3.8 29.3 - - + +
283A ARG 2.9 21.6 + - - +
284A THR 3.2 3.8 + - - +
286A CYS* 1.3 71.2 - - - +
288A LEU* 1.3 82.0 + - + +
290A LEU* 3.0 12.3 + - + +
291A VAL* 3.0 38.7 + - + +
375A PHE* 5.2 4.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 4.6 9.0 - - + -
229A ILE* 3.8 27.1 - - + +
230A LYS* 4.5 19.3 - - + -
233A TYR* 3.8 38.8 - - + -
240A PHE* 4.8 3.1 - - + -
284A THR* 2.9 32.9 + - + +
285A GLU* 3.6 13.0 - - + +
286A CYS 3.3 0.2 - - - -
287A PHE* 1.3 93.0 - - + +
289A GLN* 1.3 58.4 + - - +
291A VAL* 3.2 3.4 + - - +
292A SER* 2.9 30.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
222A LYS* 3.9 9.7 - - - +
226A LEU* 4.1 30.7 - - + +
285A GLU 3.0 14.0 + - - +
286A CYS* 3.2 14.1 + - - +
288A LEU* 1.3 74.9 - - - +
290A LEU* 1.3 59.1 + - - +
292A SER* 3.3 7.9 + - - -
293A ASP* 2.8 66.1 + - - +
392A LEU* 4.5 12.1 - - + -
394A PRO* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 4.6 3.4 - - + -
276A ILE* 4.4 20.6 - - + -
286A CYS 2.9 12.9 + - - +
287A PHE* 3.0 14.1 + - + +
289A GLN* 1.3 76.8 - - - +
291A VAL* 1.3 62.3 + - - +
293A ASP* 3.3 8.7 + - - +
294A ALA* 3.1 20.6 + - - +
375A PHE* 3.6 35.9 - - + -
390A VAL* 3.9 19.9 - - + +
392A LEU* 4.3 11.4 - - + +
399A PHE* 3.6 44.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
165A VAL* 3.7 26.7 - - + -
167A ILE* 4.6 2.9 - - + -
229A ILE* 4.0 30.1 - - + -
240A PHE* 5.3 0.2 - - + -
287A PHE* 3.0 50.6 + - + +
288A LEU 3.7 5.6 - - - +
290A LEU* 1.3 72.1 - - + +
292A SER* 1.3 67.8 + - - +
294A ALA* 3.2 2.4 + - - +
295A VAL* 2.9 31.1 + - + +
373A ILE* 4.8 4.9 - - + -
375A PHE* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 4.1 5.5 + - - +
225A VAL* 3.7 6.9 - - - +
226A LEU* 3.3 46.0 + - - +
229A ILE* 4.0 13.9 - - - +
288A LEU 2.9 17.7 + - - -
289A GLN* 3.5 9.2 + - - -
291A VAL* 1.3 77.6 - - - +
293A ASP* 1.3 63.0 + - - +
295A VAL* 3.7 2.0 - - - +
296A TYR* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 2.8 31.2 + - - +
289A GLN* 2.8 43.5 + - - +
290A LEU* 3.6 1.2 - - - +
291A VAL 3.2 0.2 - - - -
292A SER* 1.3 74.5 + - - +
294A ALA* 1.3 52.9 + - - +
296A TYR* 4.0 4.9 - - - +
297A GLY* 2.7 32.4 + - - -
390A VAL* 3.5 32.9 - - + +
391A SER 4.9 3.8 - - - +
392A LEU* 5.0 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU 3.1 8.3 + - - +
291A VAL 3.7 2.9 - - - +
293A ASP* 1.3 73.9 - - - +
295A VAL* 1.3 60.7 + - - +
297A GLY* 5.0 0.2 - - - -
298A SER* 2.9 36.8 + - - -
373A ILE* 4.3 6.7 - - + -
375A PHE* 3.7 34.5 - - + -
390A VAL* 3.8 13.4 - - + +
401A TYR* 3.9 20.5 + - + -
403A VAL* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 4.3 12.8 - - + -
217A LEU* 4.3 4.3 - - + -
225A VAL* 3.7 21.5 - - + -
229A ILE* 4.4 4.5 - - + -
291A VAL* 2.9 28.5 + - + +
292A SER 3.7 3.6 - - - +
294A ALA* 1.3 76.3 - - - +
296A TYR* 1.3 64.2 + - - +
298A SER* 3.0 19.0 + - - -
299A GLY* 3.3 8.3 + - - -
300A VAL* 4.2 3.4 + - - +
301A LEU* 3.6 37.1 + - + +
371A ILE* 6.3 0.9 - - + -
373A ILE* 3.6 25.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
220A GLY* 3.1 32.1 + - - -
221A SER 4.4 2.2 - - - -
222A LYS* 3.7 54.2 + - + +
225A VAL* 4.5 14.6 - - + -
292A SER* 3.0 15.4 + - - +
293A ASP* 4.0 3.8 - - - +
295A VAL* 1.3 81.9 - - - +
297A GLY* 1.3 68.9 + - - +
299A GLY* 3.2 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ASP 2.7 23.0 + - - -
294A ALA* 3.8 0.4 - - - -
296A TYR* 1.3 79.3 - - - +
298A SER* 1.3 62.1 + - - +
299A GLY* 3.2 1.4 + - - -
401A TYR* 4.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A HIS* 6.2 0.2 - - - -
294A ALA 2.9 18.6 + - - -
295A VAL* 3.0 16.1 + - - -
297A GLY* 1.3 71.9 - - - +
299A GLY* 1.3 62.9 + - - +
300A VAL* 3.0 27.1 + - - +
303A ARG* 5.6 4.5 + - - -
401A TYR* 3.3 28.5 + - - -
403A VAL* 4.3 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL 3.3 4.7 + - - -
296A TYR 3.2 11.9 + - - -
297A GLY 3.2 5.0 - - - -
298A SER* 1.3 78.9 + - - +
300A VAL* 1.3 61.8 + - - +
301A LEU* 3.2 5.0 + - - -
302A ASP* 3.5 33.0 + - - +
303A ARG* 4.2 8.7 + - - +
----------------------------------------------------------
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