Contacts of the helix formed by residues 302 - 314 (chain A) in PDB entry 2XGZ
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 ASP 302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PHE* 3.9 17.3 - - + -
256A GLY 5.0 2.0 - - - +
258A TYR* 2.6 36.8 + - - +
275A GLY* 5.3 0.5 - - - -
299A ALA* 3.0 19.9 + - + +
301A ASP* 1.3 73.6 - - - +
303A TRP* 1.3 64.2 + - - +
304A GLU* 3.3 5.4 + - - +
305A ALA* 3.1 27.4 + - + +
306A TRP* 3.1 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASP* 3.0 39.9 + - + +
302A ASP* 1.3 73.6 - - - +
304A GLU* 1.3 62.2 + - - +
306A TRP* 3.2 8.7 + - - +
307A SER* 3.0 27.2 + - - -
322A LEU* 3.7 39.0 - - + -
329A ARG* 3.7 44.0 - - + +
332A THR* 3.7 22.4 - - + +
333A ALA* 3.5 26.7 - - + -
336A LYS* 3.7 41.1 - - + +
338A ALA* 4.2 11.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
302A ASP* 3.3 5.3 + - - +
303A TRP* 1.3 77.4 - - - +
305A ALA* 1.3 57.4 + - - +
307A SER* 3.3 6.4 + - - +
308A HIS* 3.0 31.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
275A GLY* 4.2 16.6 - - - -
276A PRO* 6.3 0.2 - - - -
298A PHE* 3.6 28.8 - - + -
302A ASP* 3.1 33.7 + - - +
304A GLU* 1.3 77.8 - - - +
306A TRP* 1.3 61.8 + - - +
308A HIS* 3.6 5.4 + - - +
309A PHE* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASP* 3.5 38.1 - - - -
297A PRO* 3.6 16.6 - - + -
298A PHE* 3.1 37.9 + - + -
299A ALA 2.9 22.1 + - - -
302A ASP 3.1 27.0 + - - -
303A TRP* 3.2 7.3 + - - +
305A ALA* 1.3 75.5 - - - +
307A SER* 1.3 65.7 + - - +
309A PHE* 3.3 3.0 + - - +
310A PHE* 2.9 26.2 + - - +
317A ILE* 3.8 13.5 - - + -
318A VAL 3.6 12.8 - - - -
319A ALA* 3.9 7.9 - - - -
322A LEU* 3.7 32.8 - - + +
338A ALA* 3.3 37.7 - - + +
339A ALA* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A TRP 3.0 17.2 + - - -
304A GLU* 3.9 6.3 - - - -
306A TRP* 1.3 76.6 - - - +
308A HIS* 1.3 64.2 + - - +
310A PHE* 3.5 2.6 + - - +
311A LYS* 3.5 25.5 + - - +
336A LYS* 2.7 37.2 + - - +
337A LYS 3.7 12.3 + - - +
338A ALA* 4.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLY 5.2 1.0 - - - -
276A PRO* 4.1 38.7 - - + +
279A ALA* 4.8 9.1 - - + +
304A GLU 3.0 17.3 + - - +
305A ALA* 3.9 6.9 + - - +
307A SER* 1.3 77.1 - - - +
309A PHE* 1.3 64.9 + - - +
311A LYS* 3.3 34.7 + - + +
312A THR* 4.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ALA* 3.5 26.5 - - + -
282A TYR* 3.8 20.9 - + + -
283A HIS* 3.6 32.5 - + - -
286A MET* 4.1 16.4 - - - -
294A ILE* 4.6 3.8 - - + -
297A PRO* 4.2 18.2 - - + -
298A PHE* 3.3 32.5 - + + -
305A ALA 3.2 6.2 + - - +
306A TRP* 3.9 2.5 - - - +
308A HIS* 1.3 82.6 + - - +
310A PHE* 1.3 64.7 + - - +
311A LYS 3.3 0.5 + - - -
312A THR* 3.3 5.0 + - - -
313A ALA* 3.0 25.6 + - + +
317A ILE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A TRP 2.9 15.1 + - - +
307A SER 3.9 0.9 - - - +
308A HIS 3.3 0.4 - - - -
309A PHE* 1.3 81.1 - - - +
311A LYS* 1.3 65.2 + - - +
312A THR 3.1 1.0 + - - -
313A ALA* 3.6 11.5 + - + +
314A GLY 4.8 1.7 + - - -
315A ILE 5.0 2.0 - - - -
317A ILE* 4.0 17.5 - - + -
337A LYS* 3.4 40.6 - - + +
338A ALA 3.8 4.5 - - - +
339A ALA* 3.6 22.0 - - - -
340A ASP* 3.5 44.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A SER* 3.5 16.5 + - - +
308A HIS* 3.5 27.4 - - + +
309A PHE 3.2 0.6 - - - -
310A PHE* 1.3 80.9 - - + +
312A THR* 1.3 68.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A HIS* 3.4 28.6 + - - -
308A HIS 4.6 3.9 + - - +
309A PHE* 3.3 5.4 + - - -
310A PHE 3.1 0.2 - - - -
311A LYS* 1.3 88.9 - - + +
313A ALA* 1.3 68.1 + - - +
314A GLY* 3.4 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A HIS* 4.2 8.7 - - - -
286A MET* 2.9 28.1 - - - +
309A PHE* 3.0 25.0 + - + +
310A PHE* 3.6 9.4 + - + +
312A THR* 1.3 77.8 - - - +
314A GLY* 1.3 60.4 + - - +
315A ILE* 3.2 7.2 - - + +
317A ILE* 3.8 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE 4.8 2.4 + - - -
312A THR 3.4 4.0 - - - -
313A ALA* 1.3 76.5 - - - +
315A ILE* 1.3 64.8 + - - +
----------------------------------------------------------
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