Contacts of the helix formed by residues 302 - 314 (chain D) in PDB entry 2XH2
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D PHE* 3.7 18.3 - - + -
256D GLY 5.1 1.2 - - - +
258D TYR* 2.6 38.1 + - - +
275D GLY* 5.4 0.7 - - - -
299D ALA* 3.1 18.3 + - + +
301D ASP* 1.3 72.9 - - - +
303D TRP* 1.3 64.6 + - - +
304D GLU* 4.4 4.2 + - - +
305D ALA* 3.2 29.0 + - + +
306D TRP* 3.2 17.4 + - - -
322D LEU* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D GLU 4.9 0.2 - - - -
301D ASP* 3.0 30.0 + - + +
302D ASP* 1.3 75.7 - - - +
304D GLU* 1.3 65.1 + - + +
306D TRP* 3.2 7.5 + - - +
307D SER* 3.0 25.9 + - - -
322D LEU* 3.5 38.1 - - + -
329D ARG* 3.5 51.9 - - + +
332D THR* 3.8 21.3 - - + +
333D ALA* 3.6 25.6 - - + -
336D LYS* 3.7 36.8 - - + +
338D ALA* 4.2 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ASP* 3.3 5.0 + - - +
303D TRP* 1.3 78.7 - - + +
305D ALA* 1.3 56.5 + - - +
307D SER* 3.4 7.1 + - - -
308D HIS* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLY* 4.3 16.1 - - - -
298D PHE* 3.7 27.5 - - + -
302D ASP* 3.2 32.6 + - - +
304D GLU* 1.3 76.9 - - - +
306D TRP* 1.3 63.9 + - - +
308D HIS* 3.6 7.0 + - - +
309D PHE* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ASP* 3.4 38.4 - - - -
297D PRO* 3.6 14.1 - - + -
298D PHE* 3.2 38.0 + - + -
299D ALA 3.0 21.1 + - - -
302D ASP 3.2 26.7 - - - -
303D TRP* 3.2 7.0 + - - +
305D ALA* 1.3 78.0 - - - +
307D SER* 1.3 66.1 + - - +
308D HIS 3.3 0.2 + - - -
309D PHE* 3.8 2.3 - - - +
310D PHE* 2.9 25.5 + - - +
317D ILE* 3.7 16.6 - - + -
318D VAL 3.7 10.1 - - - -
319D ALA* 4.0 6.1 - - - -
322D LEU* 3.6 36.9 - - + +
338D ALA* 3.2 38.0 - - + +
339D ALA* 3.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D TRP 3.0 17.8 + - - -
304D GLU* 3.4 6.9 + - - -
306D TRP* 1.3 76.4 - - - +
308D HIS* 1.3 63.8 + - - +
310D PHE* 3.5 2.9 + - - +
311D LYS* 3.5 26.8 + - - +
336D LYS* 2.7 35.8 + - - +
337D LYS 3.9 11.9 - - - +
338D ALA* 4.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLY 5.0 1.2 - - - -
276D PRO* 3.9 41.6 - - + +
279D ALA* 4.6 10.6 - - + +
298D PHE* 6.2 0.2 - - - -
304D GLU 3.0 18.2 + - - +
305D ALA* 3.8 8.3 + - - +
307D SER* 1.3 74.9 - - - +
309D PHE* 1.3 68.1 + - - +
311D LYS* 3.2 38.0 + - + +
312D THR* 4.1 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ALA* 3.6 28.0 - - + -
282D TYR* 3.8 19.5 - + + -
283D HIS* 3.6 28.9 - + - -
286D MET* 3.6 23.1 - - + -
294D ILE* 4.5 4.5 - - + -
297D PRO* 4.2 13.2 - - + -
298D PHE* 3.4 34.3 - + + -
305D ALA 3.2 6.0 + - - +
306D TRP* 3.9 2.9 - - - +
308D HIS* 1.3 84.2 - - - +
310D PHE* 1.3 59.4 + - - +
312D THR* 3.1 6.2 + - - -
313D ALA* 2.8 34.4 + - + +
317D ILE* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D TRP 2.9 18.5 + - - +
307D SER 3.8 2.2 - - - +
308D HIS 3.2 0.4 - - - -
309D PHE* 1.3 79.3 - - - +
311D LYS* 1.3 64.3 + - - +
312D THR 3.1 1.2 + - - -
313D ALA* 3.6 11.2 + - + +
314D GLY 4.7 2.8 + - - -
315D ILE 4.9 2.5 - - - -
317D ILE* 4.0 17.7 - - + -
337D LYS* 3.4 37.2 - - + +
338D ALA 3.9 3.6 - - - +
339D ALA* 3.7 23.8 - - - -
340D ASP* 3.5 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D SER* 3.5 18.5 + - - +
308D HIS* 3.2 27.6 + - + +
310D PHE* 1.3 80.0 - - - +
312D THR* 1.3 67.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D HIS* 3.2 30.0 + - - -
308D HIS 4.7 2.6 + - - +
309D PHE* 3.1 6.5 + - - -
311D LYS* 1.3 87.8 - - + +
313D ALA* 1.3 69.2 + - - +
314D GLY* 3.3 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D HIS* 4.2 9.7 + - - -
286D MET* 3.9 18.0 - - - +
309D PHE* 2.8 44.2 + - + +
310D PHE* 3.6 7.2 + - + +
312D THR* 1.3 78.3 + - - +
314D GLY* 1.3 59.2 + - - +
315D ILE* 3.1 12.4 + - + +
317D ILE* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D PHE 4.7 3.2 + - - -
312D THR 3.3 4.4 + - - -
313D ALA* 1.3 77.7 - - - +
315D ILE* 1.3 65.5 + - - +
----------------------------------------------------------
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