Contacts of the helix formed by residues 322 - 336 (chain X) in PDB entry 2DE0
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 322 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320X HIS* 2.9 15.1 + - - -
321X GLY* 1.3 80.0 - - - +
323X PRO* 1.4 72.8 - - - +
324X ALA* 3.5 18.6 + - - +
325X VAL* 2.9 36.5 + - + +
326X TRP 3.2 4.3 + - - -
476X TYR* 4.5 4.2 + - - +
487X SER* 3.8 13.0 - - - -
497X TYR* 4.6 11.6 - - - +
562X ILE* 5.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 323 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308X VAL* 4.2 13.7 - - + +
313X ALA* 5.5 1.3 - - - +
316X LEU* 3.8 32.6 - - + +
317X VAL* 4.3 13.5 - - + +
320X HIS* 3.6 16.3 - - + +
321X GLY 4.1 2.0 - - - +
322X ASP* 1.4 85.5 - - - +
324X ALA* 1.3 64.6 + - - +
326X TRP* 2.8 22.1 + - + +
327X TRP* 2.8 15.8 + - - +
562X ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305X PRO* 5.8 0.2 - - - +
306X LEU* 3.2 55.8 - - + +
307X ALA 4.8 1.0 - - - +
308X VAL* 4.3 6.9 - - + +
322X ASP* 3.0 14.3 - - - +
323X PRO* 1.3 81.5 - - - +
325X VAL* 1.3 61.1 + - - +
327X TRP* 3.4 5.6 + - - +
328X VAL* 3.3 22.2 + - - +
562X ILE* 4.6 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320X HIS* 5.1 1.6 - - + -
322X ASP* 2.9 39.3 + - + +
324X ALA* 1.3 72.0 - - - +
326X TRP* 1.3 65.5 - - - +
328X VAL* 3.7 4.0 + - - +
329X SER* 3.1 21.7 + - - -
476X TYR* 3.5 30.5 - - + +
477X GLU* 3.8 9.2 - - + -
480X GLN* 4.3 12.4 - - + +
497X TYR* 3.4 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 326 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184X ALA* 4.6 9.2 + - - +
187X LEU* 3.8 36.3 - - + -
188X THR* 3.6 19.8 + - - -
191X VAL* 3.9 11.2 - - + -
312X LEU* 4.5 2.5 - - + -
316X LEU* 3.4 39.7 - - + +
319X VAL* 6.2 1.2 - - + +
320X HIS* 3.7 41.7 - + + +
322X ASP 3.2 2.0 + - - -
323X PRO* 2.8 12.0 + - + +
325X VAL* 1.3 79.9 - - - +
327X TRP* 1.3 67.6 + + - +
329X SER* 2.3 29.0 + - - -
330X GLN* 3.3 43.2 + - + +
480X GLN* 4.0 19.5 + - - -
481X THR* 5.9 0.4 - - - +
483X HIS 5.8 0.4 + - - -
484X PRO 5.1 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 327 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191X VAL* 3.6 25.1 - - + -
232X MET* 3.7 17.8 - - + -
235X TYR* 3.6 24.0 - + - -
305X PRO* 6.0 0.7 - - + -
307X ALA 3.4 21.3 + - - -
308X VAL* 3.9 9.4 - - + -
309X PRO* 3.5 34.6 - - + +
312X LEU* 4.2 7.4 - - + -
323X PRO 2.8 9.9 + - - +
324X ALA* 3.4 9.6 - - - +
326X TRP* 1.3 83.9 - + + +
328X VAL* 1.3 66.4 + - + +
329X SER 3.0 2.0 + - - -
330X GLN* 3.0 25.5 + - + +
331X PHE* 3.6 28.8 - + - -
567X TYR* 3.3 43.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228X VAL* 4.2 3.3 - - + +
232X MET* 3.9 15.7 - - + -
305X PRO* 3.9 31.2 - - + -
306X LEU* 6.0 0.4 - - + -
324X ALA 3.3 10.8 + - - +
325X VAL 3.8 6.1 - - - +
327X TRP* 1.3 79.6 - - + +
329X SER* 1.3 62.3 + - - +
330X GLN 3.3 0.5 + - - -
331X PHE* 3.4 5.7 + - - +
332X VAL* 3.3 21.3 + - + +
477X GLU* 3.7 25.4 - - + +
497X TYR* 3.6 25.1 - - + +
499X PHE* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 329 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325X VAL 3.1 11.8 + - - -
326X TRP* 2.3 33.9 + - - -
327X TRP 3.0 0.4 - - - -
328X VAL* 1.3 77.0 - - - +
330X GLN* 1.3 67.4 + - - +
331X PHE 3.3 0.2 - - - -
332X VAL* 3.7 8.1 - - - +
333X LYS* 2.8 29.1 + - - +
477X GLU* 2.9 31.4 - - - -
480X GLN* 3.7 8.2 - - - +
481X THR* 3.7 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 330 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188X THR* 3.4 29.3 + - - +
191X VAL* 3.6 29.6 - - + +
192X GLN* 3.0 36.9 + - - +
195X ILE* 4.3 2.5 - - + -
326X TRP* 3.3 59.7 + - + +
327X TRP* 3.0 13.8 + - + +
329X SER* 1.3 83.4 + - - +
331X PHE* 1.3 59.4 + - + +
333X LYS* 3.0 16.2 + - - +
334X TYR* 3.1 4.9 + - - +
481X THR* 4.5 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 331 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195X ILE* 4.1 20.6 - - + -
228X VAL* 3.9 20.9 - - + -
231X PHE* 3.5 50.5 - + + -
232X MET* 3.8 24.7 - - + -
235X TYR* 3.9 23.3 - + + -
327X TRP* 3.6 57.2 - + - -
328X VAL 3.4 1.3 + - - +
330X GLN* 1.3 74.8 - - + +
332X VAL* 1.3 65.3 + - - +
334X TYR* 3.4 2.3 + - - +
335X LEU* 3.2 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224X LEU* 5.1 7.2 - - + -
225X HIS* 5.0 3.4 - - + -
228X VAL* 3.5 24.2 - - + -
328X VAL* 3.3 17.0 + - + +
329X SER* 3.8 9.0 - - - +
330X GLN 3.3 0.2 - - - -
331X PHE* 1.3 77.4 - - - +
333X LYS* 1.3 63.8 + - - +
335X LEU* 3.8 2.9 - - - +
336X ILE* 3.1 32.0 + - + +
474X VAL* 4.7 9.0 - - + +
477X GLU* 3.9 22.7 - - + +
478X ILE* 3.7 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 333 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188X THR* 3.4 28.5 - - + -
192X GLN* 3.4 30.3 - - + +
329X SER 2.8 15.0 + - - +
330X GLN* 3.0 12.1 + - - +
332X VAL* 1.3 79.9 - - - +
334X TYR* 1.3 63.6 + - - +
336X ILE* 3.5 17.2 + - + +
337X ARG* 3.8 10.2 + - - +
481X THR* 4.3 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192X GLN* 3.5 21.5 + - - +
195X ILE* 3.3 30.5 - - + -
196X THR* 3.1 27.3 + - - +
199X GLN* 3.5 24.5 - - + +
200X ASN* 3.6 12.5 + - - -
231X PHE* 3.5 21.5 - + + -
261X PRO 5.3 0.2 + - - -
262X VAL* 3.4 23.1 + - + -
263X SER* 4.8 0.5 - - - -
264X GLU* 5.8 1.2 - - - +
330X GLN 3.1 9.3 + - - +
331X PHE 4.0 3.8 - - - +
332X VAL 3.4 0.2 - - - -
333X LYS* 1.3 78.3 - - - +
335X LEU* 1.3 63.1 + - - +
337X ARG* 2.4 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 335 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224X LEU* 4.4 11.7 - - + -
227X VAL* 3.9 20.9 - - + -
228X VAL* 3.6 38.8 - - + +
231X PHE* 3.7 20.0 - - + -
243X LEU* 5.4 0.2 - - + -
255X TRP* 3.6 31.3 + - + -
259X PHE* 3.9 3.5 - - - +
260X ARG 4.7 3.5 - - - +
262X VAL* 3.5 31.6 - - + -
331X PHE 3.2 18.8 + - - +
332X VAL* 3.8 4.7 - - - +
334X TYR* 1.3 78.3 - - - +
336X ILE* 1.3 58.5 + - - +
337X ARG* 2.9 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220X TYR* 3.7 24.0 - - + +
224X LEU* 3.9 18.8 - - + -
255X TRP* 5.0 1.6 - - + -
259X PHE* 3.7 23.2 - - + -
332X VAL* 3.1 27.0 + - + +
333X LYS* 3.6 11.2 - - + +
334X TYR 3.3 0.4 - - - -
335X LEU* 1.3 75.6 - - + +
337X ARG* 1.3 63.9 + - - +
338X PRO* 3.2 7.1 - - - +
454X ILE* 5.4 3.6 - - + -
474X VAL* 5.1 0.9 - - + -
478X ILE* 4.4 28.3 - - + -
----------------------------------------------------------
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