Contacts of the helix formed by residues 294 - 305 (chain D) in PDB entry 1DS5
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 294 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASP* 5.3 0.9 - - - -
134D ARG* 3.8 21.7 + - - -
292D LEU 4.1 3.2 + - - -
293D VAL* 1.3 79.3 - - - +
295D PRO* 1.3 81.2 - - - +
296D GLU* 2.5 10.1 + - - +
297D ALA* 2.7 37.2 + - - +
298D ILE* 2.8 13.1 + - - +
323D TYR* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D SER* 1.3 86.4 - - - +
296D GLU* 1.4 70.8 + - - +
298D ILE* 3.6 8.7 + - + +
299D ASP* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ARG* 5.2 5.2 + - - +
294D SER* 2.5 12.8 + - - +
295D PRO* 1.4 85.8 - - - +
297D ALA* 1.3 68.0 + - - +
298D ILE 2.9 1.6 - - - -
299D ASP* 2.7 15.4 + - - +
300D PHE* 2.9 14.6 + - - +
321D HIS* 3.6 6.8 - - + -
322D PRO* 3.7 34.0 - - + +
323D TYR* 4.0 20.2 - - + +
325D GLN* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D PHE* 3.6 17.2 - - + -
226D ILE* 4.6 8.1 - - + -
292D LEU 3.8 8.7 - - - +
293D VAL* 4.4 3.6 - - - -
294D SER* 2.7 36.2 + - - +
296D GLU* 1.3 72.1 - - - +
298D ILE* 1.3 58.5 + - - +
300D PHE* 4.6 0.2 - - - -
301D LEU* 2.9 30.0 + - - +
323D TYR* 3.4 27.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ILE* 4.9 3.8 - - + -
227D PHE* 3.7 21.5 - - + -
281D TRP* 3.6 47.6 - - + -
282D LEU* 4.6 17.7 - - + -
293D VAL* 3.9 18.6 - - + -
294D SER 2.8 15.8 + - - +
295D PRO* 3.6 9.0 - - + +
296D GLU 2.9 0.4 + - - -
297D ALA* 1.3 75.9 - - - +
299D ASP* 1.3 66.9 + - - +
301D LEU* 4.4 3.4 - - + -
302D ASP* 2.7 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D PRO 3.1 11.9 + - - +
296D GLU* 2.7 12.1 + - - +
298D ILE* 1.3 76.0 - - - +
300D PHE* 1.3 57.4 + - - +
302D ASP* 3.4 5.6 - - - +
303D LYS* 2.7 68.7 + - - +
321D HIS* 2.7 27.6 + - + +
322D PRO* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ILE* 4.4 9.0 - - + -
141D LEU* 4.3 11.0 - - + -
218D LEU* 4.4 2.0 - - + -
222D PHE* 3.7 27.8 - + - -
296D GLU 2.9 14.3 + - - +
297D ALA 3.7 2.9 - - - +
299D ASP* 1.3 74.3 - - - +
301D LEU* 1.3 70.0 + - - +
303D LYS* 2.9 11.9 + - - +
304D LEU* 3.1 34.6 + - + +
313D LEU* 3.7 15.7 - - + -
318D ALA* 3.2 32.8 - - + -
321D HIS* 3.2 30.2 + + + +
323D TYR* 4.5 5.8 - + + -
324D PHE* 3.7 32.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D GLY* 3.6 12.3 - - - +
222D PHE* 3.8 15.3 - - + -
223D ALA* 3.2 45.3 - - + +
226D ILE* 4.0 4.3 - - + -
227D PHE* 3.6 26.7 - - + -
281D TRP* 3.8 20.9 - - + -
297D ALA 2.9 18.7 + - - +
298D ILE* 3.8 4.3 - - + +
300D PHE* 1.3 73.6 - - - +
302D ASP* 1.3 56.6 + - - +
303D LYS 2.6 1.0 + - - -
304D LEU* 2.4 33.7 + - + +
305D LEU* 3.2 28.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D ARG* 3.2 20.2 + - - -
281D TRP* 2.8 40.2 + - + +
298D ILE* 2.7 22.8 + - + +
299D ASP* 3.4 7.0 - - - +
301D LEU* 1.3 72.9 - - - +
303D LYS* 1.3 64.4 + - - +
304D LEU 3.6 0.5 + - - -
305D LEU 4.0 9.8 + - - +
306D ARG* 3.2 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D ASP* 2.7 55.9 + - - +
300D PHE 2.9 4.2 + - - +
301D LEU 2.6 4.9 + - - -
302D ASP* 1.3 82.9 + - - +
304D LEU* 1.3 56.3 + - - +
306D ARG* 4.1 17.7 - - - +
311D GLU 4.2 1.3 - - - +
312D ARG* 3.5 7.4 - - - -
313D LEU* 3.0 55.6 + - + +
321D HIS* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D MET* 3.7 38.8 - - + +
216D TRP* 4.3 4.3 + - - -
218D LEU* 4.2 20.0 - - + -
219D GLY* 3.8 22.4 - - - -
222D PHE* 4.6 4.5 - - + -
300D PHE* 3.2 53.2 - - + +
301D LEU* 2.4 27.9 + - - +
303D LYS* 1.3 70.7 - - - +
305D LEU* 1.3 58.5 + - - +
306D ARG 3.0 7.7 + - - -
312D ARG* 3.1 24.7 + - - +
313D LEU* 4.6 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D TRP* 3.1 46.9 - - + -
219D GLY* 4.1 6.3 - - - -
220D CYS 4.0 14.1 - - - +
223D ALA* 4.1 9.9 - - + -
233D PHE* 4.2 15.5 - - + -
249D LEU* 3.3 16.0 - - + +
281D TRP* 3.6 36.0 - - + -
301D LEU* 3.2 34.6 + - + +
302D ASP* 4.0 6.4 + - - +
304D LEU* 1.3 72.9 - - - +
306D ARG* 1.3 63.3 + - - +
----------------------------------------------------------
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