Contacts of the helix formed by residues 244 - 251 (chain D) in PDB entry 1YXU
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 244 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLU* 1.3 92.6 - - + +
245D ASP* 1.3 66.7 + - - +
246D GLU* 3.3 20.4 - - - +
247D GLU* 3.1 30.5 + - + +
248D ILE* 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ARG* 2.8 40.6 + - - +
213D ILE* 3.8 24.3 - - + +
244D HIS* 1.3 73.3 - - - +
246D GLU* 1.3 71.0 + - - +
248D ILE* 3.1 9.2 + - - +
249D ILE* 3.0 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D HIS* 3.3 24.8 - - + +
245D ASP* 1.3 88.6 + - - +
247D GLU* 1.3 57.8 + - + +
249D ILE* 3.9 9.0 - - - +
250D ARG* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 5.8 4.0 - - - +
297C GLN* 5.9 2.6 - - - +
241D PRO 4.1 8.4 - - - +
242D PHE* 3.9 26.5 - - + -
243D GLU* 2.8 35.7 + - - +
244D HIS* 3.1 25.6 + - + +
245D ASP 3.2 0.6 - - - -
246D GLU* 1.3 77.6 - - + +
248D ILE* 1.3 65.2 + - - +
250D ARG* 3.4 5.1 + - - +
251D GLY* 3.0 20.4 + - - -
252D GLN 4.3 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ARG* 3.8 24.5 - - + +
206D VAL* 4.4 14.8 - - + +
208D SER 3.6 20.2 - - - +
209D PRO 4.1 0.4 - - - -
210D PRO* 3.7 17.5 - - + +
213D ILE* 4.1 18.6 - - + -
226D TRP* 3.6 23.9 - - + +
242D PHE* 3.7 28.0 - - + -
244D HIS 3.3 17.7 + - - +
245D ASP* 3.1 7.9 + - - +
247D GLU* 1.3 75.4 - - - +
249D ILE* 1.3 62.1 + - - +
251D GLY* 3.2 14.0 + - - -
273D LEU* 3.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D PRO* 4.2 8.5 - - + +
213D ILE* 3.7 28.0 - - + +
214D ARG* 3.3 56.9 + - + +
245D ASP* 3.0 19.3 + - + +
246D GLU* 4.0 7.4 - - - +
248D ILE* 1.3 78.9 - - - +
250D ARG* 1.3 61.1 + - + +
273D LEU* 3.5 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C SER* 4.4 4.2 - - - -
176C ASP* 5.2 0.6 + - - -
179C ARG* 3.4 49.2 - - - +
181C GLU* 2.9 41.4 + - - -
246D GLU 3.0 20.2 + - - +
247D GLU* 3.9 5.6 - - - +
248D ILE 3.3 0.2 - - - -
249D ILE* 1.3 77.9 - - + +
251D GLY* 1.3 63.1 + - - +
252D GLN* 3.1 42.2 + - + +
273D LEU* 3.9 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D TRP* 4.8 4.5 - - - -
242D PHE* 4.3 10.8 - - - -
247D GLU 3.0 10.6 + - - -
248D ILE 3.2 13.3 + - - -
249D ILE 3.2 0.2 - - - -
250D ARG* 1.3 76.2 - - - +
252D GLN* 1.3 63.7 + - - +
253D VAL* 3.7 10.0 + - - +
271D LEU 4.5 8.6 - - - +
273D LEU* 3.9 14.8 - - - +
----------------------------------------------------------
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