Contacts of the helix formed by residues 239 - 250 (chain H) in PDB entry 4U0Z
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 THR 239 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228H TYR* 4.2 4.5 - - - -
237H THR 4.4 6.1 - - - +
238H LEU* 1.3 73.8 - - - +
240H LEU* 1.3 58.0 + - - +
241H SER* 2.9 23.5 + - - -
242H GLU* 3.1 30.2 + - - +
243H ILE* 2.9 33.6 + - - +
256H LYS* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H GLU* 5.5 3.4 - - + +
224H TYR* 3.3 44.2 - - + +
225H HIS* 3.9 9.2 - - + +
228H TYR* 3.7 33.4 - - + -
239H THR* 1.3 73.4 - - - +
241H SER* 1.4 58.4 + - - +
243H ILE* 3.8 5.1 - - + +
244H ARG* 2.9 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H THR* 2.9 16.6 + - - -
240H LEU* 1.4 77.1 - - - +
242H GLU* 1.4 59.2 + - - +
244H ARG* 3.5 7.9 + - - +
245H HIS* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238H LEU* 3.4 21.3 - - + +
239H THR* 3.1 44.5 + - - +
241H SER* 1.4 73.9 - - - +
243H ILE* 1.4 59.8 + - - +
245H HIS* 3.2 5.0 + - - +
246H ILE* 2.9 35.7 + - - +
253H VAL* 3.3 38.2 - - + +
254H PRO 4.9 2.1 - - - +
256H LYS* 4.0 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H TYR* 4.1 16.6 - - + +
227H ILE* 4.1 14.8 - - + -
228H TYR* 3.6 40.8 - - + +
231H VAL* 4.4 11.7 - - + -
238H LEU* 4.2 16.6 - - + +
239H THR 2.9 21.4 + - - +
240H LEU* 3.8 5.8 - - + +
242H GLU* 1.4 72.4 - - - +
244H ARG* 1.3 58.7 + - - +
246H ILE* 3.4 6.8 + - - +
247H LEU* 3.1 49.2 + - + +
264H VAL* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 244 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H TYR* 3.9 31.8 - - + -
240H LEU* 2.9 23.1 + - + +
241H SER* 3.6 9.6 - - - +
243H ILE* 1.3 76.7 - - - +
245H HIS* 1.4 58.3 + - - +
247H LEU 4.0 0.3 + - - -
248H GLU* 3.1 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 245 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H SER 3.0 14.8 + - - +
242H GLU* 3.4 10.1 - - - +
243H ILE 3.2 0.2 - - - -
244H ARG* 1.4 74.6 - - - +
246H ILE* 1.4 57.5 + - - +
248H GLU* 3.0 4.0 + - - -
249H THR* 2.9 75.5 + - + +
251H TYR* 3.7 23.6 + - + +
252H ALA 4.2 8.7 - - - -
253H VAL* 3.5 21.1 - - + +
254H PRO* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.9 17.1 - - + +
238H LEU* 3.9 17.5 - - + -
242H GLU 2.9 25.3 + - - +
243H ILE* 3.4 5.8 + - - +
245H HIS* 1.4 70.1 - - - +
247H LEU* 1.3 58.4 + - + +
250H ARG* 3.1 31.0 + - - -
251H TYR 4.0 13.9 - - - +
253H VAL* 3.8 19.5 - - + -
261H GLN* 3.6 44.9 - - + +
264H VAL* 3.9 21.3 - - + -
265H ILE* 4.4 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H TYR* 5.0 0.9 - - + -
224H TYR* 3.7 37.2 + - + +
227H ILE* 3.9 24.2 - - + -
243H ILE* 3.1 26.0 + - + +
246H ILE* 1.3 77.5 - - + +
248H GLU* 1.4 58.6 + - - +
250H ARG* 3.3 33.0 + - - +
264H VAL* 3.9 21.5 - - + +
265H ILE* 4.6 5.2 - - + -
268H HIS* 3.5 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H TYR* 3.6 21.8 + - - +
244H ARG* 3.1 42.1 + - - +
245H HIS* 3.0 4.0 + - - +
247H LEU* 1.4 78.1 - - - +
249H THR* 1.3 67.0 + - + +
250H ARG* 3.6 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H HIS* 2.9 59.1 + - + +
248H GLU* 1.3 78.2 - - + +
250H ARG* 1.4 66.6 + - - +
251H TYR* 3.0 43.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 250 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B SER* 3.7 7.8 - - - -
258B LEU* 3.1 31.6 + - + +
259B GLU 5.0 0.3 + - - -
246H ILE 3.1 22.7 + - - -
247H LEU* 3.3 29.9 + - - +
248H GLU 4.6 4.6 + - - +
249H THR* 1.4 79.8 + - - +
251H TYR* 1.4 60.1 + - - +
265H ILE* 5.2 14.1 - - - +
268H HIS* 3.4 38.6 + - - -
----------------------------------------------------------
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