Contacts of the helix formed by residues 231 - 243 (chain G) in PDB entry 5T0J
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 231 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G ARG* 2.6 29.0 + - - -
229G ILE 3.4 2.6 + - - -
230G LEU* 1.3 73.4 - - - +
232G GLU* 1.3 70.6 + - + +
233G ALA* 3.1 18.5 + - + +
234G GLU* 3.1 16.4 + - - +
235G ILE* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G LYS* 3.7 12.1 + - - +
212G PRO* 3.3 31.1 - - - +
213G SER* 3.0 36.3 + - - +
215G ILE 5.0 0.3 - - - +
230G LEU 3.8 1.8 + - - -
231G THR* 1.3 77.1 - - + +
233G ALA* 1.3 63.0 + - - +
235G ILE* 4.1 9.4 - - - +
236G ASP* 3.4 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G THR* 3.0 14.3 - - + +
232G GLU* 1.3 80.8 - - - +
234G GLU* 1.3 61.1 + - - +
236G ASP* 3.7 4.1 + - - +
237G ALA* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G PHE* 4.8 7.7 - - - -
228G ARG* 2.5 38.4 + - - -
230G LEU* 3.2 20.1 - - + +
231G THR* 3.1 26.3 + - - +
233G ALA* 1.3 76.9 - - - +
235G ILE* 1.3 60.1 + - - +
237G ALA* 3.4 8.6 - - + +
238G HIS* 2.9 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G VAL* 5.7 4.1 - - + +
199G ILE* 6.4 2.5 - - + -
212G PRO* 3.6 22.2 - - + -
215G ILE* 3.8 23.1 - - + +
216G GLU* 5.5 0.2 - - - -
217G VAL* 4.5 21.1 - - + +
230G LEU* 3.6 47.3 - - + +
231G THR 3.1 14.5 + - - +
232G GLU* 4.1 15.5 - - - +
233G ALA 3.4 0.2 - - - -
234G GLU* 1.3 78.1 - - - +
236G ASP* 1.3 57.0 + - - +
238G HIS* 3.3 4.7 + - - +
239G LEU* 2.9 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 236 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G PRO* 3.9 24.4 - - + +
232G GLU* 3.4 15.5 + - + +
233G ALA* 4.2 3.6 - - - +
234G GLU 3.4 0.2 - - - -
235G ILE* 1.3 79.6 - - - +
237G ALA* 1.3 60.1 + - - +
239G LEU* 4.0 11.3 - - - +
240G VAL* 3.2 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233G ALA 3.4 13.9 + - - +
234G GLU* 3.2 13.2 + - + +
235G ILE 3.2 0.6 - - - -
236G ASP* 1.3 79.7 - - - +
238G HIS* 1.3 64.2 + - + +
240G VAL* 3.3 11.1 - - - +
241G ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 238 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G PHE* 3.3 39.3 - + - -
192G GLU* 3.6 36.7 - - + +
195G VAL* 3.9 24.7 - - + -
230G LEU* 5.0 3.6 - - + -
234G GLU* 2.9 40.3 + - + +
235G ILE* 4.0 3.1 - - - +
237G ALA* 1.3 76.8 - - + +
239G LEU* 1.3 64.2 + - - +
241G ALA* 3.6 9.1 - - - +
242G LEU* 3.2 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G VAL* 5.5 0.2 - - - +
199G ILE* 4.1 31.9 - - + -
209G ASP* 5.9 6.7 - - + +
210G PHE 4.6 7.9 - - - +
212G PRO* 3.8 35.2 - - + -
235G ILE* 2.9 18.6 + - + +
236G ASP* 3.8 11.4 - - - +
237G ALA 3.3 0.2 - - - -
238G HIS* 1.3 77.9 - - - +
240G VAL* 1.3 62.4 + - + +
242G LEU* 3.4 28.3 - - + +
243G ALA* 3.5 10.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G ASP* 3.2 27.5 + - - +
237G ALA* 3.3 18.6 - - - +
239G LEU* 1.3 77.5 - - + +
241G ALA* 1.3 60.4 + - - +
243G ALA* 2.8 23.9 - - - +
244G GLU* 4.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G GLU* 5.7 6.5 - - + -
237G ALA 3.2 16.9 + - - +
238G HIS* 3.6 15.3 - - - +
239G LEU 3.2 0.8 - - - -
240G VAL* 1.3 79.2 - - - +
242G LEU* 1.3 61.5 + - - +
244G GLU* 2.9 23.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G GLU 5.6 0.9 - - - +
195G VAL* 4.1 2.9 - - + +
196G GLU* 3.8 33.7 - - + +
199G ILE* 3.7 48.0 - - + -
200G THR* 6.0 4.3 - - + -
238G HIS 3.2 18.8 + - - +
239G LEU* 3.4 15.0 - - + +
241G ALA* 1.3 79.3 - - - +
243G ALA* 1.3 68.4 + - + +
244G GLU* 2.9 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G LEU* 3.5 13.5 + - + +
240G VAL* 2.8 23.7 - - - +
241G ALA 3.3 0.2 - - - -
242G LEU* 1.3 85.3 - - + +
244G GLU* 1.3 61.9 + - - +
----------------------------------------------------------
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