Contacts of the helix formed by residues 230 - 246 (chain B) in PDB entry 2PO5
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 230 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TRP* 3.5 19.7 + - + +
228B PRO 3.8 0.4 - - - -
229B THR* 1.3 75.0 - - - +
231B HIS* 1.3 96.4 + + - +
232B LEU* 3.1 36.5 + - + +
233B LEU* 2.9 24.9 + - + +
234B ILE* 3.1 10.4 + - - +
380B ALA* 4.2 14.5 - - - +
383B ASP* 4.2 12.6 - - + +
384B LEU* 3.4 39.8 + - + +
387B SER* 5.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B THR 3.0 6.7 + - - -
230B HIS* 1.3 99.3 + + - +
232B LEU* 1.3 79.6 + - + +
234B ILE* 3.7 5.6 + - - +
235B GLN* 3.1 27.8 + - - +
286B LYS* 4.3 14.1 - - - +
290B ARG* 5.3 2.1 + - - -
383B ASP* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B HIS* 3.1 15.7 + - + +
231B HIS* 1.3 96.6 - - + +
233B LEU* 1.3 65.2 + - - +
234B ILE 3.2 0.2 - - - -
235B GLN* 3.8 20.0 - - - +
236B CYS* 3.0 28.2 + - - -
376B LEU* 3.5 25.0 - - + +
379B LYS* 3.8 26.9 - - + -
380B ALA* 3.6 23.1 - - + +
383B ASP* 3.3 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PRO* 3.8 22.7 - - + -
227B TRP* 3.7 47.3 - - + +
228B PRO 3.9 13.9 - - - +
230B HIS* 2.9 15.3 + - + +
232B LEU* 1.3 78.4 - - - +
234B ILE* 1.3 64.6 + - + +
236B CYS* 3.2 8.0 + - - +
237B PHE* 3.2 42.5 + - + -
283B THR* 4.7 4.0 - - + -
338B THR* 4.7 0.7 - - + -
371B LEU* 3.6 28.5 - - + -
377B PHE* 4.2 5.2 - - + -
380B ALA* 4.3 5.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO 4.0 9.2 - - - +
229B THR* 3.9 2.0 - - - +
230B HIS 3.1 12.7 + - - +
231B HIS* 3.8 8.3 - - - +
233B LEU* 1.3 81.1 - - + +
235B GLN* 1.3 56.5 + - - +
237B PHE* 3.3 3.3 + - - +
238B ALA* 2.9 26.7 + - - +
283B THR* 3.7 31.9 - - + +
286B LYS* 3.6 64.6 - - + +
287B VAL* 3.7 11.6 - - + +
290B ARG* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B HIS* 3.1 20.1 + - - +
232B LEU* 3.8 23.0 - - - +
233B LEU 3.3 0.4 - - - -
234B ILE* 1.3 76.5 - - - +
236B CYS* 1.3 58.5 + - - +
238B ALA* 3.7 0.5 - - - +
239B ASP* 2.9 46.1 + - - +
290B ARG* 3.5 43.2 + - - +
376B LEU* 3.6 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU 3.0 21.2 + - - -
233B LEU 3.2 9.4 + - - +
235B GLN* 1.3 77.0 - - - +
237B PHE* 1.3 62.6 + - - +
239B ASP* 3.4 1.9 + - - +
240B HIS* 3.0 30.3 + - - -
371B LEU* 3.6 22.9 - - + -
374B ASN* 3.7 12.1 - - - +
376B LEU* 3.5 30.3 - - - -
377B PHE* 3.6 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PRO* 5.8 2.0 - - + -
193B GLN* 5.4 0.4 - - - -
233B LEU* 3.2 40.5 + - + -
234B ILE* 3.3 5.6 + - - +
236B CYS* 1.3 75.2 - - - +
238B ALA* 1.3 67.5 + - - +
240B HIS* 3.2 5.3 + - + +
241B ILE* 2.9 31.6 + - + +
283B THR* 4.2 7.2 - - + -
287B VAL* 3.8 19.5 - - + -
333B VAL* 4.6 9.4 - - + -
334B PRO* 3.6 20.4 - - + -
335B ILE* 3.6 43.7 - - + -
337B PHE 3.6 19.3 - - - -
338B THR* 5.9 0.2 - - + -
369B GLU 5.9 1.3 - - - -
370B SER* 6.4 0.9 - - - -
371B LEU* 4.0 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE 2.9 17.4 + - - +
235B GLN 3.7 4.0 - - - +
237B PHE* 1.3 76.1 - - - +
239B ASP* 1.3 62.3 + - - +
241B ILE* 3.2 9.1 + - - +
242B LEU* 2.9 29.5 + - + +
287B VAL* 4.4 4.2 - - + +
290B ARG* 4.0 31.9 - - + +
291B LEU* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLN* 2.9 39.3 + - - +
236B CYS* 3.6 5.6 - - - +
238B ALA* 1.3 76.7 - - - +
240B HIS* 1.3 64.3 + - + +
242B LEU* 3.4 10.6 + - - +
243B LYS* 3.0 30.9 + - - +
290B ARG* 4.0 14.7 + - - -
374B ASN* 5.3 3.5 - - - +
376B LEU* 4.0 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B CYS 3.0 20.3 + - - +
237B PHE* 3.8 6.3 - - + +
239B ASP* 1.3 79.1 - - + +
241B ILE* 1.3 65.4 + - - +
243B LYS* 3.5 25.2 - - + +
244B GLU* 3.1 24.9 + - - +
368B ALA* 4.1 7.8 - - + +
369B GLU* 2.7 43.6 + - + +
370B SER 3.2 22.5 + - - -
371B LEU* 3.6 23.5 - - + +
374B ASN* 3.4 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B PHE* 2.9 24.7 + - + +
238B ALA 3.5 3.4 - - - +
240B HIS* 1.3 76.3 - - - +
242B LEU* 1.3 57.0 + - - +
244B GLU* 3.1 3.9 + - - +
245B LEU* 2.9 39.0 + - + +
258B ILE* 4.2 7.9 - - + -
260B PHE* 4.0 17.3 - - + -
287B VAL* 3.4 31.6 - - + -
291B LEU* 3.7 21.8 - - + -
331B LEU* 3.8 19.4 - - + +
333B VAL* 4.0 24.9 - - + -
368B ALA* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ALA* 2.9 23.8 + - + +
239B ASP* 3.7 11.2 - - - +
241B ILE* 1.3 77.1 - - - +
243B LYS* 1.3 61.1 + - - +
245B LEU* 3.1 13.6 + - + +
246B ASP* 3.1 28.6 + - - +
253B ARG* 3.7 21.0 + - - +
290B ARG* 5.6 4.5 - - - +
291B LEU* 3.4 24.7 - - + -
294B CYS* 4.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP 3.0 14.5 + - - +
240B HIS* 3.5 31.2 - - + +
242B LEU* 1.3 74.8 - - - +
244B GLU* 1.3 73.5 + - - +
246B ASP* 3.4 23.1 - - - +
247B HIS* 3.2 27.6 + - - +
369B GLU* 2.7 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B HIS 3.1 18.4 + - - +
241B ILE 3.1 4.2 + - - +
243B LYS* 1.3 88.3 + - - +
245B LEU* 1.3 62.1 + - - +
246B ASP 3.1 1.8 - - - -
247B HIS* 3.0 36.0 + - - +
248B PHE* 3.4 10.0 - - - -
331B LEU* 3.6 26.9 - - + -
366B ARG* 2.9 38.3 + - + +
367B ARG 3.5 22.1 + - - +
368B ALA* 4.1 4.5 - - - -
369B GLU* 4.4 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ILE* 2.9 29.8 + - + +
242B LEU* 3.5 11.9 - - + +
244B GLU* 1.3 77.1 - - - +
246B ASP* 1.3 60.5 + - - +
248B PHE* 3.1 27.7 + - + +
253B ARG* 3.7 42.4 + - + +
256B VAL* 4.0 28.3 - - + -
258B ILE* 5.0 2.5 - - + -
294B CYS* 4.2 11.9 - - - -
295B ASN* 3.8 23.1 - - - +
331B LEU* 3.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.1 14.3 + - - +
243B LYS* 3.4 18.0 - - - +
244B GLU 3.1 0.4 - - - -
245B LEU* 1.3 77.6 - - - +
247B HIS* 1.3 62.0 + - + +
248B PHE 3.2 7.7 + - - +
253B ARG* 2.8 26.0 + - - +
----------------------------------------------------------
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