Contacts of the helix formed by residues 231 - 244 (chain B) in PDB entry 1AO5
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 LEU 231 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.1 27.8 - - + -
103B LEU* 4.1 20.2 - - + -
123B LEU* 4.8 3.4 - - + -
124B PRO* 4.0 15.5 - - + -
209B LEU* 3.8 36.3 - - + -
210B GLN 3.0 20.2 + - - +
211B GLY* 3.7 21.3 - - - +
212B THR* 4.6 2.2 - - + +
229B THR* 3.1 8.0 + - - +
230B ASN* 1.3 68.6 - - - +
232B ILE* 1.3 65.5 + - - +
234B PHE* 2.9 17.0 + - + +
235B ASN* 3.4 11.4 + - - +
238B ILE* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 3.4 22.5 - - + +
125B THR* 3.7 20.2 - - - +
128B LYS 3.8 15.9 - - - +
129B GLU* 4.6 16.6 - - + -
130B PRO* 4.5 11.0 - - + -
210B GLN* 4.5 1.9 + - - +
230B ASN* 3.3 22.8 + - - +
231B LEU* 1.3 77.3 - - - +
233B LYS* 1.3 76.5 + - + +
234B PHE 3.1 1.6 + - - -
235B ASN* 3.0 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 5.3 8.4 + - - -
178B ASP* 3.8 30.7 - - + +
179B VAL* 3.9 23.8 - - + -
230B ASN* 3.6 31.0 - - - +
231B LEU 3.1 0.8 - - - -
232B ILE* 1.3 83.1 - - + +
234B PHE* 1.3 62.0 + - + +
235B ASN 3.6 0.4 - - - -
236B SER* 5.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B HIS* 3.6 30.7 - + - -
101B ASP* 3.1 42.6 - - - -
102B ASP 5.2 0.4 - - - -
103B LEU* 3.6 28.5 - - + -
179B VAL* 3.5 37.5 - - + -
229B THR* 4.5 8.1 - - - -
230B ASN 3.3 31.2 - - - -
231B LEU* 2.9 10.2 + - + +
233B LYS* 1.3 80.2 - - - +
235B ASN* 1.3 65.4 + - - +
236B SER* 3.2 3.4 - - - -
237B TRP* 3.1 10.4 + + + +
238B ILE* 3.1 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.5 35.4 - - + +
124B PRO* 3.3 12.5 + - - +
231B LEU 3.4 7.5 + - - +
232B ILE* 3.0 47.8 + - - +
233B LYS 3.6 0.4 - - - -
234B PHE* 1.3 74.5 - - - +
236B SER* 1.3 64.4 + - - +
238B ILE* 3.4 5.0 + - - +
239B LYS* 3.1 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LYS 5.3 1.1 + - - -
234B PHE 3.1 1.2 + - - -
235B ASN* 1.3 77.6 - - - +
237B TRP* 1.3 58.4 + - - +
239B LYS* 3.2 4.8 + - - +
240B ASP* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 5.4 0.7 - - + -
89B PHE* 3.5 28.3 - - + -
90B PRO 4.2 2.9 - - - -
91B HIS* 3.6 54.1 - + + +
92B PRO* 3.8 17.7 - - + +
103B LEU* 4.0 17.9 - - + -
104B MET* 4.6 1.8 - - - -
105B LEU* 4.4 17.9 - - + -
234B PHE* 3.1 10.8 + - + +
236B SER* 1.3 79.8 - - - +
238B ILE* 1.3 90.0 + - + +
240B ASP* 3.8 8.8 - - + +
241B THR* 2.8 48.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.2 8.7 - - + -
53B LEU* 4.5 10.3 - - + -
103B LEU* 4.2 9.0 - - + -
105B LEU* 4.1 11.4 - - + +
123B LEU* 4.1 24.9 - - + -
231B LEU* 4.1 26.0 - - + -
234B PHE 3.1 18.4 + - - +
235B ASN* 3.7 6.7 - - - +
237B TRP* 1.3 96.0 - - + +
239B LYS* 1.3 56.9 + - - +
241B THR* 2.8 26.3 + - - -
242B MET* 3.0 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.9 27.3 - - + +
235B ASN* 3.1 24.5 + - + +
236B SER* 3.7 4.5 - - - +
238B ILE* 1.3 78.7 - - + +
240B ASP* 1.3 63.7 + - - +
242B MET* 3.2 11.8 + - - +
243B MET* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER 2.8 22.6 + - - +
237B TRP* 3.8 10.2 - - + +
239B LYS* 1.3 71.9 - - - +
241B THR* 1.3 57.6 + - - +
243B MET* 4.0 4.0 - - - +
244B LYS* 2.9 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TRP* 4.2 4.4 - - + -
89B PHE* 4.1 24.9 - - + -
105B LEU* 3.6 22.0 - - + -
237B TRP* 2.8 37.4 + - + -
238B ILE 2.8 14.6 + - - -
240B ASP* 1.3 70.7 - - - +
242B MET* 1.3 63.4 + - - -
244B LYS* 4.7 1.1 - - - -
245B ASN* 2.7 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.5 37.7 - - + -
48B ASP* 4.8 7.9 - - + -
51B TRP* 3.6 55.0 + - + +
105B LEU* 4.3 7.2 - - + -
123B LEU* 5.9 2.7 - - + -
238B ILE* 3.0 30.6 + - + +
239B LYS* 3.2 12.8 + - - +
241B THR* 1.3 74.4 - - - +
243B MET* 1.3 64.1 + - - +
245B ASN 3.4 18.0 + - - +
246B ALA 4.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS 3.0 16.2 + - - +
240B ASP* 4.0 4.0 - - - +
242B MET* 1.3 78.5 - - - +
244B LYS* 1.3 64.0 + - + +
245B ASN 3.3 0.9 + - - -
246B ALA* 4.3 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASP* 2.9 48.6 + - - +
241B THR* 4.7 0.7 - - - -
243B MET* 1.3 82.2 - - + +
245B ASN* 1.3 69.3 + - - +
246B ALA 3.7 3.6 + - - -
----------------------------------------------------------
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