Contacts of the helix formed by residues 209 - 218 (chain B) in PDB entry 3IO6
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 ASP 209 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASN* 3.4 15.4 - - - +
152B GLN* 3.8 15.3 - - + -
207B ASP 3.6 3.4 + - - +
208B THR* 1.3 77.5 - - - +
210B TYR* 1.3 64.3 + - - +
211B SER* 3.7 17.0 + - - -
212B ILE* 3.1 31.0 + - - +
213B ALA* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASN* 3.3 21.0 - - + +
156B PHE* 3.8 25.6 - + - -
209B ASP* 1.3 76.2 - - - +
211B SER* 1.3 63.5 + - - +
213B ALA* 3.3 3.6 + - + +
214B GLU* 2.9 63.1 + - + +
227B ASN* 3.3 35.5 + - - -
230B TRP* 3.3 28.2 + + - -
231B ALA* 3.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASP* 3.5 14.6 + - - -
210B TYR* 1.3 81.3 - - - +
212B ILE* 1.3 65.9 + - - +
214B GLU* 4.2 3.4 - - - +
215B ALA* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 5.7 2.2 - - + -
205B ASN* 5.7 1.3 - - - +
207B ASP* 3.4 24.9 - - + +
208B THR* 3.7 24.9 - - + +
209B ASP* 3.1 22.0 + - - +
211B SER* 1.3 77.5 - - - +
213B ALA* 1.3 63.3 + - - +
215B ALA* 4.0 2.2 - - - +
216B ALA* 3.0 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 3.6 28.1 - - - +
149B PHE* 3.9 15.9 - - - -
150B ASN 4.1 2.2 - - - +
208B THR* 4.2 5.4 - - + -
209B ASP 3.1 17.4 + - - +
210B TYR* 3.7 5.2 - - + +
211B SER 3.3 0.2 - - - -
212B ILE* 1.3 80.0 - - - +
214B GLU* 1.3 62.5 + - - +
216B ALA* 3.4 4.8 + - - +
217B PHE* 3.1 23.6 + - - +
222B THR* 4.7 0.9 - - - +
225B THR* 4.5 6.4 + - - +
227B ASN* 6.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B TYR* 2.9 55.0 + - + +
211B SER* 4.3 3.1 - - - +
213B ALA* 1.3 73.6 - - - +
215B ALA* 1.3 53.1 + - - +
217B PHE* 3.1 4.3 + - - +
218B ASN* 2.8 56.2 + - - +
225B THR* 5.7 2.0 - - - -
227B ASN* 5.0 9.8 - - - +
231B ALA* 4.1 12.2 - - + +
234B ASN* 3.1 35.7 - - - +
235B ILE* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B SER 3.1 17.8 + - - +
212B ILE* 4.2 2.2 - - - +
214B GLU* 1.3 78.5 - - - +
216B ALA* 1.3 57.2 + - - +
218B ASN* 3.8 7.7 - - - -
219B LYS* 3.3 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 5.7 4.5 - - + -
212B ILE* 3.0 25.4 + - + +
213B ALA* 3.8 4.7 - - - +
214B GLU 3.2 0.4 - - - -
215B ALA* 1.3 75.0 - - - +
217B PHE* 1.3 61.6 + - - +
219B LYS* 4.1 1.1 - - - +
220B GLY 3.8 0.5 + - - -
221B GLU* 3.0 48.4 + - + +
222B THR* 3.2 17.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 3.7 22.0 - - + -
117B TYR* 3.5 25.6 - - - -
118B ASN* 3.6 12.3 + - + -
213B ALA 3.1 13.9 + - - +
214B GLU* 3.1 4.7 + - - +
216B ALA* 1.3 73.9 - - - +
218B ASN* 1.3 71.6 + - - +
219B LYS 3.1 4.9 - - - -
220B GLY* 3.1 18.0 + - - -
222B THR* 3.5 24.2 - - + +
223B ALA 3.5 22.9 - - - -
224B MET* 4.1 8.7 - - - -
225B THR* 3.6 23.3 - - + -
235B ILE* 4.0 15.5 - - + -
240B VAL* 4.1 12.4 - - + +
242B TYR* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLU* 2.8 33.4 + - - +
215B ALA* 3.7 6.9 + - - +
216B ALA 3.4 0.2 - - - -
217B PHE* 1.3 86.2 - - - +
219B LYS* 1.3 60.9 + - + +
220B GLY 3.5 0.2 - - - -
234B ASN* 3.4 29.3 - - - +
235B ILE* 3.5 24.6 - - - +
238B SER* 3.4 34.7 + - - +
240B VAL* 3.4 10.5 - - - +
----------------------------------------------------------
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