Contacts of the helix formed by residues 176 - 189 (chain D) in PDB entry 2BKU
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 SER 176 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D MET* 3.6 35.6 - - - +
140D VAL* 4.8 2.6 - - - +
172D ALA* 2.7 20.6 + - - -
173D LEU 3.7 4.0 - - - -
175D SER* 1.3 73.9 - - - +
177D SER* 1.3 63.3 + - - +
178D ASN* 3.4 2.2 - - - -
179D ASN* 3.3 21.0 + - - +
180D ILE* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D GLN* 5.6 2.7 - - - -
173D LEU 3.2 11.6 + - - -
174D VAL* 2.6 25.9 + - - +
175D SER 3.4 0.6 - - - -
176D SER* 1.3 73.8 - - - +
178D ASN* 1.3 71.6 + - - +
180D ILE* 3.0 11.3 + - - +
181D LEU* 2.8 31.6 + - - +
211D PHE 5.7 4.5 - - - -
212D ILE* 5.7 3.9 - - - +
215D ASN* 4.9 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D VAL 5.0 0.5 - - - +
175D SER 5.2 4.4 + - - +
176D SER 3.4 0.6 - - - -
177D SER* 1.3 83.5 + - - +
179D ASN* 1.3 64.2 + - - +
181D LEU* 3.2 5.7 + - - +
182D ILE* 2.9 39.9 + - + +
215D ASN* 4.5 10.6 + - - +
218D ARG* 5.1 5.7 + - - +
221D GLU* 4.6 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D VAL* 4.3 27.3 - - + +
175D SER 5.8 0.4 - - - -
176D SER* 3.3 20.7 + - - +
178D ASN* 1.3 81.1 - - - +
180D ILE* 1.3 62.2 + - - +
182D ILE* 3.9 6.5 - - - +
183D ALA* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D MET* 4.3 11.0 - - - -
140D VAL* 4.2 13.0 - - + -
159D LEU* 3.8 31.2 - - + -
163D CYS* 4.0 28.9 - - - -
173D LEU* 4.8 6.1 - - + +
176D SER* 3.1 30.7 + - - +
177D SER* 3.0 13.4 + - - +
179D ASN* 1.3 74.5 - - - +
181D LEU* 1.3 60.3 + - - +
183D ALA* 3.2 7.8 + - - +
184D ILE* 2.9 50.4 + - + +
208D SER* 5.4 1.6 - - - +
212D ILE* 6.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D SER 2.8 19.5 + - - +
178D ASN* 3.7 6.7 - - - +
180D ILE* 1.3 73.6 - - - +
182D ILE* 1.3 69.8 + - + +
184D ILE* 3.3 6.4 + - + +
185D VAL* 2.8 49.8 + - + +
205D LEU* 3.9 17.3 - - + -
208D SER* 6.1 0.7 - - - -
212D ILE* 3.7 43.1 - - + -
215D ASN* 4.6 20.4 - - + +
221D GLU* 5.1 13.7 - - + +
224D TYR* 5.7 3.6 - - + -
225D LEU* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ASN* 2.9 29.9 + - + +
179D ASN* 3.9 5.8 - - - +
181D LEU* 1.3 87.4 - - + +
183D ALA* 1.3 55.8 + - - +
185D VAL* 3.0 4.3 + - - +
186D GLN* 2.5 66.1 + - + +
221D GLU* 5.6 8.1 - - + -
224D TYR* 5.2 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D VAL* 5.3 9.9 - - + -
143D THR* 3.7 32.8 - - + +
156D LEU* 3.7 13.6 - - + +
159D LEU* 4.8 7.0 - - + -
179D ASN 3.0 17.6 + - - +
180D ILE* 3.4 6.3 - - - +
182D ILE* 1.3 79.8 - - - +
184D ILE* 1.3 61.5 + - - +
186D GLN* 3.8 7.3 - - - +
187D GLY 3.1 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D LEU* 4.1 11.9 - - + +
159D LEU* 4.4 14.6 - - + -
160D GLY 4.7 0.2 - - - +
180D ILE* 2.9 48.3 + - + +
181D LEU* 3.5 9.9 - - + +
183D ALA* 1.3 69.7 - - + +
185D VAL* 1.3 68.7 + - + +
187D GLY 3.1 10.7 + - - -
188D ALA* 3.3 9.8 + - + +
201D ALA* 3.2 32.7 - - - +
204D ALA* 3.4 30.1 - - + +
205D LEU* 3.6 24.9 - - + +
208D SER* 4.4 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D LEU* 2.8 49.8 + - + +
182D ILE* 3.8 1.8 - - - +
184D ILE* 1.3 74.5 - - - +
186D GLN* 1.3 64.7 + - - +
188D ALA* 3.1 17.6 + - - +
189D GLN* 3.4 9.7 + - - +
205D LEU* 4.5 11.4 - - + -
224D TYR* 3.3 34.5 - - + -
225D LEU* 4.3 21.8 - - + -
228D VAL* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D THR* 6.1 0.9 - - + -
182D ILE* 2.5 45.4 + - + +
183D ALA* 3.8 8.0 - - - +
185D VAL* 1.3 72.7 - - - +
187D GLY* 1.3 61.3 + - - +
189D GLN* 3.1 31.5 + - + +
192D GLU* 4.9 2.4 - - - +
224D TYR* 4.4 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D THR* 6.0 1.8 - - - -
156D LEU* 4.8 3.1 - - - -
183D ALA 3.1 8.8 + - - -
184D ILE 3.1 8.2 + - - -
186D GLN* 1.3 77.6 - - - +
188D ALA* 1.3 56.0 + - - +
189D GLN 3.5 0.4 - - - -
192D GLU* 3.1 29.4 - - - +
197D VAL* 3.9 8.4 - - - +
198D ARG* 3.4 15.1 + - - -
201D ALA* 3.4 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE 3.3 9.0 + - - +
185D VAL* 3.1 8.5 + - - +
187D GLY* 1.3 75.4 - - - +
189D GLN* 1.3 69.0 + - - +
190D SER 3.6 0.3 + - - -
198D ARG* 3.1 24.0 + - - +
201D ALA* 4.0 9.6 - - + +
202D LEU* 3.7 24.5 - - + +
205D LEU* 5.9 3.6 - - + -
228D VAL* 3.5 27.7 - - + +
232D ALA* 4.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D VAL 3.4 7.5 + - - +
186D GLN* 3.1 27.9 + - + +
187D GLY 3.5 0.2 - - - -
188D ALA* 1.3 80.6 - - - +
190D SER* 1.3 66.5 + - - +
191D THR* 3.5 20.0 - - - +
192D GLU* 3.1 21.0 + - + +
198D ARG* 3.4 2.8 + - - -
224D TYR* 2.9 34.1 + - - -
228D VAL* 3.5 23.1 - - - +
----------------------------------------------------------
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