Contacts of the helix formed by residues 218 - 233 (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 ARG 218 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LYS* 5.6 1.8 - - - +
264B GLU* 6.1 1.3 - - - +
178D ASN* 5.1 6.8 + - - +
214D ASN* 3.5 32.0 + - - +
215D ASN* 3.5 17.5 + - - +
216D MET 3.3 4.0 + - - -
217D GLU* 1.3 83.9 - - - +
219D GLU* 1.4 67.4 + - - +
220D GLY 2.7 4.1 + - - +
221D GLU* 2.7 49.2 + - + +
222D ARG* 2.9 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLU* 2.3 45.7 - - - +
261B PRO* 6.6 0.4 - - + -
218D ARG* 1.4 68.4 - - - +
220D GLY* 1.3 53.0 + - - +
222D ARG* 3.7 24.1 - - - +
223D ASN* 2.7 69.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D ARG* 2.7 7.4 + - - +
219D GLU* 1.3 75.6 - - - +
221D GLU* 1.3 59.9 + - - -
223D ASN* 3.9 4.1 - - - +
224D TYR* 3.3 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ASN* 4.6 10.7 + - - -
181D LEU* 5.1 13.4 - - + +
182D ILE* 5.6 7.6 - - + -
215D ASN* 3.0 34.1 - - + +
218D ARG* 2.7 47.1 + - + +
220D GLY* 1.3 72.5 - - - +
222D ARG* 1.3 66.1 + - - +
223D ASN 3.3 0.2 + - - -
224D TYR* 3.4 9.1 + - + +
225D LEU* 3.1 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D ASN 3.9 3.2 + - - -
216D MET* 2.7 70.4 + - + +
217D GLU* 3.8 0.6 - - - +
218D ARG 2.9 30.5 + - - +
219D GLU* 3.7 26.2 - - - +
221D GLU* 1.3 77.1 - - - +
223D ASN* 1.3 57.6 + - - +
225D LEU* 3.7 5.4 - - - +
226D MET* 3.0 37.9 + - + +
258D PHE* 3.4 55.5 + - - +
259D MET* 4.9 0.4 - - - -
261D PRO* 6.4 0.6 - - - +
262D TYR* 2.9 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D GLU* 2.7 59.7 + - - +
220D GLY* 3.9 5.1 - - - +
222D ARG* 1.3 70.7 - - - +
224D TYR* 1.3 65.9 + - - +
226D MET* 3.3 1.4 + - - +
227D GLN* 2.9 24.4 + - - +
262D TYR* 2.5 42.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D LEU* 5.7 2.9 - - + -
182D ILE* 5.2 18.5 - - + +
185D VAL* 3.3 31.5 - - + +
186D GLN* 4.4 14.6 - - - +
189D GLN* 2.9 32.6 + - - -
220D GLY 3.3 14.3 + - - +
221D GLU* 3.4 7.8 + - + +
223D ASN* 1.3 76.5 - - - +
225D LEU* 1.3 64.4 + - + +
227D GLN* 3.1 19.3 + - + +
228D VAL* 3.3 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D LEU* 4.2 13.9 - - + -
185D VAL* 4.3 18.6 - - + -
205D LEU* 3.9 23.9 - - + +
209D LEU* 5.3 0.9 - - + -
212D ILE* 3.7 29.2 - - + -
215D ASN* 6.1 1.3 - - + -
216D MET* 4.0 18.4 - - + +
221D GLU* 3.1 15.7 + - + +
222D ARG* 3.7 3.1 - - - +
224D TYR* 1.3 79.7 - - - +
226D MET* 1.3 87.3 + - + +
228D VAL* 3.2 5.4 + - - +
229D VAL* 3.1 34.0 + - + +
251D ILE* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D MET* 5.1 1.1 - - + -
222D ARG* 3.0 32.8 + - + +
223D ASN 3.3 3.8 + - - +
225D LEU* 1.3 82.5 - - + +
227D GLN* 1.3 63.7 + - - +
229D VAL* 3.9 13.5 - - + +
230D CYS* 3.0 34.0 + - - -
248D LEU* 4.0 15.3 - - + -
251D ILE* 3.3 38.1 - - + -
259D MET* 3.9 27.8 - - - +
262D TYR* 3.8 37.7 - - + -
267D LEU* 5.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D ASN 2.9 13.6 + - - +
224D TYR* 3.1 12.7 + - + +
226D MET* 1.3 77.4 - - - +
228D VAL* 1.3 63.8 + - + +
230D CYS* 3.4 11.2 + - - +
231D GLU* 3.1 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D VAL* 3.7 27.1 - - + +
188D ALA* 3.5 44.3 - - + +
189D GLN* 3.5 29.8 - - - +
190D SER 5.6 0.2 - - - +
198D ARG* 5.3 0.3 + - - -
202D LEU* 5.1 1.8 - - + -
205D LEU* 6.1 1.6 - - + -
224D TYR* 3.3 12.1 + - + +
225D LEU 3.2 8.4 + - - +
227D GLN* 1.3 77.1 - - + +
229D VAL* 1.3 69.4 + - + +
230D CYS 3.2 0.2 + - - -
231D GLU* 3.3 7.6 + - - +
232D ALA* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D LEU* 4.9 5.6 - - + -
205D LEU* 3.9 25.6 - - + -
225D LEU* 3.3 24.5 - - + +
226D MET* 3.9 12.1 - - + +
227D GLN 3.4 0.2 - - - -
228D VAL* 1.3 78.5 - - + +
230D CYS* 1.3 62.8 + - - +
232D ALA* 3.4 8.4 + - - +
233D THR* 3.3 21.1 + - - +
244D ALA* 3.7 15.8 - - - +
247D CYS* 4.0 11.9 - - + -
248D LEU* 3.7 33.0 - - + +
251D ILE* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D MET* 3.0 30.5 + - - +
227D GLN* 3.7 14.1 - - - +
228D VAL 3.1 0.2 - - - -
229D VAL* 1.3 74.3 - - - +
231D GLU* 1.3 63.0 + - - +
233D THR* 2.5 31.8 + - - -
234D GLN* 3.8 1.7 + - - +
248D LEU* 5.0 3.8 - - - -
262D TYR* 5.5 4.5 - - - -
266D ALA* 4.6 12.3 - - + -
267D LEU* 3.6 37.0 - - - -
270D LEU* 3.7 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D SER* 3.7 31.0 + - - +
198D ARG* 4.3 4.9 + - - +
227D GLN* 3.1 40.3 + - - +
228D VAL* 3.6 6.7 - - - +
230D CYS* 1.3 75.8 - - - +
232D ALA* 1.3 57.3 + - - +
234D GLN* 2.9 33.2 + - - +
235D ALA* 3.6 0.3 + - - -
270D LEU* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ALA 4.9 1.6 - - - +
198D ARG* 3.7 19.4 - - - +
202D LEU* 4.0 26.0 - - + -
228D VAL 3.0 13.2 + - - +
229D VAL 3.5 5.4 - - - +
231D GLU* 1.3 72.2 - - - +
233D THR* 1.3 64.0 + - - +
234D GLN 3.0 2.0 - - - -
235D ALA* 3.0 19.8 + - - +
240D VAL* 4.5 1.8 - - + -
241D GLN* 3.6 10.2 + - - -
244D ALA* 3.4 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D VAL 3.4 14.4 - - - +
230D CYS* 2.5 19.9 + - - +
232D ALA* 1.3 76.3 - - - +
234D GLN* 1.3 69.8 + - - +
235D ALA 3.4 0.4 - - - -
241D GLN* 2.7 31.7 + - - +
244D ALA* 3.3 13.9 - - + +
245D PHE* 3.8 32.6 - - + +
248D LEU* 3.7 28.7 - - + -
267D LEU* 5.0 2.7 - - + +
270D LEU* 4.2 6.1 - - - +
274D THR* 4.3 1.0 - - - +
----------------------------------------------------------
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