Contacts of the helix formed by residues 212 - 234 (chain D) in PDB entry 2B05
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 ASN 212 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D THR 3.7 3.2 + - - +
211D LEU* 1.3 73.5 - - - +
213D GLU* 1.3 54.7 + - - +
214D ASP* 2.8 16.7 + - + +
215D SER* 2.7 39.4 + - - +
216D TYR* 3.0 8.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU 4.1 1.6 + - - -
212D ASN* 1.3 70.0 - - - +
214D ASP* 1.3 61.6 + - - +
215D SER 3.2 0.9 + - - -
216D TYR* 3.8 17.9 + - + +
217D LYS* 4.8 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D ASN* 2.8 11.6 + - + -
213D GLU* 1.3 80.0 - - - +
215D SER* 1.3 58.0 + - - +
217D LYS 5.5 0.4 - - - -
218D ASP* 4.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D THR 5.3 0.2 - - - -
170D PRO* 4.2 18.4 - - - -
210D THR 5.1 0.9 + - - -
211D LEU* 3.4 7.7 - - - +
212D ASN* 2.7 37.7 + - - +
214D ASP* 1.3 75.7 - - - +
216D TYR* 1.3 62.4 + - - +
217D LYS 3.3 2.7 - - - -
218D ASP* 3.1 7.3 + - - +
219D SER* 2.8 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 3.9 21.5 - - + -
212D ASN 3.0 12.9 + - - +
213D GLU* 3.8 13.7 + - + +
214D ASP 3.8 0.6 - - - -
215D SER* 1.3 75.0 + - - +
217D LYS* 1.3 52.8 + - - +
219D SER* 4.0 0.3 - - - -
220D THR* 2.7 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D GLU 4.8 3.8 + - - +
214D ASP 5.5 0.2 - - - -
215D SER 3.3 0.4 - - - -
216D TYR* 1.3 79.3 - - - +
218D ASP* 1.3 68.2 + - - +
220D THR* 3.3 6.6 + - - -
221D LEU* 3.2 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D PRO* 4.3 18.2 - - + +
214D ASP 4.7 7.7 + - - +
215D SER* 3.1 10.3 + - - +
217D LYS* 1.3 83.6 - - - +
219D SER* 1.3 61.7 + - - +
221D LEU* 4.0 8.5 - - - +
222D ILE* 3.2 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D THR* 3.0 27.1 + - - -
170D PRO* 3.5 13.3 - - - +
173D LEU* 3.6 14.8 - - - +
211D LEU* 3.4 20.8 - - - +
215D SER 2.8 17.4 + - - -
216D TYR 4.0 0.2 - - - -
218D ASP* 1.3 74.4 - - - +
220D THR* 1.3 60.7 + - - +
222D ILE* 3.3 2.6 + - - -
223D MET* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D LEU* 5.4 4.5 - - + -
211D LEU* 4.4 15.3 - - + -
216D TYR* 2.7 29.6 + - + +
217D LYS* 3.3 10.9 + - - -
219D SER* 1.3 75.1 - - - +
221D LEU* 1.3 57.0 + - - +
223D MET* 3.4 17.5 + - + +
224D GLN* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D LYS* 3.2 27.3 + - + +
218D ASP* 4.0 9.2 - - - +
219D SER 3.2 0.4 - - - -
220D THR* 1.3 76.9 + - - +
222D ILE* 1.3 70.4 + - + +
224D GLN* 3.3 9.7 + - - +
225D LEU* 3.2 43.4 + - + +
506J LEU* 5.9 0.2 - - + -
507J PRO* 5.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D PRO* 3.5 35.2 - - + +
173D LEU* 3.7 33.7 - - + +
174D GLY* 3.8 4.9 - - - +
177D LEU* 4.4 14.6 - - + -
218D ASP* 3.2 20.6 + - + +
219D SER 3.3 5.2 + - - +
221D LEU* 1.3 80.7 - - + +
223D MET* 1.3 61.3 + - - +
225D LEU* 3.1 9.4 + - - +
226D LEU* 2.9 28.5 + - + +
506J LEU* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D THR* 5.8 2.0 - - - -
173D LEU* 4.0 21.8 - - + -
201D PHE* 3.1 31.6 - - + +
204D ALA* 3.9 20.6 - - + -
205D ILE* 3.8 30.5 - - + -
208D LEU* 4.2 20.0 - - + -
211D LEU* 5.6 1.6 - - - -
219D SER* 3.0 29.3 + - - +
220D THR* 3.5 15.9 - - + +
221D LEU 3.2 0.2 - - - -
222D ILE* 1.3 74.0 - - - +
224D GLN* 1.3 64.2 + - - +
226D LEU* 3.3 5.9 + - + -
227D ARG 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PHE* 5.8 2.4 - - - -
220D THR 3.0 15.9 + - - +
221D LEU* 3.5 11.9 - - + +
222D ILE 3.3 0.2 - - - -
223D MET* 1.3 76.8 - - - +
225D LEU* 1.3 58.3 + - + +
227D ARG* 3.2 24.1 + - - +
228D ASP* 2.7 59.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
177D LEU* 3.8 26.7 - - + -
221D LEU* 3.2 24.8 + - + +
222D ILE* 3.1 10.0 + - - +
224D GLN* 1.3 76.7 - - + +
226D LEU* 1.3 64.0 + - - +
228D ASP* 3.6 17.0 - - + +
229D ASN* 2.9 29.5 + - - +
504J ILE* 4.1 28.7 - - + +
506J LEU* 4.9 0.7 - - + -
507J PRO* 3.6 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU* 4.0 33.9 - - + +
176D ALA* 4.2 4.9 - - + -
177D LEU* 3.8 38.8 - - + +
180D SER* 4.7 0.7 - - - +
197D ALA* 3.8 34.7 - - + +
200D ALA* 4.3 10.8 - - + -
201D PHE* 4.2 15.7 - - + +
222D ILE* 2.9 19.1 + - + +
223D MET* 3.6 11.2 - - - +
225D LEU* 1.3 75.3 - - - +
227D ARG* 1.3 58.6 + - - +
229D ASN* 3.4 4.5 + - - +
230D LEU* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PHE* 3.8 33.2 - - + -
223D MET 3.1 13.6 + - - +
224D GLN* 3.5 28.7 - - - +
226D LEU* 1.3 76.2 - - - +
228D ASP* 1.3 59.3 + - - +
230D LEU* 3.1 11.0 + - + +
231D THR* 2.8 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D GLN* 2.7 46.1 + - - +
225D LEU* 3.3 18.4 + - + +
227D ARG* 1.3 74.0 - - - +
229D ASN* 1.3 63.7 + - - +
231D THR* 3.3 8.4 + - - -
232D LEU* 3.0 23.4 + - - +
504J ILE* 5.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D LEU* 3.1 21.0 - - + +
180D SER* 5.0 0.4 + - - +
181D VAL* 3.7 10.9 - - - +
197D ALA* 5.8 0.9 - - + -
225D LEU 2.9 12.4 + - - +
226D LEU* 3.7 5.4 - - - +
228D ASP* 1.3 76.2 - - - +
230D LEU* 1.3 57.4 + - - +
232D LEU* 3.3 7.1 + - - +
233D TRP* 2.9 54.5 + - + -
503J ALA* 3.3 14.0 - - - -
504J ILE* 2.8 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D CYS* 3.5 47.3 - - + +
197D ALA* 4.1 12.6 - - + +
198D LYS* 3.8 29.4 - - + -
201D PHE* 5.5 7.4 - - + -
226D LEU 2.9 15.9 + - - +
227D ARG* 3.5 14.6 - - + +
229D ASN* 1.3 73.0 - - - +
231D THR* 1.3 58.0 + - - +
233D TRP* 3.4 3.4 + - + -
234D THR* 2.6 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D ARG* 2.8 30.2 + - - +
228D ASP* 3.6 10.4 + - - -
230D LEU* 1.3 72.0 - - - +
232D LEU* 1.3 64.9 + - - +
234D THR* 3.2 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D ASP 3.0 11.7 + - - +
229D ASN* 3.6 11.4 - - - +
231D THR* 1.3 78.7 - - - +
233D TRP* 1.3 70.0 + - + +
234D THR 3.2 4.5 + - - +
502J ARG* 5.4 8.7 - - + +
503J ALA* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D SER* 3.7 38.8 - - - -
181D VAL* 3.8 7.4 - - + -
184D TYR* 3.4 62.8 + + + -
190D PRO* 5.9 1.4 - - - +
193D ALA* 4.0 23.8 - - + -
194D CYS* 3.9 26.4 - - - -
197D ALA* 4.6 4.7 - - + -
229D ASN* 2.9 41.0 + - + +
230D LEU* 4.1 3.8 - - + +
232D LEU* 1.3 78.0 - - + +
234D THR* 1.3 63.3 + - - +
503J ALA* 3.3 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D CYS* 3.9 19.1 - - - -
230D LEU* 2.6 25.3 + - + +
231D THR* 3.3 16.5 + - - -
232D LEU 3.1 4.1 - - - +
233D TRP* 1.3 84.7 - - - +
----------------------------------------------------------
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