Contacts of the helix formed by residues 208 - 222 (chain D) in PDB entry 3HUU
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 208 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLU* 5.5 0.9 - - - +
37D ASN* 2.6 32.8 + - - +
39D PHE* 5.6 1.0 - - - +
150D GLU* 3.3 25.3 - - - +
160D ARG* 4.5 6.0 + - - +
206D THR* 3.1 4.0 + - - -
207D SER* 1.3 82.9 + - - +
209D VAL* 1.3 74.3 + - - +
210D MET* 3.3 10.3 + - - +
211D LEU* 3.3 9.7 + - + +
212D ASN* 2.9 22.5 + - - +
234D THR* 3.2 11.9 + - - -
235D PHE* 4.1 8.5 - - - +
236D ASN* 4.4 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASN* 3.8 23.1 - - - +
38D PRO* 4.1 10.3 - - + -
208D ASP* 1.3 74.3 + - - +
210D MET* 1.3 78.4 + - + +
212D ASN* 3.1 8.8 + - - +
213D MET* 2.8 31.6 + - - +
234D THR* 3.5 3.1 + - + -
235D PHE 3.0 20.8 + - - +
236D ASN* 3.2 22.2 - - + +
238D SER* 4.5 3.1 - - - +
240D LEU* 4.8 8.1 - - + -
241D THR* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C PHE* 3.5 56.4 - - + -
240C LEU* 4.5 5.2 - - + -
33D GLU* 3.8 33.4 - - - +
36D GLN* 3.7 30.3 - - + +
37D ASN* 3.7 27.8 - - - +
208D ASP* 3.3 5.2 + - - +
209D VAL* 1.3 77.5 - - + +
211D LEU* 1.3 65.2 + - - +
213D MET* 3.2 14.4 + - - +
214D GLN* 3.4 11.4 + - - +
240D LEU* 3.9 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D LEU* 3.6 35.0 - - + +
149D GLN 3.8 5.2 - - - +
150D GLU* 3.7 30.7 - - + +
180D ILE* 4.2 26.0 - - + +
186D LEU* 4.3 9.2 - - + -
206D THR* 4.2 11.4 - - + -
207D SER* 4.2 4.0 - - - +
208D ASP* 3.3 13.1 + - + +
210D MET* 1.3 78.9 - - - +
212D ASN* 1.3 63.6 + - - +
214D GLN* 3.2 23.5 + - - +
215D LEU* 3.0 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D THR* 2.6 36.0 + - - +
208D ASP 2.9 10.8 + - - +
209D VAL* 3.1 11.2 + - - +
211D LEU* 1.3 79.1 - - - +
213D MET* 1.3 62.3 + - - +
215D LEU* 3.1 10.4 + - - +
216D LEU* 3.0 32.4 + - - +
232D THR* 4.5 1.0 - - - -
233D ALA 4.0 3.6 - - - +
234D THR* 3.6 18.0 - - - +
241D THR* 5.7 0.6 - - - +
244D ALA* 5.4 0.4 - - - +
248D GLN* 3.1 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C MET* 4.0 24.2 - - + -
239C PHE* 4.2 17.7 - - + +
240C LEU* 3.5 51.1 - - + +
243C ASN* 3.5 25.5 - - + +
244C ALA* 4.5 4.3 - - + -
245C THR* 4.8 0.7 + - - -
209D VAL 2.8 19.5 + - - +
210D MET* 3.2 9.6 + - - +
212D ASN* 1.3 76.4 - - - +
214D GLN* 1.3 61.9 + - - +
216D LEU* 3.3 10.7 + - + +
217D ASN 3.1 17.3 + - - -
240D LEU* 3.9 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C PHE* 3.7 21.4 - - + -
243C ASN* 3.5 25.3 - - - +
33D GLU* 4.9 5.8 + - - +
180D ILE* 5.5 1.0 - - - +
182D SER 5.3 2.4 - - - -
183D MET* 3.6 35.6 + - + +
186D LEU* 3.6 11.4 - - + +
210D MET 3.6 8.5 - - - +
211D LEU* 3.2 31.3 + - - +
213D MET* 1.3 76.6 - - - +
215D LEU* 1.3 62.3 + - - +
217D ASN* 3.3 3.7 + - - +
218D VAL* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D LEU* 4.1 16.8 - - + -
186D LEU* 3.6 21.0 - - + +
190D ILE 5.4 2.7 - - - +
204D ILE* 3.8 25.4 - - + +
206D THR* 3.6 26.0 - - + -
211D LEU 3.0 12.7 + - - +
212D ASN* 3.1 14.1 + - - +
214D GLN* 1.3 74.5 - - - +
216D LEU* 1.3 60.7 + - + +
218D VAL* 3.2 3.6 + - + -
219D LEU* 2.9 57.4 + - + +
232D THR* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C THR* 3.6 14.4 + - - +
212D ASN* 3.0 26.8 + - - +
213D MET* 3.8 8.7 - - - +
215D LEU* 1.3 77.0 - - + +
217D ASN* 1.3 61.9 + - - +
219D LEU* 4.0 4.3 - - + +
220D TYR* 3.1 24.9 + - - +
226D ILE* 3.6 28.1 - - + +
232D THR* 3.8 16.2 - - + +
244D ALA* 3.8 19.3 - - + -
245D THR* 3.7 19.3 - - - +
248D GLN* 3.5 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C GLU 4.5 1.0 + - - -
243C ASN* 4.0 10.9 - - - +
244C ALA 2.7 26.3 + - - +
245C THR* 3.6 8.9 + - - +
246C PRO* 4.1 3.1 - - - +
247C SER* 3.6 20.6 - - - +
183D MET* 4.2 15.9 - - + +
187D ARG* 4.7 6.3 + - - -
213D MET 3.1 13.2 + - - +
214D GLN* 3.5 11.2 - - - +
215D LEU 3.1 0.2 - - - -
216D LEU* 1.3 77.8 - - - +
218D VAL* 1.3 60.9 + - - +
220D TYR* 3.3 6.8 + - - +
221D GLU* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D MET* 3.6 24.0 - - - -
186D LEU* 4.1 13.9 - - + +
187D ARG* 3.9 28.7 - - + +
190D ILE 4.2 15.5 - - - +
214D GLN 3.1 16.7 + - - +
215D LEU* 3.7 5.4 - - + +
217D ASN* 1.3 79.6 - - - +
219D LEU* 1.3 65.9 + - + +
221D GLU* 3.1 6.1 + - - +
222D TYR* 3.1 45.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ILE 4.6 11.7 - - - +
204D ILE* 4.7 9.4 - - + -
215D LEU* 2.9 42.7 + - + +
216D LEU* 4.0 3.8 - - + +
218D VAL* 1.3 75.4 - - + +
220D TYR* 1.3 62.3 + - - +
222D TYR* 3.3 2.8 + - - -
223D GLN 3.0 4.9 + - - -
224D LEU* 2.8 66.2 + - + +
226D ILE* 3.7 27.1 - - + -
230D ILE* 4.1 13.2 - - + -
232D THR* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C TYR* 3.8 33.0 - + + -
224C LEU 4.1 2.9 + - - -
225C ARG* 3.0 54.5 + - - -
226C ILE* 3.0 39.4 + - - +
245C THR* 3.3 26.5 - - + -
246C PRO* 3.8 32.5 - - + -
216D LEU 3.1 19.3 + - - +
217D ASN* 3.4 4.7 - - - +
219D LEU* 1.3 75.6 - - - +
221D GLU* 1.3 63.9 + - - +
223D GLN* 3.1 11.5 + - - +
224D LEU 4.8 2.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
225C ARG* 4.0 11.9 + - - +
187D ARG* 2.8 36.5 + - - +
217D ASN* 3.0 20.4 + - - +
218D VAL* 3.1 10.5 + - - +
220D TYR* 1.3 80.0 - - - +
222D TYR* 1.3 82.2 + - + +
223D GLN* 3.3 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ARG* 4.0 28.7 + - - +
190D ILE* 5.4 18.2 - - + -
218D VAL* 3.1 46.1 + - + +
219D LEU* 4.2 2.5 - - - +
221D GLU* 1.3 101.5 + - + +
223D GLN* 1.3 69.7 + - - +
224D LEU* 3.4 20.4 + - + +
----------------------------------------------------------
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