Contacts of the helix formed by residues 178 - 193 (chain D) in PDB entry 3QEL
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 GLY 178 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ALA* 3.6 10.1 - - - +
136D ASP* 4.9 3.0 + - - -
150D ILE* 3.4 21.9 - - - +
177D PRO* 1.3 73.6 - - - +
179D TYR* 1.3 66.7 + - - +
180D GLN 3.1 3.9 - - - +
181D ASP* 2.9 13.4 + - - +
182D PHE* 2.7 23.7 + - - +
231D TYR* 3.6 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASP* 5.7 0.7 + - - -
132C SER* 4.3 10.9 - - - -
173D THR* 3.7 24.4 - - + +
174D THR 3.3 15.9 - - - +
175D TYR* 3.5 52.4 - + - -
176D PHE 3.0 11.0 + - - +
178D GLY* 1.3 79.3 - - - +
180D GLN* 1.3 97.7 + - + +
182D PHE* 3.3 2.9 + - - +
183D VAL* 3.0 35.8 + - + +
204D LEU* 3.8 21.7 - - + +
231D TYR* 3.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D GLY* 3.1 1.0 - - - +
179D TYR* 1.3 122.4 + - + +
181D ASP* 1.3 68.9 + - - +
183D VAL* 4.5 4.3 - - - +
184D ASN* 3.1 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ALA* 4.9 7.5 - - - +
136D ASP* 4.5 13.1 + - - +
150D ILE* 4.1 18.0 - - + +
151D GLU* 5.3 6.5 - - + +
178D GLY* 2.9 21.4 + - - +
180D GLN* 1.3 79.9 - - - +
182D PHE* 1.3 61.8 + - - +
184D ASN* 4.2 3.9 - - - +
185D LYS* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 3.8 20.1 - - + +
153D GLN* 5.0 0.9 - - + -
154D ALA* 3.7 27.8 - - + -
157D MET* 3.2 38.8 - - + -
171D ILE* 4.2 24.9 - - + -
173D THR* 4.3 2.2 - - + -
178D GLY 2.7 13.9 + - - +
179D TYR* 3.4 9.4 - - - +
181D ASP* 1.3 75.1 - - - +
183D VAL* 1.3 65.3 + - - +
185D LYS* 3.3 4.2 + - - +
186D ILE* 3.2 36.0 + - + +
229D LEU* 4.2 12.6 - - + -
230D LEU 5.2 2.5 - - - -
231D TYR* 3.8 38.4 - + + -
259D PRO* 5.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ILE* 4.0 37.5 - - + -
173D THR* 4.2 11.2 - - + +
179D TYR* 3.0 19.9 + - + +
180D GLN* 4.3 4.5 - - - +
182D PHE* 1.3 78.5 - - + +
184D ASN* 1.3 57.9 + - - +
186D ILE* 3.2 4.7 + - - +
187D ARG* 2.8 71.2 + - + +
202D VAL* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D GLN* 3.1 32.6 + - - +
181D ASP* 4.2 3.9 - - - +
183D VAL* 1.3 81.9 - - - +
185D LYS* 1.3 56.7 + - - +
187D ARG* 3.7 10.3 - - - +
188D SER* 2.8 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D GLU* 3.6 44.5 + - + +
152D GLN* 5.6 0.2 - - - +
154D ALA* 4.1 12.1 - - + -
155D SER* 4.4 16.5 + - - +
158D LEU* 5.3 0.7 - - + -
181D ASP 3.2 17.6 + - - +
182D PHE 3.7 4.0 - - - +
184D ASN* 1.3 74.7 - - - +
186D ILE* 1.3 60.6 + - - +
188D SER* 3.8 8.5 + - - +
189D THR* 2.5 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ALA* 3.6 37.2 - - + +
157D MET* 4.8 0.2 - - + -
158D LEU* 4.0 18.6 - - + +
169D PHE* 3.7 34.1 - - + -
171D ILE* 3.9 21.3 - - + -
182D PHE* 3.3 23.6 - - + +
183D VAL 3.2 6.8 + - - +
185D LYS* 1.3 77.3 - - - +
187D ARG* 1.3 63.0 + - - +
189D THR* 3.2 3.3 + - - -
190D ILE* 3.1 30.4 + - + +
199D LEU* 4.8 2.0 - - + -
229D LEU* 4.3 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D VAL* 2.8 47.4 + - + +
184D ASN* 3.9 10.3 + - - +
186D ILE* 1.3 75.3 - - + +
188D SER* 1.3 60.2 + - - +
190D ILE* 3.9 8.0 + - + +
191D GLU* 3.4 22.2 + - - +
199D LEU* 4.1 20.3 - - + +
202D VAL* 3.3 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ASN 2.8 21.1 + - - -
185D LYS* 3.8 12.6 + - - +
187D ARG* 1.3 73.3 - - - +
189D THR* 1.3 65.3 + - - +
191D GLU* 3.9 6.0 + - - +
192D ASN* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D SER* 6.0 1.0 - - - -
158D LEU* 3.5 26.7 - - + +
185D LYS* 2.5 40.5 + - - -
186D ILE 3.2 4.6 + - - -
188D SER* 1.3 78.7 + - - +
190D ILE* 1.3 66.0 + - - +
192D ASN* 3.3 15.9 + - + +
193D SER* 3.3 13.4 + - - -
197D TRP* 5.6 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 5.2 4.0 - - + -
169D PHE* 3.8 28.3 - - + -
186D ILE* 3.1 22.8 + - + +
187D ARG* 3.9 6.5 - - + +
189D THR* 1.3 79.2 - - - +
191D GLU* 1.3 59.7 + - - +
193D SER* 2.8 27.0 + - - +
197D TRP* 3.9 45.6 - - + +
199D LEU* 4.3 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ARG 3.4 14.8 + - - +
188D SER* 4.1 7.6 - - - +
189D THR 3.3 1.0 - - - -
190D ILE* 1.3 82.5 - - + +
192D ASN* 1.3 63.1 + - - +
193D SER 3.4 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D SER* 2.9 20.3 + - - +
189D THR* 3.3 12.2 + - + +
190D ILE 3.2 0.4 - - - -
191D GLU* 1.3 79.0 - - - +
193D SER* 1.3 60.7 + - - +
194D PHE* 4.0 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D THR* 3.6 10.3 - - - -
190D ILE 2.8 20.3 + - - +
191D GLU 4.4 2.3 - - - +
192D ASN* 1.3 81.1 - - - +
194D PHE* 1.3 60.3 + - - +
195D VAL* 3.2 6.9 + - - -
196D GLY* 4.6 2.8 + - - -
197D TRP* 3.6 29.2 - - - -
----------------------------------------------------------
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