Contacts of the helix formed by residues 169 - 190 (chain D) in PDB entry 2Q9Q
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 169 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 3.6 32.4 - - + +
110D HIS* 4.5 0.7 - - - +
114D PRO* 3.3 12.4 - - - +
115D HIS* 3.6 4.3 - - - -
116D PHE* 3.0 26.5 + - + -
117D TYR* 3.5 19.1 + - - -
118D GLY 5.0 0.7 + - - -
168D LEU* 1.3 77.6 - - - +
170D GLU* 1.3 63.5 + - - +
171D MET* 2.7 29.1 + - - +
172D GLU* 2.9 25.1 + - - +
173D ARG* 3.0 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C HIS* 4.7 12.6 + - - -
23D ASP* 4.4 13.5 - - - +
110D HIS* 4.7 1.5 + - - -
114D PRO* 2.7 33.9 + - + +
115D HIS* 3.5 32.4 - - + +
169D ASP* 1.3 72.2 - - - +
171D MET* 1.3 61.9 + - - +
173D ARG* 3.4 35.3 + - - +
174D GLY* 3.2 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A HIS* 3.7 28.2 - - + +
170A LEU* 4.8 2.7 - - + -
13D LEU* 3.6 31.6 - - + -
117D TYR* 3.5 36.3 - - + -
142D PHE* 3.4 45.5 - - + -
169D ASP* 2.7 19.7 + - - +
170D GLU* 1.3 73.6 - - - +
172D GLU* 1.3 63.2 + - + +
174D GLY* 3.2 4.0 + - - -
175D LEU* 3.1 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 3.6 3.1 - - - +
117D TYR* 2.8 36.8 + - + -
142D PHE* 4.6 2.4 - - + -
145D ARG* 2.8 40.2 + - - +
149D ILE* 3.7 28.7 - - + +
168D LEU* 3.4 11.7 - - + +
169D ASP* 2.9 29.6 + - - +
171D MET* 1.3 80.1 - - + +
173D ARG* 1.3 59.3 + - - +
175D LEU* 3.2 11.3 + - - +
176D PHE* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D HIS* 3.0 46.9 + - - +
165D VAL* 3.0 32.5 + - + +
166D ALA* 3.3 19.2 + - - +
168D LEU* 3.0 18.6 + - + +
169D ASP 3.0 16.0 + - - +
170D GLU* 3.4 28.9 + - - +
171D MET 3.2 0.4 - - - -
172D GLU* 1.3 76.2 - - - +
174D GLY* 1.3 57.8 + - - +
176D PHE* 3.2 10.4 + - - +
177D GLN* 2.8 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ARG* 6.3 1.6 - - - -
170D GLU 3.2 6.8 + - - -
171D MET 3.2 8.2 + - - -
173D ARG* 1.3 74.9 - - - +
175D LEU* 1.3 65.6 + - - +
177D GLN* 2.8 22.6 + - - +
178D THR* 2.9 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.3 39.2 - - + +
162A GLN* 3.7 31.0 - - + -
163A ALA* 3.8 15.3 - - + +
166A HIS* 4.3 12.0 - - + +
142D PHE* 3.3 41.5 - - + -
146D PHE* 5.5 1.1 - - + -
149D ILE* 4.4 7.6 - - + -
171D MET* 3.1 15.2 + - + +
172D GLU* 3.3 11.4 - - - +
174D GLY* 1.3 74.8 - - - +
176D PHE* 1.3 63.3 + - - +
178D THR* 3.3 4.9 + - - -
179D GLY 3.1 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ILE* 4.2 6.5 - - + +
152D SER* 3.6 18.2 - - - -
153D SER* 3.4 43.0 - - - -
161D THR* 3.7 19.3 - - + -
164D LEU* 4.4 4.9 - - + -
165D VAL* 3.4 38.6 - - + -
168D LEU* 4.3 6.1 - - + -
172D GLU 2.8 14.2 + - - +
173D ARG* 3.2 13.9 - - - +
175D LEU* 1.3 77.4 - - - +
177D GLN* 1.3 69.1 + - - +
179D GLY 3.4 0.3 + - - -
180D GLN* 2.9 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D VAL* 5.9 1.3 - - - +
173D ARG* 2.8 31.5 + - - +
174D GLY* 2.8 15.5 + - - +
176D PHE* 1.3 85.5 - - - +
178D THR* 1.3 56.6 + - - +
180D GLN* 3.1 11.0 + - - +
181D LYS* 2.7 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 3.4 51.3 - - + +
159A PHE* 3.8 5.4 - - - +
162A GLN* 4.6 10.0 - - + +
174D GLY 2.9 13.4 + - - -
175D LEU* 3.6 9.5 - - - -
177D GLN* 1.3 74.6 - - - +
179D GLY* 1.3 65.3 + - - +
181D LYS* 3.3 7.7 + - - +
182D GLY* 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A THR 4.9 2.6 - - - +
156A SER* 6.2 0.7 - - - -
159A PHE* 3.6 26.4 - - - -
153D SER* 3.8 14.0 - - - +
154D GLN* 4.6 9.7 + - - +
175D LEU 3.1 8.5 + - - -
176D PHE 3.8 2.2 - - - -
178D THR* 1.3 79.2 - - - +
180D GLN* 1.3 62.2 + - - +
182D GLY* 3.5 1.1 + - - -
183D LEU* 3.2 22.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
152D SER 5.2 1.2 - - - +
153D SER 3.4 17.1 + - - +
161D THR* 4.8 6.1 + - - +
176D PHE* 2.9 46.8 + - + +
177D GLN* 3.1 11.2 + - - +
179D GLY* 1.3 73.8 - - - +
181D LYS* 1.3 61.3 + - - +
183D LEU* 3.3 2.8 + - - +
184D ASN* 2.9 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D GLN 2.7 21.0 + - - +
178D THR* 3.6 7.6 - - - +
180D GLN* 1.3 73.9 - - - +
182D GLY* 1.3 64.2 + - - +
184D ASN* 4.1 4.4 - - - +
185D ASP* 2.9 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN 5.5 2.0 - - - -
155A THR* 3.6 26.7 - - - +
178D THR 2.9 15.6 + - - -
179D GLY 3.9 0.7 - - - -
180D GLN 3.2 0.2 - - - -
181D LYS* 1.3 79.3 - - - +
183D LEU* 1.3 60.8 + - - +
185D ASP* 3.7 7.5 - - - +
186D PHE* 3.2 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TRP* 5.5 4.5 - - + +
125A ILE* 6.0 5.4 - - + -
155A THR* 4.1 14.9 + - + -
153D SER 4.5 3.6 - - - +
154D GLN* 3.1 46.4 - - + +
155D ASN* 4.8 5.8 - - + -
179D GLY 3.2 16.8 + - - +
180D GLN 3.8 3.1 - - - +
182D GLY* 1.3 75.5 - - - +
184D ASN* 1.3 64.9 + - - +
186D PHE* 3.1 15.6 + - + +
187D GLN* 3.0 57.1 + - + +
----------------------------------------------------------
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* 2.9 51.5 + - - +
181D LYS* 4.1 4.6 - - - +
183D LEU* 1.3 73.3 - - - +
185D ASP* 1.3 65.4 + - - +
187D GLN* 3.3 19.9 + - - +
188D CYS* 3.0 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP* 3.7 22.3 - - - +
3A ALA* 2.9 30.3 + - - +
4A ALA 5.2 0.3 + - - -
154A ASN* 5.3 0.5 - - - +
181D LYS* 2.9 23.5 + - + +
182D GLY* 3.7 7.6 - - - +
184D ASN* 1.3 75.9 - - - +
186D PHE* 1.3 63.6 + - - +
188D CYS* 3.5 6.2 + - - +
189D TRP* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 4.2 9.4 - - + -
93A MET* 4.2 9.2 - - + -
121A TRP* 3.2 64.4 - + - -
151A MET* 3.6 19.7 - - + -
155A THR* 3.8 14.4 - - + +
182D GLY 3.2 10.1 + - - +
183D LEU* 3.1 14.6 + - + +
185D ASP* 1.3 82.1 - - - +
187D GLN* 1.3 72.1 + - + +
189D TRP* 3.5 21.0 + + - +
190D GLU* 3.0 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LEU* 3.0 41.7 + - + +
184D ASN* 3.3 22.0 + - - +
186D PHE* 1.3 89.3 - - + +
188D CYS* 1.3 63.3 + - - +
190D GLU* 3.8 10.2 + - - +
191D LYS* 3.4 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ASN* 3.0 24.9 + - - +
185D ASP* 3.9 6.3 - - - +
186D PHE 3.3 0.2 - - - -
187D GLN* 1.3 74.3 - - - +
189D TRP* 1.3 66.9 + - - +
191D LYS* 3.1 26.8 + - - +
192D GLY* 4.2 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.7 21.3 - - + -
4A ALA* 4.1 12.3 - - + +
7A GLU* 3.0 49.1 + - + +
93A MET* 4.0 10.1 - - + -
94A GLU* 3.9 38.1 - - + -
97A LYS* 3.7 34.6 + - + +
151A MET* 3.3 26.7 - - + -
144C LYS* 5.4 1.8 - - - -
185D ASP* 3.1 15.6 + - - +
186D PHE* 3.6 19.7 - + - +
188D CYS* 1.3 76.3 - - - +
190D GLU* 1.3 79.9 + - + +
191D LYS 2.8 15.1 + - - -
192D GLY* 3.1 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A MET* 5.1 7.2 - - - -
97A LYS* 4.4 17.2 - - + +
101A ASN* 5.0 3.1 - - - +
114A ARG* 5.5 4.3 + - - -
118A LYS* 4.6 22.0 + - - -
186D PHE* 3.0 40.1 + - + +
187D GLN* 4.0 10.4 - - - +
189D TRP* 1.3 92.2 - - + +
191D LYS* 1.3 58.0 + - - +
192D GLY 3.6 1.8 + - - -
----------------------------------------------------------
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