Contacts of the helix formed by residues 175 - 200 (chain B) in PDB entry 1RQ2
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 SER 175 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 1.4 73.3 - - - +
176B LEU* 1.3 59.2 + - - +
177B MET* 3.4 10.6 + - - +
178B ASP* 3.1 34.6 + - - -
179B ALA* 2.8 29.2 + - - +
181B ARG* 5.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS 5.6 1.1 - - - +
121A LEU* 3.5 27.1 - - - +
135B PHE* 3.5 43.5 - - + -
175B SER* 1.3 73.6 - - - +
177B MET* 1.3 73.1 + - + +
179B ALA* 3.2 6.2 + - + +
180B PHE* 3.1 43.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLY* 3.9 9.0 - - - +
93A ALA 3.2 27.1 - - - +
94A ASP* 3.4 20.6 - - - +
121A LEU* 3.9 9.6 - - + +
122A GLY* 3.3 36.6 - - - +
123A ALA* 3.7 5.8 - - - +
212A LYS* 5.8 3.4 - - - +
175B SER* 3.4 7.6 + - - +
176B LEU* 1.3 86.3 - - + +
178B ASP* 1.3 62.7 + - - +
180B PHE* 3.4 5.1 + - + +
181B ARG* 3.0 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 3.9 10.9 - - + -
175B SER* 3.1 39.3 + - - +
177B MET* 1.3 78.7 - - - +
179B ALA* 1.3 53.1 + - - +
181B ARG* 2.8 27.4 + - - +
182B SER* 2.8 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.4 27.8 - - + -
135B PHE* 4.8 8.3 - - + -
166B LEU* 5.7 0.2 - - - -
167B LEU* 3.9 19.7 - - + -
174B VAL* 3.8 5.6 - - - +
175B SER 2.8 14.2 + - - +
176B LEU* 3.2 13.7 + - + +
178B ASP* 1.3 76.5 - - - +
180B PHE* 1.3 56.5 + - - +
182B SER* 2.6 22.6 + - - -
183B ALA 3.0 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 5.6 1.6 - - - -
91A ARG* 3.5 57.5 + - + +
92A GLY* 3.6 25.1 - - - +
121A LEU* 3.8 25.4 - - + -
133B PHE* 4.0 9.4 - + - -
135B PHE* 3.8 32.3 - + - -
136B GLU* 4.6 4.0 - - + -
176B LEU* 3.1 36.8 + - + -
177B MET* 3.9 3.6 - - + +
179B ALA* 1.3 77.1 - - - +
181B ARG* 1.3 64.5 + - - +
183B ALA* 3.3 5.5 + - - +
184B ASP* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU 5.6 4.4 - - - -
10A VAL* 3.6 24.0 - - - +
92A GLY* 2.8 43.7 + - - +
94A ASP* 2.8 27.2 + - - -
175B SER* 5.1 0.4 + - - -
177B MET* 3.0 30.0 + - - +
178B ASP* 2.8 35.1 + - - +
180B PHE* 1.3 73.0 - - - +
182B SER* 1.3 66.2 + - - +
184B ASP* 3.3 11.2 + - - +
185B GLU* 2.9 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.6 26.5 + - - +
174B VAL* 5.1 3.4 - - - +
178B ASP 2.8 19.3 + - - -
179B ALA* 2.6 26.3 + - - -
181B ARG* 1.3 73.0 - - - +
183B ALA* 1.3 56.6 + - - +
185B GLU* 3.2 10.3 + - - +
186B VAL* 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 4.5 2.2 - - - +
102B GLU* 3.1 19.1 - - - +
133B PHE* 4.0 7.0 - - + -
163B ASN* 3.7 30.8 - - - +
166B LEU* 3.5 13.5 - - + -
179B ALA 3.0 12.4 + - - +
180B PHE* 3.6 6.1 - - - +
181B ARG 3.2 0.2 - - - -
182B SER* 1.3 81.6 + - - +
184B ASP* 1.3 62.3 + - - +
186B VAL* 3.3 4.6 - - - +
187B LEU 3.0 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 4.5 10.2 - - - +
91A ARG* 4.3 19.7 + - - +
22B ASN* 5.5 1.9 + - - -
26B ARG* 3.5 44.7 + - - +
102B GLU* 3.3 26.1 - - - +
180B PHE 3.1 15.5 + - - +
181B ARG* 3.3 10.4 + - - +
183B ALA* 1.3 76.4 - - - +
185B GLU* 1.3 63.6 + - + +
187B LEU* 3.4 7.1 + - - +
188B LEU* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ARG* 5.2 6.5 - - - +
30B GLN* 5.7 7.0 - - - +
181B ARG* 2.9 37.7 + - - +
182B SER* 3.6 8.1 - - - +
184B ASP* 1.3 77.8 - - + +
186B VAL* 1.3 65.4 + - + +
188B LEU* 3.3 12.5 + - + +
189B ASN* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 3.7 26.9 - - + -
163B ASN* 4.6 0.2 - - - +
166B LEU* 3.7 25.6 - - + -
169B MET* 4.7 0.9 - - + -
182B SER* 2.9 20.9 + - - +
183B ALA* 3.3 20.0 - - - +
185B GLU* 1.3 74.9 - - + +
187B LEU* 1.3 61.1 + - - +
189B ASN* 3.2 6.7 + - - +
190B GLY 2.9 23.9 + - - -
223B MET* 3.3 13.3 - - + +
225B ILE* 3.8 27.6 - - + -
246B LEU* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 3.8 22.7 - - + -
27B MET* 5.2 2.4 - - + +
99B THR* 3.9 15.3 - - + +
101B GLY* 3.7 24.5 - - - -
102B GLU* 3.6 20.6 - - + +
128B VAL* 3.6 24.4 - - + +
130B THR* 4.0 16.2 - - + -
161B ILE* 3.7 9.4 - - + -
183B ALA 3.0 16.9 + - - +
184B ASP* 3.5 8.5 - - - +
186B VAL* 1.3 78.3 - - - +
188B LEU* 1.3 62.8 + - - +
190B GLY* 3.0 15.2 + - - -
191B VAL* 3.7 8.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA 5.9 0.2 - - - +
26B ARG* 4.3 11.4 - - - -
27B MET* 3.5 42.6 - - + +
30B GLN* 3.9 35.4 - - + +
32B LEU* 4.4 5.2 - - + -
184B ASP 3.2 11.4 + - - +
185B GLU* 3.5 12.6 - - + +
186B VAL 3.2 0.2 - - - -
187B LEU* 1.3 80.6 - - - +
189B ASN* 1.3 57.1 + - - +
191B VAL* 2.9 8.7 + - - +
192B GLN* 2.9 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU 3.1 12.7 + - - +
186B VAL* 3.4 13.2 - - + +
188B LEU* 1.3 79.4 - - - +
190B GLY* 1.3 62.0 + - - +
191B VAL 3.0 1.6 + - - -
192B GLN* 4.2 7.0 - - - +
193B GLY* 3.0 22.0 + - - +
194B ILE 4.5 0.5 + - - -
223B MET* 3.8 8.5 - - - +
225B ILE* 3.5 28.7 - - + +
304B ARG* 5.9 7.9 - - - +
305B VAL 5.5 0.4 + - - -
306B THR* 2.9 28.4 + - - +
308B ILE* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 4.0 5.9 - - - -
128B VAL* 4.3 13.3 - - - +
159B ILE* 3.6 26.7 - - - +
161B ILE* 4.7 0.7 - - - -
186B VAL 2.9 13.1 + - - -
187B LEU 3.0 9.2 + - - -
189B ASN* 1.3 74.5 - - - +
191B VAL* 1.3 61.3 + - - +
194B ILE* 4.0 6.2 - - - +
223B MET* 3.7 19.0 - - - -
308B ILE* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.9 22.4 - - + -
27B MET* 3.8 25.6 - - + -
32B LEU* 4.0 13.0 - - + -
97B PHE* 3.9 25.6 - - + -
99B THR* 5.5 4.3 - - + -
128B VAL* 4.1 11.9 - - + -
187B LEU* 4.4 5.6 - - + +
188B LEU 2.9 7.6 + - - +
190B GLY* 1.3 80.2 - - - +
192B GLN* 1.3 62.0 + - - +
193B GLY 3.3 1.8 - - - -
194B ILE* 3.2 7.1 + - - +
195B THR* 2.9 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLN* 5.7 3.9 + - - +
31B GLY 5.7 0.6 + - - -
32B LEU* 3.5 32.2 - - + +
188B LEU* 2.9 40.3 + - + +
189B ASN* 4.5 4.0 + - - -
191B VAL* 1.3 74.1 - - - +
193B GLY* 1.3 66.3 + - - +
195B THR* 3.6 7.9 - - - -
196B ASP* 2.8 48.6 + - - +
296B ASP* 5.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ASN* 3.0 18.5 + - - -
192B GLN* 1.3 79.2 - - - +
194B ILE* 1.3 60.9 + - - +
196B ASP* 4.4 1.4 - - - +
197B LEU* 3.4 19.8 + - - +
260B SER* 3.7 12.4 + - - -
306B THR* 3.7 28.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B MET* 3.9 7.2 - - + -
97B PHE* 3.8 20.0 - - + -
159B ILE* 3.6 31.6 - - + -
189B ASN 4.5 0.6 + - - +
190B GLY 4.0 7.2 - - - +
191B VAL 3.2 7.2 + - - +
193B GLY* 1.3 76.4 - - - +
195B THR* 1.3 66.3 + - - +
197B LEU* 3.2 15.3 + - - +
198B ILE* 3.2 30.3 + - + +
211B VAL* 5.0 0.2 - - + -
215B MET* 3.9 21.1 - - + -
258B LEU* 4.0 20.0 - - + -
306B THR* 5.1 0.2 - - - +
308B ILE* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.1 12.8 - - + -
32B LEU* 3.6 15.2 - - - +
33B LYS 4.7 0.4 + - - -
35B VAL* 3.8 27.8 - - + +
97B PHE* 3.4 32.3 - - + -
191B VAL* 2.9 32.0 + - + +
192B GLN* 3.6 9.5 - - - -
194B ILE* 1.3 72.8 - - - +
196B ASP* 1.3 60.1 + - - +
198B ILE* 3.1 2.7 + - - -
199B THR* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.6 18.7 - - - +
33B LYS* 4.5 5.5 + - - +
192B GLN* 2.8 44.0 + - - +
193B GLY* 4.4 2.0 - - - +
195B THR* 1.3 77.9 + - - +
197B LEU* 1.3 66.0 + - - +
199B THR* 3.8 6.2 + - - -
200B THR* 2.9 40.2 + - - +
260B SER* 5.6 0.2 - - - +
294B VAL* 3.5 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLY 3.4 13.3 + - - +
194B ILE 3.2 10.3 + - - +
196B ASP* 1.3 81.3 - - - +
198B ILE* 1.3 61.9 + - + +
200B THR 4.3 6.1 - - - +
204B ILE 4.9 0.9 - - - +
205B ASN* 5.2 4.3 - - - +
206B VAL* 3.9 24.5 + - + +
211B VAL* 5.5 1.3 - - + -
258B LEU* 3.5 35.2 - - + -
259B MET 4.1 13.0 - - - +
260B SER* 3.7 13.5 - - - +
290B ILE* 4.3 12.6 - - + -
292B GLY* 3.5 39.0 - - - +
293B THR 4.1 5.3 - - - +
294B VAL* 3.7 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 4.1 20.2 - - + -
11B ILE* 4.1 18.4 - - + -
95B MET* 3.7 30.1 - - - -
194B ILE* 3.2 24.2 + - + +
195B THR 3.1 7.0 + - - +
197B LEU* 1.3 82.1 - - + +
199B THR* 1.3 63.1 + - + +
200B THR 5.4 0.2 - - - -
206B VAL* 4.6 9.9 - - + +
208B PHE* 4.1 15.7 - - + +
211B VAL* 4.1 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 5.5 3.6 - - + +
11B ILE* 3.7 27.1 - - + -
33B LYS 3.8 10.0 + - - -
34B GLY* 3.7 29.1 - - - +
195B THR* 2.8 32.4 + - - +
196B ASP* 3.8 0.9 + - - -
198B ILE* 1.3 77.2 - - + +
200B THR* 1.3 70.6 + - - +
201B PRO* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 5.1 8.1 - - - +
196B ASP* 2.9 29.8 + - - +
197B LEU 4.3 4.5 - - - +
198B ILE 3.7 0.4 - - - -
199B THR* 1.3 90.1 + - - +
201B PRO* 1.3 76.8 - - + +
202B GLY 3.5 1.7 + - - -
205B ASN* 4.1 3.9 - - - +
293B THR 4.2 6.2 - - - +
294B VAL* 3.7 24.6 - - + +
295B ILE 3.8 13.9 - - - +
----------------------------------------------------------
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