Contacts of the helix formed by residues 168 - 187 (chain E) in PDB entry 2RCY
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 CYS 168 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 4.4 0.6 - - - +
229A ILE* 3.6 33.0 - - - -
230A THR* 3.2 32.8 - - - +
163E THR* 2.9 18.6 + - - -
164E ALA* 3.4 17.3 - - - +
167E GLY* 1.3 74.1 - - - +
169E GLY* 1.3 65.6 + - - +
170E PRO* 3.3 2.7 - - - -
171E ALA* 3.0 24.4 + - - +
172E TYR* 3.4 21.7 + - + +
253E ALA* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 5.9 2.0 - - - -
201A THR* 3.6 9.0 - - - -
164E ALA 3.8 0.4 + - - -
165E ILE 2.8 27.6 + - - -
167E GLY 3.4 0.2 - - - -
168E CYS* 1.3 77.3 - - - +
170E PRO* 1.4 64.9 - - - +
172E TYR* 3.0 27.1 + - - +
173E VAL* 3.1 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A THR* 3.5 7.8 - - + -
205A SER* 3.2 24.5 - - - +
223A ILE* 3.1 22.2 - - + -
115E ASN* 4.0 10.1 - - + +
117E PRO* 3.9 23.3 - - + -
166E SER 3.4 8.5 - - - +
167E GLY 3.4 10.8 - - - +
168E CYS 3.3 6.3 - - - +
169E GLY* 1.4 88.3 - - - +
171E ALA* 1.3 48.8 + - - -
173E VAL* 3.1 2.5 + - + +
174E TYR* 2.7 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LYS* 3.8 12.5 - - + +
223A ILE* 3.4 13.0 - - + +
230A THR* 3.6 25.1 - - + -
234A LEU* 3.8 21.1 - - + +
168E CYS 3.0 12.7 + - - +
170E PRO* 1.3 77.6 - - - +
172E TYR* 1.3 61.8 + - - +
174E TYR* 4.0 9.4 - - - -
175E LEU* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 3.8 19.1 - - + -
180A LEU* 4.3 16.2 - - + -
230A THR 5.0 1.1 - - - -
233A GLY* 3.8 25.2 - - - -
234A LEU* 3.7 9.2 - - + -
237A LEU* 3.6 27.1 - - + -
242A PHE* 4.1 4.0 - - - -
164E ALA 3.1 21.6 + - - -
165E ILE* 5.0 0.2 - - - -
168E CYS* 3.4 17.0 - - + +
169E GLY* 3.0 21.9 + - - +
171E ALA* 1.3 75.3 - - + +
173E VAL* 1.3 59.3 + - + +
175E LEU* 3.5 3.3 + - - +
176E PHE* 3.0 27.0 + - - +
246E VAL* 6.1 1.6 - - + -
249E ALA* 3.6 13.9 + - + -
250E VAL* 4.0 14.1 - - + -
253E ALA* 3.3 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 3.9 14.8 - - + -
180A LEU* 5.3 2.2 - - + -
201A THR* 4.6 3.1 - - + +
202A ILE* 3.8 42.2 - - + +
205A SER* 3.7 27.6 - - - +
206A VAL* 5.1 1.3 - - + -
169E GLY 3.1 16.3 + - - +
170E PRO 3.5 5.4 - - - +
172E TYR* 1.3 73.8 - - - +
174E TYR* 1.3 59.6 + - - +
176E PHE* 3.1 9.1 + - + +
177E ILE* 2.8 42.4 + - + +
202E ILE* 5.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A SER* 3.3 32.4 - - - -
208A MSE 3.2 32.2 - - + +
209A VAL* 3.9 19.3 - - + -
216A VAL* 3.9 14.5 - - + +
219A LEU* 3.4 21.9 - - + +
220A LYS* 3.6 36.3 - - + -
223A ILE* 3.3 23.8 - - + -
265A GOL 4.4 0.6 + - - -
116E THR* 4.0 8.7 + - - -
117E PRO* 4.5 0.3 - - - +
170E PRO* 2.7 32.2 + - + +
171E ALA* 3.9 2.0 - - - +
173E VAL* 1.3 73.1 - - - +
175E LEU* 1.3 56.6 + - - +
177E ILE* 3.4 7.1 + - + +
178E GLU* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LYS* 4.3 13.4 - - - +
234A LEU* 4.9 9.2 - - + -
237A LEU* 3.8 23.3 - - + -
238A GLU* 3.8 24.9 - - - +
242A PHE* 3.8 25.6 - - + -
243A LYS* 4.5 12.8 - - + +
171E ALA 3.1 18.9 + - - +
172E TYR 3.8 3.6 - - - +
174E TYR* 1.3 73.8 - - - +
176E PHE* 1.3 57.1 + - - +
178E GLU* 3.5 29.4 + - - +
179E SER* 2.6 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 3.8 33.2 - - + -
173A VAL* 4.1 17.9 - - + -
176A PHE* 4.0 27.6 - + + -
242A PHE* 3.6 26.0 - + + -
246A VAL* 3.9 21.3 - - + -
172E TYR 3.0 15.5 + - - +
173E VAL* 3.1 12.7 + - + +
175E LEU* 1.3 76.7 - - - +
177E ILE* 1.3 62.0 + - - +
179E SER* 3.4 3.0 + - - -
180E LEU* 3.1 49.5 + - + +
202E ILE* 4.3 12.3 - - + -
237E LEU* 6.4 0.2 - - + -
242E PHE* 3.9 17.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A SER 4.8 0.2 - - - +
206A VAL* 4.5 9.2 - - + -
209A VAL* 4.0 21.1 - - + -
216A VAL* 3.8 14.8 - - + -
173E VAL* 2.8 39.2 + - + +
174E TYR* 3.6 9.2 - - + +
176E PHE* 1.3 70.3 - - + +
178E GLU* 1.3 63.6 + - - +
180E LEU* 3.3 3.5 + - - +
181E ILE* 3.0 43.2 + - + +
198E VAL* 4.1 15.2 - - + +
199E LEU* 4.0 19.3 - - + -
202E ILE* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 4.2 14.1 - - + -
217A GLN* 3.5 34.0 + - + +
220A LYS* 3.2 32.2 + - - -
243A LYS* 2.7 30.6 + - - +
220B LYS* 4.4 5.4 + - - -
178C GLU* 4.9 2.9 - - - +
174E TYR 2.8 19.8 + - - +
175E LEU* 3.5 17.9 - - - +
177E ILE* 1.3 74.4 - - - +
179E SER* 1.3 55.7 - - - +
181E ILE* 3.5 5.2 + - - +
182E ASP* 3.1 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 4.4 1.7 - - - -
243A LYS* 3.3 40.3 - - - +
246A VAL* 3.8 26.1 - - - +
247A MSE 3.4 11.3 - - - +
175E LEU* 2.6 33.4 + - - +
176E PHE 3.8 4.0 - - - -
177E ILE 3.3 0.2 - - - -
178E GLU* 1.3 71.7 - - - +
180E LEU* 1.3 60.5 + - - +
182E ASP* 3.4 2.7 + - - +
183E ALA* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE* 3.8 20.9 - - + +
169A GLY* 5.9 0.9 - - - -
172A TYR* 4.1 19.3 - - + -
173A VAL* 5.3 3.1 - - + -
246A VAL* 3.8 20.9 - - + -
250A VAL* 3.8 18.8 - - + -
176E PHE* 3.1 49.3 + - + +
177E ILE 3.3 2.7 + - - +
179E SER* 1.3 75.2 - - - +
181E ILE* 1.3 64.2 + - - +
183E ALA* 3.5 6.0 + - - +
184E GLY 3.3 14.7 + - - -
198E VAL* 3.6 34.3 - - + -
202E ILE* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 4.8 10.8 - - + -
177E ILE* 3.0 40.1 + - + +
178E GLU* 3.8 7.4 - - - +
180E LEU* 1.3 73.9 - - - +
182E ASP* 1.3 61.2 + - - +
184E GLY* 3.0 3.3 + - - -
185E VAL* 2.9 29.0 + - + +
191E ARG* 3.9 35.2 - - + +
194E SER* 3.9 22.0 - - - +
195E LYS* 3.8 42.0 - - + +
198E VAL* 4.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 182 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 5.6 0.7 + - - -
243A LYS* 2.9 33.6 + - - -
247A MSE 3.5 20.7 - - + +
220B LYS* 5.4 0.5 + - - +
221B ASP* 4.3 7.1 - - - +
224B VAL* 5.8 1.2 - - - +
234B LEU* 5.9 3.3 - - - +
178E GLU* 3.1 21.5 + - - +
179E SER* 3.6 7.0 - - - +
181E ILE* 1.3 75.5 - - - +
183E ALA* 1.3 57.7 + - - +
185E VAL* 3.9 6.1 - - - +
186E LYS* 3.0 29.6 + - - +
191E ARG* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 3.4 5.7 - - - +
247A MSE 3.8 26.0 - - - +
250A VAL* 3.7 31.9 - - + -
179E SER 3.1 16.6 + - - +
180E LEU 3.7 5.8 - - - +
181E ILE 3.2 0.2 - - - -
182E ASP* 1.3 74.4 - - - +
184E GLY* 1.3 63.1 + - - +
186E LYS* 3.7 1.8 + - - +
187E ASN* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 184 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 3.8 6.0 - - - +
165A ILE* 3.4 25.1 - - - +
180E LEU 3.3 4.6 + - - -
181E ILE 3.0 6.7 + - - -
183E ALA* 1.3 77.3 - - - +
185E VAL* 1.3 62.6 + - - +
187E ASN 3.4 3.1 + - - -
188E GLY 3.4 5.4 + - - -
189E LEU* 2.9 26.8 + - - +
194E SER* 3.7 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 3.5 39.3 - - + +
226B PRO* 3.0 18.6 - - + +
227B GLY 2.9 23.0 + - - -
181E ILE* 2.9 20.8 + - + +
182E ASP 3.9 4.3 - - - +
184E GLY* 1.3 75.5 - - - +
186E LYS* 1.3 58.0 + - - +
187E ASN 3.2 0.9 + - - -
188E GLY 3.2 3.5 + - - -
189E LEU 3.3 8.1 - - - +
191E ARG* 3.7 57.4 - - - +
194E SER* 3.7 1.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 186 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A MSE 3.9 7.2 - - + -
251A GLU* 2.7 40.2 + - - +
224B VAL* 5.3 0.2 - - - +
227B GLY* 3.1 20.6 - - - -
228B GLY 5.1 0.2 - - - +
231B ALA* 3.6 36.6 - - + +
232B VAL* 4.0 22.3 - - + +
235B TYR* 3.5 43.4 - - + -
182E ASP 3.0 20.7 + - - +
183E ALA* 3.9 5.6 - - - +
184E GLY 3.3 0.4 - - - -
185E VAL* 1.3 75.2 - - - +
187E ASN* 1.3 62.9 + - - +
188E GLY 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 187 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS* 5.5 2.6 + - - +
158A ASP* 5.0 1.2 - - - +
161A ILE* 3.5 42.2 - - + +
251A GLU* 3.5 45.2 + - - +
254A CYS* 4.3 13.8 - - - -
258A LYS* 5.3 8.5 + - - +
227B GLY* 4.5 2.7 - - - -
183E ALA* 3.0 18.1 + - - +
184E GLY 3.4 5.5 + - - -
185E VAL 3.2 1.4 - - - -
186E LYS* 1.3 84.5 + - - +
188E GLY* 1.3 55.2 + - - +
189E LEU 3.7 0.4 - - - -
----------------------------------------------------------
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