Contacts of the helix formed by residues 170 - 195 (chain E) in PDB entry 4P9U
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 LEU 170 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E LYS* 3.2 13.8 + - + +
169E GLU* 1.3 80.9 - - - +
171E LYS* 1.3 64.3 + - - +
172E ARG 3.3 1.3 - - - -
173E GLN* 4.1 5.5 - - - +
174E GLU* 3.1 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E GLN* 4.2 0.4 + - - -
160E HIS* 2.9 64.2 - - + +
167E LYS* 2.9 18.4 + - + +
168E ASP* 3.5 4.7 + - - -
170E LEU* 1.3 79.5 - - + +
172E ARG* 1.3 91.5 + - - +
174E GLU* 3.1 10.0 + - - +
175E ILE* 3.0 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E GLN* 2.8 57.5 + - - +
160E HIS* 4.3 7.2 - - + +
168E ASP* 3.2 33.1 + - - +
169E GLU* 4.5 4.3 - - - +
170E LEU 3.3 0.4 - - - -
171E LYS* 1.3 94.9 - - - +
173E GLN* 1.3 61.4 + - + +
175E ILE 3.3 1.4 + - - -
176E LEU* 2.9 55.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E PRO* 3.2 45.9 - - + +
143E SER* 4.8 7.3 - - - -
169E GLU* 3.0 26.2 + - - +
170E LEU* 4.2 6.0 - - - +
171E LYS 3.2 0.4 - - - -
172E ARG* 1.3 82.1 + - + +
174E GLU* 1.3 63.3 + - - +
176E LEU* 3.4 20.1 - - + +
177E ILE* 2.9 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E PRO* 6.0 2.6 - - - +
170E LEU* 3.1 35.1 + - + +
171E LYS* 3.1 10.0 + - + +
173E GLN* 1.3 80.8 - - - +
175E ILE* 1.3 66.5 + - + +
177E ILE* 3.1 21.4 + - - +
178E ALA* 3.0 21.3 + - - +
221E SER* 5.1 7.0 - - - -
226E ARG* 5.0 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E GLN* 3.2 39.3 - - - +
160E HIS* 5.1 0.7 - - - +
171E LYS* 3.0 39.7 + - + +
172E ARG 3.6 1.1 - - - +
174E GLU* 1.3 77.4 - - + +
176E LEU* 1.3 55.7 + - - +
178E ALA* 3.3 6.0 + - - +
179E LYS* 2.9 41.8 + - + +
217E SER* 5.0 8.5 - - - +
221E SER* 5.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E ASP* 5.3 7.9 - - - +
156E LYS* 3.6 28.0 - - + +
157E ILE* 5.6 0.2 - - - -
158E GLN* 3.4 39.7 - - + +
172E ARG* 2.9 50.4 + - + +
173E GLN* 3.4 25.4 - - + +
174E GLU 3.1 0.2 - - - -
175E ILE* 1.3 76.7 - - - +
177E ILE* 1.3 57.8 + - + +
179E LYS* 3.3 5.8 + - + +
180E THR* 2.9 28.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
137E ALA* 4.6 20.2 - - + +
138E LEU* 5.7 4.3 - - + -
140E ASN 6.0 1.1 - - - +
142E PRO* 5.3 17.7 - - + +
144E TRP* 6.1 4.0 - - + -
173E GLN* 2.9 20.5 + - + +
174E GLU* 3.4 24.5 - - - +
176E LEU* 1.3 76.0 - - + +
178E ALA* 1.3 66.0 + - - +
180E THR* 3.0 27.9 - - + +
181E PHE* 3.0 10.0 + - + +
226E ARG* 3.7 37.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E GLU 3.0 10.6 + - - +
175E ILE* 3.3 9.6 + - - +
177E ILE* 1.3 76.2 - - - +
179E LYS* 1.3 58.3 + - - +
182E ASN* 3.0 30.0 + - - +
216E GLY 3.9 0.2 - - - +
217E SER* 3.1 28.0 - - - +
220E PHE* 3.2 35.8 + - - +
221E SER* 3.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLU 5.4 1.5 + - - +
156E LYS* 4.4 24.7 - - + +
157E ILE 3.1 26.8 + - - +
158E GLN* 3.6 20.1 - - + +
175E ILE* 2.9 36.3 + - + +
176E LEU* 3.6 7.0 - - + +
178E ALA* 1.3 77.2 - - - +
180E THR* 1.3 56.7 + - - +
182E ASN* 3.5 5.8 + - - +
183E PHE* 2.9 27.0 + - - +
217E SER* 3.8 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E ALA* 4.4 21.3 - - + +
144E TRP* 3.9 10.3 - - - +
156E LYS* 3.2 31.8 + - - +
176E LEU 2.9 15.3 + - - +
177E ILE* 3.0 30.3 - - + +
179E LYS* 1.3 73.7 - - - +
181E PHE* 1.3 68.4 + - + +
183E PHE* 3.0 9.4 + - - +
184E TYR* 3.0 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E CYS* 3.8 15.7 - - + -
137E ALA* 6.1 1.1 - - + -
138E LEU* 3.5 33.7 - - + -
177E ILE* 3.0 16.8 + - + +
178E ALA 4.0 2.5 - - - +
180E THR* 1.3 79.3 - - + +
182E ASN* 1.3 58.2 + - - +
184E TYR* 3.4 5.9 + - - +
185E ASP* 2.9 24.8 + - - +
220E PHE* 3.5 29.8 - + + -
226E ARG* 3.2 36.6 - - + -
229E ALA* 3.3 25.8 - - + -
230E MET* 3.6 19.3 - - + -
233E TYR* 3.9 15.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 182 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E ALA 3.0 18.2 + - - +
179E LYS* 3.6 7.7 + - - +
181E PHE* 1.3 75.3 - - - +
183E PHE* 1.3 68.9 + - - +
185E ASP* 3.6 0.2 - - - +
186E TYR* 2.9 23.7 + - - +
212E TYR* 3.2 28.9 - - - +
213E ASP* 2.8 38.7 + - - +
216E GLY* 3.2 27.6 - - - -
217E SER* 4.0 4.4 + - - +
220E PHE* 3.5 12.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 183 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E PRO 4.8 3.1 - - - -
153E TYR* 3.9 31.2 - + - -
155E GLU* 3.9 42.4 - - + -
156E LYS* 5.4 5.8 - - + -
179E LYS 2.9 16.5 + - - +
180E THR* 3.1 13.0 - - - +
182E ASN* 1.3 81.1 - - - +
184E TYR* 1.3 77.7 + + - +
186E TYR* 3.6 5.8 + - - +
187E MET* 3.0 54.6 + - + +
209E LYS* 6.3 1.3 - - - -
213E ASP* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 184 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ASN* 4.5 7.2 - - - -
131E VAL* 3.8 19.7 - - + +
134E SER* 3.4 47.2 + - - -
135E CYS* 3.8 26.5 - - - -
144E TRP* 4.3 5.3 - + - -
148E ILE* 3.9 8.7 - - - +
153E TYR* 2.7 28.3 + + - -
180E THR* 3.0 40.5 + - - +
181E PHE 4.0 1.1 - - - +
183E PHE* 1.3 86.9 - + - +
185E ASP* 1.3 60.2 + - - +
187E MET* 3.3 27.8 + - + +
188E LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ARG* 3.7 7.0 + - - -
181E PHE 2.9 16.4 + - - +
182E ASN* 3.6 4.7 - - - +
184E TYR* 1.3 76.7 - - - +
186E TYR* 1.3 62.6 + - - +
188E LEU* 3.1 5.2 + - - +
189E PHE* 3.0 38.6 + - - -
212E TYR* 2.6 34.9 + - + -
220E PHE* 3.6 25.4 - - + -
233E TYR* 2.4 35.1 + - - +
255E TYR* 4.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 186 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E ASN 2.9 16.6 + - - +
183E PHE* 3.8 5.2 - - - +
185E ASP* 1.3 76.3 + - - +
187E MET* 1.3 70.9 + - + +
189E PHE* 4.2 0.8 - - - +
190E GLN* 2.9 47.8 + - + +
205E PHE* 3.2 39.2 + + + -
206E ASN* 3.5 19.2 + - - -
209E LYS* 3.5 45.8 - - + +
212E TYR* 3.5 41.0 - + + -
213E ASP* 4.2 9.2 - - - +
76F GLU 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 187 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E ILE* 5.7 1.8 - - + +
130E ASN* 4.2 19.1 - - - +
131E VAL* 4.6 7.4 - - + -
183E PHE* 3.0 47.3 + - + +
184E TYR* 3.4 23.8 - - + +
186E TYR* 1.3 82.1 - - + +
188E LEU* 1.3 61.4 + - - +
190E GLN* 5.0 1.3 - - - -
191E ARG* 2.9 76.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E MET* 4.4 1.8 - - + -
127E ILE* 5.9 2.7 - - - -
128E MET* 4.7 18.8 - - + +
131E VAL* 3.7 30.5 - - + +
184E TYR 2.9 13.8 + - - +
185E ASP* 3.1 10.7 + - - +
187E MET* 1.3 76.6 - - - +
189E PHE* 1.3 88.2 + - + +
191E ARG* 4.1 1.9 - - - +
192E LEU* 2.9 49.9 + - + +
233E TYR* 3.5 36.8 - - + -
236E LEU* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E ARG* 3.6 35.2 - - + -
109E SER* 3.6 21.1 - - - -
112E PHE* 3.7 8.6 - + - -
113E MET* 3.6 21.5 - - + -
185E ASP* 3.0 32.1 + - - +
186E TYR 4.2 1.6 - - - +
188E LEU* 1.3 93.2 - - + +
190E GLN* 1.3 57.9 + - - +
192E LEU* 3.6 1.7 + - - -
193E ALA* 2.9 29.0 + - - +
205E PHE* 3.4 22.9 - + + -
212E TYR* 3.1 23.8 - - + +
232E PHE* 3.7 28.3 - + - -
233E TYR* 4.7 1.8 - + - -
255E TYR* 4.8 3.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E TYR* 2.9 48.6 + - + +
187E MET* 4.3 1.9 - - - +
189E PHE* 1.3 75.4 - - - +
191E ARG* 1.3 76.5 + - - +
193E ALA* 2.9 21.2 + - - +
194E PHE* 3.0 35.0 + - + -
202E GLY* 4.2 6.1 - - - +
205E PHE* 3.7 19.2 - - + -
206E ASN* 3.0 24.5 + - - -
76F GLU* 3.3 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E ILE* 3.6 36.9 - - + +
187E MET* 2.9 66.3 + - - +
188E LEU* 5.1 0.2 - - - -
190E GLN* 1.3 89.2 + - - +
192E LEU* 1.3 61.0 + - - +
194E PHE* 3.4 4.1 + - - +
195E HIS* 2.8 36.7 + - + +
76F GLU* 5.7 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E PHE* 3.6 13.6 - - + +
113E MET* 4.1 19.7 - - + -
116E ALA* 3.6 23.4 - - + +
117E PHE* 4.1 10.8 - - + -
124E ALA* 3.7 31.0 - - + -
127E ILE* 3.8 16.4 - - + -
128E MET* 4.0 24.9 - - + -
188E LEU* 2.9 41.7 + - + +
189E PHE* 3.9 3.8 - - - +
191E ARG* 1.3 78.0 - - - +
193E ALA* 1.3 60.9 + - - +
195E HIS* 3.5 10.7 + - + +
196E SER 3.8 1.4 + - - -
236E LEU* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E PHE* 3.4 16.2 - - + -
189E PHE 2.9 19.2 + - - +
190E GLN 2.9 7.9 + - - +
192E LEU* 1.3 78.3 - - - +
194E PHE* 1.3 55.3 + - - +
195E HIS 3.5 0.2 - - - -
196E SER* 2.9 18.3 + - - -
198E ASN 3.6 1.6 - - - +
201E TYR* 3.4 36.4 - - + +
202E GLY* 3.6 6.4 + - - +
205E PHE* 3.7 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E GLN* 3.0 35.5 + - - +
191E ARG* 4.0 6.3 - - - +
192E LEU 3.2 0.2 - - - -
193E ALA* 1.3 76.1 - - - +
195E HIS* 1.3 62.5 + - + +
196E SER 3.0 9.6 + - - -
197E GLY* 3.5 10.9 + - - -
198E ASN 4.5 3.8 + - - +
199E GLN* 3.6 34.1 - - + -
202E GLY* 3.5 19.3 - - - -
203E LEU* 3.8 12.8 - - + -
206E ASN* 3.1 28.3 - - - -
75F MET* 3.1 28.7 - - + -
76F GLU* 4.2 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E TYR 4.6 0.2 - - - +
116E ALA* 3.2 24.4 - - + -
119E LEU* 4.8 1.0 - - - +
120E ASN* 3.6 36.8 + - + +
123E SER* 3.5 37.0 + - - -
124E ALA* 5.5 1.1 - - - +
126E ARG* 5.1 6.2 + - - -
127E ILE* 4.7 15.3 - - + -
191E ARG* 2.8 29.8 + - + +
192E LEU* 3.5 8.8 + - + +
194E PHE* 1.3 80.9 - - + +
196E SER* 1.3 58.6 + - - +
197E GLY 3.3 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