Contacts of the helix formed by residues 188 - 209 (chain X) in PDB entry 6JM9
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 ALA 188 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X GLU* 3.1 36.1 - - - +
186X GLU* 3.0 12.3 + - - +
187X LYS* 1.3 80.2 - - - +
189X ASP* 1.4 65.5 + - - +
190X ILE 3.5 1.0 + - - -
191X PRO* 3.5 22.8 - - + +
192X ALA* 3.6 13.6 + - - +
500X SAM 3.8 4.7 - - - +
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Residues in contact with ASP 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187X LYS 4.2 7.2 - - - +
188X ALA* 1.4 70.8 - - - +
190X ILE* 1.4 61.6 + - + +
192X ALA* 3.7 4.0 - - - +
193X LYS* 3.0 32.6 + - - +
220X ARG* 4.8 14.6 - - - +
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Residues in contact with ILE 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125X LEU* 4.0 11.2 - - + -
189X ASP* 1.4 78.5 - - + +
191X PRO* 1.3 66.8 - - + +
193X LYS* 3.5 26.5 + - - +
194X TYR* 3.3 37.0 + - + +
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Residues in contact with PRO 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125X LEU* 3.8 17.9 - - + -
134X GLU 5.7 0.9 - - - +
136X TYR* 3.7 33.7 - - + -
165X GLY 3.4 20.2 - - - +
166X VAL* 3.8 4.7 - - + +
186X GLU* 3.9 15.3 - - + +
188X ALA* 3.5 24.9 - - + +
190X ILE* 1.3 92.3 - - + +
192X ALA* 1.4 53.5 + - - +
194X TYR* 3.4 10.5 - - + +
195X ALA* 3.1 19.1 + - - +
500X SAM 4.9 1.8 - - - +
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Residues in contact with ALA 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186X GLU* 3.7 28.7 - - + +
188X ALA 3.6 17.8 + - - +
189X ASP* 3.5 4.0 + - - +
190X ILE 3.4 0.4 - - - -
191X PRO* 1.4 70.9 - - - +
193X LYS* 1.4 66.1 + - - +
194X TYR 3.2 0.7 - - - -
195X ALA* 3.1 23.5 + - - +
196X GLU* 3.5 7.3 + - - +
219X GLU 4.9 0.2 - - - +
220X ARG* 3.8 32.8 + - + +
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Residues in contact with LYS 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189X ASP* 3.0 16.5 + - - +
190X ILE* 3.5 38.7 + - - +
192X ALA* 1.4 76.7 - - - +
194X TYR* 1.4 84.1 + - + +
196X GLU* 3.5 16.5 + - - +
197X THR* 3.6 10.0 + - - +
200X ARG* 5.0 0.3 + - - -
220X ARG* 4.0 23.3 - - - +
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Residues in contact with TYR 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118X SER* 3.4 29.2 - - - +
119X VAL* 3.9 38.1 - - + -
120X THR* 4.3 6.3 + - - -
121X ASP* 4.3 20.8 + - - +
125X LEU* 4.4 12.8 - - + -
166X VAL* 4.3 5.2 - - + -
190X ILE* 3.3 36.7 + - + +
191X PRO* 3.4 12.1 - - + +
193X LYS* 1.4 95.4 + - + +
195X ALA* 1.4 57.7 + - - +
197X THR* 3.1 11.1 + - - -
198X MET* 3.0 30.4 + - + +
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Residues in contact with ALA 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X SER* 5.5 2.2 - - - +
165X GLY 4.1 4.3 - - - +
166X VAL 3.7 25.8 + - - +
167X GLY* 4.5 1.3 - - - +
186X GLU* 5.7 0.7 - - + -
191X PRO 3.1 10.8 + - - +
192X ALA* 3.1 22.3 + - + +
194X TYR* 1.4 74.9 - - - +
196X GLU* 1.4 59.0 + - - +
198X MET* 3.5 0.7 - - - +
199X ASP 3.1 9.0 + - - -
218X LEU* 3.1 40.8 - - + +
219X GLU 5.1 6.1 - - - +
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Residues in contact with GLU 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192X ALA 3.5 7.6 + - - +
193X LYS* 3.7 10.5 - - - +
194X TYR 3.2 1.2 - - - -
195X ALA* 1.4 79.2 - - - +
197X THR* 1.3 58.2 - - - +
199X ASP* 3.6 8.1 + - - +
200X ARG* 3.1 45.4 + - - +
218X LEU 4.2 17.0 - - - +
220X ARG* 3.5 49.7 + - + +
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Residues in contact with THR 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117X HIS 4.7 2.9 - - - +
118X SER* 3.5 28.3 - - - +
193X LYS* 3.6 12.1 + - - +
194X TYR* 3.1 12.4 + - - -
196X GLU* 1.3 71.6 - - - +
198X MET* 1.4 53.6 + - - +
200X ARG* 3.3 24.9 + - + +
201X GLU* 2.9 46.2 + - + +
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Residues in contact with MET 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X LEU* 4.8 5.6 - - + +
114X VAL* 3.6 18.7 - - + +
115X TYR* 3.7 33.2 - - + -
118X SER* 3.3 28.1 + - - +
119X VAL* 5.3 0.2 - - + -
166X VAL* 3.4 27.6 - - + +
168X GLN* 3.9 24.0 - - + -
171X LEU* 3.8 21.5 - - + -
194X TYR* 3.0 15.8 + - + +
195X ALA 3.5 9.4 - - - +
197X THR* 1.4 74.2 - - - +
199X ASP* 1.3 54.7 + - - +
201X GLU* 4.5 0.9 - - - -
202X PHE* 2.9 35.8 + - - +
218X LEU* 4.1 3.8 - - + -
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Residues in contact with ASP 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171X LEU* 4.3 6.5 - - - -
195X ALA 3.1 13.0 + - - +
196X GLU* 3.6 12.1 - - - +
198X MET* 1.3 73.0 - - - +
200X ARG* 1.4 64.4 + - - +
203X ARG* 3.2 34.7 + - - +
216X TYR* 3.2 35.2 - - - +
217X THR* 3.7 6.4 - - - +
218X LEU* 3.5 36.1 + - + +
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Residues in contact with ARG 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X LYS 5.0 0.6 + - - -
196X GLU* 3.1 26.3 + - - +
197X THR* 3.3 42.5 + - + +
199X ASP* 1.4 80.6 - - + +
201X GLU* 1.4 58.7 + - + +
203X ARG* 3.2 12.5 + - - +
204X LYS* 3.1 25.9 + - - +
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Residues in contact with GLU 201 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X VAL* 4.2 9.6 - - + +
117X HIS* 3.2 34.9 + - - +
118X SER* 3.7 17.3 - - - +
197X THR* 2.9 35.8 + - + +
198X MET 4.0 1.1 - - - +
200X ARG* 1.4 71.2 - - + +
202X PHE* 1.3 58.7 + - - +
204X LYS* 3.3 17.4 + - - +
205X TRP* 2.9 44.2 + - + +
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Residues in contact with PHE 202 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X LEU* 4.1 15.7 - - + -
110X ILE* 3.7 22.7 - - + -
111X LEU* 3.9 25.6 - - + -
114X VAL* 4.0 23.2 - - + +
171X LEU* 3.6 46.9 - - + -
175X ALA* 4.2 6.3 - - + -
198X MET 2.9 23.5 + - - +
199X ASP 3.9 2.9 - - - +
201X GLU* 1.3 69.2 - - - +
203X ARG* 1.4 62.6 + - - +
205X TRP 3.8 0.3 - - - -
206X MET* 2.9 60.6 + - + +
213X HIS* 4.9 1.1 - - + -
216X TYR* 3.5 22.0 - + - -
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Residues in contact with ARG 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199X ASP* 3.2 31.1 + - - +
200X ARG* 3.2 11.4 + - - +
202X PHE* 1.4 76.4 - - - +
204X LYS* 1.4 62.4 + - - +
206X MET* 3.4 2.5 + - - +
207X LYS* 3.3 38.1 + - - +
213X HIS* 3.5 27.8 + - + -
215X GLU* 3.6 23.2 - - - +
216X TYR* 3.2 61.8 + - + +
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Residues in contact with LYS 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X ALA* 5.5 3.1 - - + +
16X GLU* 3.9 27.9 + - + +
17X PRO 4.8 5.5 + - - -
18X ALA* 4.8 2.8 - - - +
200X ARG 3.1 13.7 + - - +
201X GLU* 3.3 19.7 + - - +
203X ARG* 1.4 74.6 - - - +
205X TRP* 1.4 97.2 + - + +
207X LYS* 3.4 10.4 + - - +
208X TRP* 3.1 36.7 + - + +
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Residues in contact with TRP 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X ALA* 3.6 29.6 - - + -
20X TYR* 4.4 6.3 - - - -
40X THR* 5.2 2.9 - - + -
110X ILE* 4.2 8.1 - - + -
113X GLN* 4.9 7.2 - - + -
114X VAL* 3.5 26.9 - - + -
117X HIS* 3.4 34.5 + + - -
201X GLU* 2.9 36.3 + - + +
202X PHE 4.1 0.7 - - - +
204X LYS* 1.4 100.3 - - + +
206X MET* 1.4 62.3 + - - +
208X TRP* 3.2 41.0 - + - +
209X TYR* 3.1 69.4 + + - -
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Residues in contact with MET 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X PRO* 4.0 9.9 - - + -
107X LEU* 4.8 0.7 - - + -
110X ILE* 3.8 20.6 - - + -
175X ALA* 3.9 15.9 - - + -
202X PHE* 2.9 61.9 + - + +
203X ARG 3.4 2.0 + - - +
205X TRP* 1.4 69.1 - - - +
207X LYS* 1.4 63.4 + - - +
209X TYR* 3.7 2.5 + - - +
210X GLY 3.3 2.9 + - - -
211X LYS* 3.0 50.5 + - + +
212X LYS 3.4 26.5 - - - +
213X HIS* 3.6 26.2 - - + +
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Residues in contact with LYS 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X VAL* 3.5 12.9 - - - +
15X ALA* 5.2 5.6 - - + -
98X LEU* 3.7 19.3 - - + +
203X ARG* 3.3 27.1 + - - +
204X LYS* 3.7 9.0 - - - +
206X MET* 1.4 76.8 - - - +
208X TRP* 1.4 56.6 + - - +
210X GLY* 2.9 22.2 + - - -
213X HIS* 3.8 27.1 - - + +
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Residues in contact with TRP 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 3.6 24.5 - - + -
10X LYS 3.7 15.9 - - - -
11X SER* 3.2 36.5 + - - -
12X PRO* 3.4 26.0 - - + +
13X VAL* 3.8 3.1 - - - +
15X ALA* 4.2 11.1 - - + +
16X GLU 3.2 27.7 + - - -
17X PRO* 3.9 1.2 - - - +
18X ALA* 3.7 10.4 - - + +
40X THR* 4.2 11.0 - - + -
44X VAL* 4.5 1.6 - - + -
78X TYR* 3.8 12.3 - - - -
204X LYS* 3.1 31.2 + - + +
205X TRP* 3.2 46.9 - + + +
207X LYS* 1.4 74.2 - - - +
209X TYR* 1.4 83.5 + + - +
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Residues in contact with TYR 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X PRO* 4.6 9.7 - - + +
13X VAL* 5.0 0.4 - - - -
40X THR* 3.8 8.5 + - + +
44X VAL* 3.9 15.0 - - + -
47X GLU* 3.0 39.3 - - - +
48X ILE* 6.2 0.2 - - - +
96X MET* 4.2 6.6 - - - +
106X LEU* 4.8 1.8 - - + -
109X HIS* 3.1 30.9 + + - -
110X ILE* 3.5 44.9 - - + -
113X GLN* 3.6 10.8 - - + +
205X TRP* 3.1 57.2 + + - +
206X MET 4.2 3.8 - - - +
208X TRP* 1.4 95.2 - + - +
210X GLY* 1.4 64.2 - - - +
211X LYS* 4.1 4.7 - - + +
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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
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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) + - + + + + + -
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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