Contacts of the helix formed by residues 191 - 212 (chain F) in PDB entry 2VUU
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 191 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154F ASN* 2.6 35.8 + - - +
155F ASN* 5.8 2.7 - - - +
190F LEU* 1.3 77.1 - - - +
192F ALA* 1.3 55.6 + - - +
193F GLU* 4.5 1.6 + - - +
194F HIS* 3.3 9.9 + - + +
195F ASP* 2.7 53.6 + - - +
196F VAL 3.9 0.2 + - - -
220F PHE* 5.4 0.6 - - - -
329F ARG* 2.7 52.1 + - - +
334F TYR* 3.7 10.1 - - - +
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Residues in contact with ALA 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ARG* 3.9 31.4 - - + +
17F GLN 4.9 0.2 - - - +
20F SER* 3.0 14.9 + - - -
153F TYR* 3.9 31.1 - - + +
154F ASN 5.3 0.2 - - - +
155F ASN* 4.8 3.9 + - - +
190F LEU* 3.3 6.8 + - - +
191F ASP* 1.3 71.0 - - - +
193F GLU* 1.3 63.2 + - - +
196F VAL* 3.1 31.7 + - + +
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Residues in contact with GLU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ARG* 4.4 26.2 - - + +
20F SER* 2.9 24.3 + - - -
23F ARG* 3.3 31.9 + - - +
24F VAL* 5.9 1.0 - - - +
43F ILE* 5.2 4.2 - - - +
155F ASN* 4.3 11.6 + - - +
191F ASP* 3.5 1.6 + - - +
192F ALA* 1.3 78.8 - - - +
194F HIS* 1.3 60.7 + - - +
198F PRO* 5.3 0.5 - - - +
329F ARG* 4.8 9.6 + - - +
338F VAL* 5.6 2.8 - - - +
342F GLU* 4.2 14.0 - - - +
708N ARG* 5.7 0.3 + - - -
711N SER* 3.4 19.0 + - - +
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Residues in contact with HIS 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F ASP* 3.3 24.1 + - - +
193F GLU* 1.3 80.9 - - - +
195F ASP* 1.3 79.3 + - - +
198F PRO* 3.5 19.4 - - - +
325F TRP* 4.4 2.9 + + - -
327F GLY 2.9 26.5 - - - -
328F TRP 4.0 0.7 - - - -
329F ARG* 3.5 46.3 - - + +
333F GLU* 4.8 5.7 + - - -
676N CYS* 5.9 0.2 - - - -
696N ALA* 3.6 21.5 - - + +
708N ARG* 3.7 32.4 + - - +
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Residues in contact with ASP 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F LEU* 4.6 1.8 - - + -
191F ASP* 2.7 32.8 + - - +
194F HIS* 1.3 97.8 + - - +
196F VAL* 1.3 63.4 + - - +
197F GLY 3.4 2.2 - - - -
198F PRO* 3.8 3.4 - - - -
199F ALA* 3.3 25.8 + - - +
220F PHE* 3.9 19.9 - - + +
325F TRP* 2.9 26.7 + - + -
328F TRP* 3.0 18.8 - - - +
329F ARG 2.9 18.2 + - - +
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLN* 3.7 36.6 - - + +
20F SER* 3.9 2.7 - - - +
78F PHE* 4.9 1.1 - - + -
190F LEU* 3.9 25.8 - - + -
192F ALA* 3.1 35.9 + - + +
195F ASP* 1.3 74.8 - - - +
197F GLY* 1.3 68.8 + - - +
199F ALA* 3.9 3.5 - - - +
200F LEU* 3.2 39.0 + - + +
218F LEU* 4.5 13.9 - - + -
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Residues in contact with GLY 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F SER* 2.7 25.3 + - - -
21F LEU* 3.5 26.5 - - - +
24F VAL* 4.0 7.0 - - - -
196F VAL* 1.3 75.6 - - - +
198F PRO* 1.3 69.8 - - - +
200F LEU* 3.7 2.1 - - - +
201F LEU* 3.0 22.9 + - - +
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Residues in contact with PRO 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F SER* 4.5 1.1 - - - +
24F VAL* 3.9 19.5 - - + -
193F GLU 5.3 0.4 - - - +
194F HIS 3.5 24.7 - - - +
195F ASP 3.8 3.1 - - - +
197F GLY* 1.3 87.1 - - - +
199F ALA* 1.3 63.3 + - - +
201F LEU* 3.0 10.7 + - + +
202F GLN* 2.9 21.7 + - - +
325F TRP* 3.4 49.4 - - + +
700N PHE* 4.5 11.7 - - + -
704N HIS* 5.3 3.9 + - - +
708N ARG* 5.4 5.2 - - + +
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Residues in contact with ALA 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ASP 3.3 17.7 + - - +
196F VAL 3.9 2.2 - - - +
198F PRO* 1.3 78.5 - - - +
200F LEU* 1.3 64.7 + - - +
202F GLN* 3.0 16.8 + - - +
203F ILE* 3.0 19.4 + - + +
218F LEU* 3.8 28.3 - - + -
220F PHE* 4.2 11.9 - - + -
324F LEU* 4.7 8.1 - - + +
325F TRP* 4.1 11.1 - - + +
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Residues in contact with LEU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU* 4.2 19.7 - - + -
78F PHE* 3.4 46.9 - - + -
109F ILE* 3.7 38.5 - - + +
148F VAL* 4.2 7.4 - - + -
196F VAL* 3.2 30.4 + - + +
197F GLY 3.7 2.5 - - - +
199F ALA* 1.3 78.7 - - - +
201F LEU* 1.3 57.1 + - - +
203F ILE* 3.3 14.1 + - + +
204F PHE* 3.0 37.1 + - + -
218F LEU* 5.0 3.8 - - + -
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Residues in contact with LEU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ILE* 5.3 3.4 - - + -
21F LEU* 4.8 7.2 - - + +
24F VAL* 2.9 39.3 - - + +
25F ALA* 4.5 9.9 - - + +
28F VAL* 4.2 13.9 - - + -
30F HIS* 3.9 30.7 - - + +
197F GLY 3.0 9.7 + - - +
198F PRO* 3.0 10.3 + - + +
200F LEU* 1.3 78.0 - - - +
202F GLN* 1.3 57.0 + - - +
204F PHE* 3.4 9.1 + - + +
205F LYS* 2.9 31.3 + - - +
704N HIS* 3.9 27.8 - - + +
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Residues in contact with GLN 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F PRO 2.9 10.7 + - - +
199F ALA 3.4 8.1 - - - +
201F LEU* 1.3 75.0 - - - +
203F ILE* 1.3 65.9 + - - +
205F LYS* 3.1 36.6 + - - +
206F ASP* 2.9 52.3 + - - +
323F LYS 5.4 0.4 - - - +
324F LEU* 3.2 46.8 - - + +
325F TRP* 6.4 0.2 - - + -
703N LEU* 5.1 9.0 - - - +
704N HIS* 5.0 2.8 + - + -
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Residues in contact with ILE 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F HIS* 3.8 12.9 - - + -
109F ILE* 3.9 15.7 - - + -
146F THR* 4.3 8.1 - - + -
148F VAL* 3.9 28.3 - - + -
199F ALA* 3.0 18.7 + - + +
200F LEU* 3.6 17.5 - - + +
202F GLN* 1.3 75.1 - - - +
204F PHE* 1.3 64.8 + - - +
206F ASP* 3.0 13.7 + - - +
207F GLY 3.2 9.2 + - - -
211F TRP* 3.9 24.7 - - + -
216F ILE* 4.1 12.8 - - + -
218F LEU* 5.5 2.5 - - + -
324F LEU* 3.9 25.4 - - + -
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Residues in contact with PHE 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LYS* 5.9 1.0 + - - -
8F ILE* 4.4 23.1 - - + -
21F LEU* 4.7 8.1 - - + -
30F HIS* 6.2 2.2 - - + -
76F LEU* 3.7 31.2 - - + +
77F ALA 3.4 29.8 - - - -
78F PHE* 4.3 9.4 - - + -
107F HIS* 3.3 40.5 + - + +
109F ILE* 3.4 27.8 - - + -
200F LEU* 3.0 26.9 + - + +
201F LEU* 3.7 10.3 - - + +
203F ILE* 1.3 75.3 - - - +
205F LYS* 1.3 59.4 + - - +
207F GLY* 2.9 21.0 + - - -
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Residues in contact with LYS 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLN* 5.7 8.1 + - - +
201F LEU* 2.9 17.3 + - - +
202F GLN* 3.4 33.4 + - - +
204F PHE* 1.3 75.3 - - - +
206F ASP* 1.3 59.8 + - - +
207F GLY 3.5 0.2 - - - -
209F GLN* 5.6 0.3 + - - -
703N LEU* 4.1 21.2 + - - +
704N HIS* 3.1 39.8 + - - -
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Residues in contact with ASP 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F GLN* 2.9 34.0 + - - -
203F ILE 3.0 3.3 + - - +
205F LYS* 1.3 81.7 - - - +
207F GLY* 1.3 61.3 + - - +
209F GLN* 3.2 22.9 + - - +
210F LYS* 3.6 21.3 + - + +
211F TRP* 2.8 40.7 + - + +
324F LEU* 3.5 14.9 - - - +
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Residues in contact with GLY 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F HIS* 3.7 10.3 - - - -
203F ILE 3.2 3.8 + - - -
204F PHE 2.9 16.1 + - - -
205F LYS 3.5 0.2 - - - -
206F ASP* 1.3 81.2 - - - +
208F PRO* 1.3 67.4 - - - +
209F GLN* 2.9 18.3 + - - -
210F LYS 3.2 7.3 + - - -
211F TRP* 3.3 12.6 + - - +
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Residues in contact with PRO 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E PRO* 3.8 20.2 - - + +
281E GLU* 4.0 6.6 + - - +
106F GLN* 3.8 19.5 - - + +
107F HIS* 3.8 21.9 - - + +
144F PRO* 4.2 8.1 - - + -
207F GLY* 1.3 75.7 - - - +
209F GLN* 1.3 73.0 + - - +
210F LYS 2.9 6.2 - - - -
211F TRP 3.9 0.2 - - - +
212F ASN* 2.9 56.5 + - + +
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Residues in contact with GLN 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E PRO 4.1 11.4 - - - +
281E GLU* 3.7 28.4 - - - +
205F LYS 5.6 0.6 + - - -
206F ASP 3.2 25.7 + - - +
207F GLY* 2.9 4.5 - - - -
208F PRO* 1.3 100.0 - - - +
210F LYS* 1.3 58.0 + - + +
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Residues in contact with LYS 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E HIS* 5.7 1.0 - - - -
206F ASP* 3.6 22.8 + - + +
207F GLY 3.2 4.5 + - - +
208F PRO 2.9 0.2 - - - -
209F GLN* 1.3 83.3 - - + +
211F TRP* 1.3 106.1 + - + +
212F ASN 3.7 1.1 - - - -
214F HIS* 3.4 18.7 + - - -
324F LEU* 5.7 0.2 - - - -
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Residues in contact with TRP 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F HIS* 4.2 1.3 - - + -
146F THR* 3.1 27.1 + - + +
203F ILE* 3.9 17.7 - - + -
206F ASP* 2.8 43.3 + - + -
207F GLY 3.3 9.1 + - - +
208F PRO* 4.3 0.2 - - - -
210F LYS* 1.3 111.3 - - + +
212F ASN* 1.3 64.6 + - - +
214F HIS* 3.0 44.4 + + + +
216F ILE* 3.5 25.1 - - + -
320F GLU* 3.5 40.8 - - + -
324F LEU* 4.0 21.8 - - + +
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Residues in contact with ASN 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ARG* 5.6 0.3 + - - -
213E GLY 5.2 1.7 - - - +
215E ARG* 3.3 17.7 + - - +
279E LEU* 5.6 0.2 - - - +
280E PRO* 4.1 12.9 - - + +
281E GLU* 3.0 39.8 + - - +
143F LEU 4.2 0.7 - - - +
144F PRO* 3.2 8.0 - - - +
145F SER* 2.7 36.7 + - - +
208F PRO* 2.9 37.1 + - + +
210F LYS 3.7 1.0 - - - -
211F TRP* 1.3 75.1 - - - +
213F GLY* 1.3 59.9 + - - +
214F HIS* 3.2 9.2 + - - -
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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