Contacts of the helix formed by residues 172 - 197 (chain L) in PDB entry 5FUR
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 TYR 172 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237J ALA* 3.1 36.8 - - + +
238J LYS* 3.5 11.8 + - + +
241J GLU* 2.8 63.3 + - + +
173L GLN* 1.3 71.0 + - + +
174L VAL* 3.2 5.8 - - - +
175L LEU* 3.1 10.6 + - - +
176L ARG* 3.0 38.1 + - - +
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Residues in contact with GLN 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L TYR* 1.3 76.2 - - + +
174L VAL* 1.3 66.7 + - + +
176L ARG* 3.1 20.4 + - - +
177L GLU* 3.0 22.1 + - - +
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Residues in contact with VAL 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837I LEU* 3.5 51.4 - - + +
838I ASN* 4.5 7.4 - - - +
172L TYR 3.2 3.9 - - - +
173L GLN* 1.3 78.6 - - + +
175L LEU* 1.3 64.5 + - - +
177L GLU* 3.1 9.5 + - - +
178L LYS* 3.0 20.5 + - + +
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Residues in contact with LEU 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838I ASN* 5.0 0.9 - - - -
223J TYR* 3.1 30.2 - - + -
226J GLU* 2.7 36.6 - - + +
227J ILE* 5.3 10.3 - - + -
238J LYS* 2.5 34.8 - - - +
241J GLU* 2.6 22.9 - - - +
245J SER* 5.2 12.3 - - - +
172L TYR* 3.1 13.4 + - - +
174L VAL* 1.3 79.2 - - - +
176L ARG* 1.3 64.4 + - + +
178L LYS* 3.1 1.0 + - - -
179L ALA* 3.0 21.7 + - + +
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Residues in contact with ARG 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241J GLU* 5.5 9.8 - - + +
244J GLN* 4.9 16.7 - - - +
245J SER* 6.3 3.1 - - - -
249J ASP* 4.3 6.1 - - - +
172L TYR* 3.0 30.3 + - - +
173L GLN* 3.1 19.4 + - - +
175L LEU* 1.3 77.7 - - + +
177L GLU* 1.3 63.2 + - - +
179L ALA* 3.1 9.1 + - - +
180L ALA* 3.0 22.4 + - - +
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Residues in contact with GLU 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831I GLU* 5.5 7.7 - - + +
834I THR* 4.1 15.6 + - - -
835I ARG 5.3 1.0 - - - +
837I LEU* 3.3 30.1 - - - +
173L GLN 3.0 12.2 + - - +
174L VAL* 3.3 10.0 - - - +
176L ARG* 1.3 76.0 - - - +
178L LYS* 1.3 62.9 + - - +
180L ALA* 3.1 9.1 + - + +
181L SER* 3.0 29.1 + - - +
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Residues in contact with LYS 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836I PHE* 6.1 5.8 - - + -
837I LEU* 6.1 1.1 - - + +
838I ASN* 0.8 69.4 - - + +
219J GLU* 4.9 2.7 - - + +
222J LEU* 2.3 49.5 - - - +
223J TYR* 0.6 201.7 + - + +
226J GLU* 1.7 27.2 + - - +
174L VAL* 3.0 12.0 + - + +
175L LEU 3.1 2.4 + - - +
177L GLU* 1.3 76.6 - - - +
179L ALA* 1.3 57.3 + - - +
181L SER* 3.1 10.3 + - - -
182L GLN* 3.0 25.4 + - + +
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Residues in contact with ALA 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223J TYR* 2.3 27.9 - - + -
227J ILE* 6.4 0.9 - - + -
245J SER* 4.9 4.0 - - - +
249J ASP* 2.6 36.6 - - + +
252J LEU* 5.9 2.5 - - + -
175L LEU* 3.0 9.4 + - + +
176L ARG* 3.1 9.8 + - - +
178L LYS* 1.3 73.3 - - - +
180L ALA* 1.3 60.9 + - - +
182L GLN* 3.1 6.3 + - - +
183L ARG* 3.0 25.1 + - - +
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Residues in contact with ALA 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827I ARG* 4.4 20.0 - - - +
249J ASP* 3.9 1.7 + - - +
250J PRO* 5.8 0.9 - - - -
176L ARG 3.0 11.7 + - - +
177L GLU* 3.4 12.3 - - + +
179L ALA* 1.3 75.7 - - - +
181L SER* 1.3 63.3 + - - +
183L ARG* 3.1 15.0 + - - +
184L ARG* 3.0 31.6 + - - +
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Residues in contact with SER 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783I ASP* 5.8 0.2 - - - -
831I GLU* 3.5 31.5 + - - +
836I PHE* 4.2 26.4 - - - -
219J GLU* 5.4 1.1 - - - -
177L GLU* 3.0 20.4 + - - +
178L LYS* 3.1 12.7 + - - -
180L ALA* 1.3 75.7 - - - +
182L GLN* 1.3 63.1 + - - +
184L ARG* 3.1 5.3 + - - +
185L ASP* 3.0 28.6 + - - +
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Residues in contact with GLN 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219J GLU* 1.5 61.8 + - + +
220J GLN* 3.5 6.1 - - + +
223J TYR* 1.7 72.9 - - + +
255J MET* 3.8 13.3 - - + +
178L LYS* 3.0 12.7 + - - +
179L ALA* 3.1 6.6 + - - +
181L SER* 1.3 75.4 - - - +
183L ARG* 1.3 64.7 + - + +
185L ASP* 3.1 4.7 + - - +
186L VAL* 3.0 27.6 + - - +
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Residues in contact with ARG 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248J THR 3.2 3.8 + - - -
249J ASP* 0.7 141.8 + - - +
250J PRO* 1.0 118.1 + - + +
251J GLY* 3.3 16.6 - - - -
252J LEU* 4.3 3.7 - - + +
179L ALA 3.0 17.3 + - - +
180L ALA* 3.1 12.3 + - - +
182L GLN* 1.3 76.6 - - + +
184L ARG* 1.3 64.1 + - + +
186L VAL* 3.1 6.1 + - - +
187L GLU* 3.0 21.8 + - - +
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Residues in contact with ARG 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783I ASP* 5.1 0.9 - - - +
827I ARG* 1.9 65.0 - - - +
828I LEU* 3.5 21.5 - - - +
831I GLU* 1.5 65.9 + - - +
180L ALA* 3.0 20.6 + - - +
181L SER* 3.1 7.4 + - - +
183L ARG* 1.3 75.6 - - + +
185L ASP* 1.3 65.0 + - - +
187L GLU* 3.1 14.9 + - - +
188L ARG* 3.0 37.7 + - - +
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Residues in contact with ASP 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783I ASP* 2.1 48.9 - - - +
784I ASN* 4.4 5.7 - - - +
836I PHE* 4.9 5.4 - - - -
219J GLU* 2.9 40.8 - - - +
220J GLN* 5.1 0.7 - - - +
181L SER* 3.0 14.7 + - - +
182L GLN 3.4 8.3 - - - +
184L ARG* 1.3 73.2 - - - +
186L VAL* 1.3 65.2 + - - +
188L ARG* 3.1 11.5 + - - +
189L ALA* 3.0 22.1 + - - +
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Residues in contact with VAL 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220J GLN* 2.8 50.0 - - + +
251J GLY* 3.9 25.6 - - - +
253J TYR* 6.3 0.9 - - + -
254J GLN* 4.8 14.1 - - + +
182L GLN 3.0 17.0 + - - +
183L ARG 3.4 8.3 - - - +
185L ASP* 1.3 74.1 - - - +
187L GLU* 1.3 64.4 + - - +
189L ALA* 3.1 9.3 + - + +
190L LEU* 3.0 22.9 + - + +
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Residues in contact with GLU 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L ARG 3.0 12.2 + - - +
184L ARG* 3.4 17.3 - - - +
186L VAL* 1.3 76.5 - - - +
188L ARG* 1.3 66.0 + - + +
190L LEU* 3.1 12.6 + - + +
191L THR* 3.0 31.2 + - - +
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Residues in contact with ARG 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779I ILE* 4.6 20.6 + - - +
780I LYS* 4.6 9.6 + - - +
782I ASN 2.8 19.4 + - - -
783I ASP* 2.2 55.6 + - - +
784I ASN* 4.1 17.7 - - - +
828I LEU* 5.6 6.7 - - - +
831I GLU* 5.1 11.1 + - - -
832I GLU* 5.2 7.3 + - - +
184L ARG* 3.0 27.8 + - - +
185L ASP* 3.4 10.8 - - - +
187L GLU* 1.3 77.7 - - + +
189L ALA* 1.3 62.0 + - - +
191L THR* 3.1 10.0 + - - -
192L ARG* 3.0 27.8 + - - +
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Residues in contact with ALA 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734I ASN* 6.2 2.2 - - - +
784I ASN* 4.8 4.0 + - - +
220J GLN* 6.1 1.3 - - - +
254J GLN* 6.1 2.2 - - - +
185L ASP 3.0 12.4 + - - +
186L VAL* 3.4 12.6 - - + +
188L ARG* 1.3 75.7 - - - +
190L LEU* 1.3 63.4 + - - +
192L ARG* 3.1 15.1 + - - +
193L PHE* 3.0 22.2 + - - +
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Residues in contact with LEU 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L VAL* 3.0 14.3 + - + +
187L GLU* 3.1 15.0 + - + +
189L ALA* 1.3 74.5 - - - +
191L THR* 1.3 64.5 + - - +
193L PHE* 3.1 19.3 + - + +
194L MET* 3.0 41.5 + - + +
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Residues in contact with THR 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L GLU* 3.0 21.4 + - - +
188L ARG* 3.4 11.8 - - - -
190L LEU* 1.3 75.4 - - - +
192L ARG* 1.3 65.7 + - + +
194L MET* 3.1 15.6 + - + +
195L ALA* 3.0 22.3 + - + +
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Residues in contact with ARG 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729I CYS* 4.3 17.5 + - - +
730I LYS* 4.1 10.1 - - - +
732I CYS 4.3 2.2 + - - -
733I PRO* 2.4 40.4 - - - +
734I ASN* 4.6 10.6 + - - +
780I LYS 3.8 6.9 + - - -
781I TYR* 3.1 21.2 + - - +
784I ASN* 1.6 61.0 + - - +
188L ARG* 3.0 18.6 + - - +
189L ALA* 3.1 14.0 + - - +
191L THR* 1.3 76.9 - - + +
193L PHE* 1.3 63.6 + - - +
195L ALA* 3.1 9.4 + - - +
196L LYS* 3.0 22.2 + - - +
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Residues in contact with PHE 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L ALA 3.0 12.2 + - - +
190L LEU* 3.1 22.0 + - + +
192L ARG* 1.3 76.5 - - - +
194L MET* 1.3 67.0 + - + +
196L LYS* 3.1 17.1 + - + +
197L THR* 3.0 49.0 + - + +
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Residues in contact with MET 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L LEU* 3.0 40.7 + - + +
191L THR* 3.1 14.8 + - + +
193L PHE* 1.3 79.7 - - + +
195L ALA* 1.3 61.8 + - - +
197L THR* 2.2 31.9 + - - +
198L GLY 3.0 4.7 + - - -
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Residues in contact with ALA 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730I LYS* 1.8 48.1 + - - +
191L THR* 3.0 14.0 + - + +
192L ARG* 3.4 9.2 - - - +
194L MET* 1.3 75.0 - - - +
196L LYS* 1.3 63.5 + - - +
198L GLY 3.2 9.2 + - - -
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Residues in contact with LYS 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730I LYS* 3.8 36.8 + - + +
192L ARG 3.0 12.6 + - - +
193L PHE* 3.1 20.2 + - + +
195L ALA* 1.3 77.2 - - - +
197L THR* 1.3 67.0 + - + +
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Residues in contact with THR 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193L PHE* 3.0 45.5 + - + +
194L MET* 2.2 31.3 + - - +
196L LYS* 1.3 79.1 - - + +
198L GLY 1.2 50.2 + - - +
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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
------------------------------------------------------------
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