Contacts of the helix formed by residues 192 - 213 (chain F) in PDB entry 1M06
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 192 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184F MET* 4.1 9.3 - - + +
186F ILE* 5.1 0.4 - - - +
187F GLU* 3.9 17.4 + - - +
191F ILE* 1.3 74.0 - - - +
193F ILE* 1.3 57.6 + - - +
194F MET* 2.9 23.4 + - - +
195F GLY* 2.8 38.0 + - - +
196F LEU* 2.9 12.5 + - - +
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Residues in contact with ILE 193 (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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191F ILE* 3.1 19.6 + - + +
192F ASP* 1.3 72.2 + - - +
194F MET* 1.3 71.9 + - + +
196F LEU* 3.6 18.5 + - + +
197F GLN* 3.2 19.2 + - - +
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Residues in contact with MET 194 (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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192F ASP* 2.9 15.2 + - - +
193F ILE* 1.3 84.8 - - + +
195F GLY* 1.3 66.3 + - - +
197F GLN* 3.2 9.7 + - - +
198F ALA* 3.1 19.2 + - - +
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Residues in contact with GLY 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F MET* 3.9 12.3 - - - -
192F ASP* 2.8 21.9 + - - -
194F MET* 1.3 77.5 - - - +
196F LEU* 1.3 54.0 + - - +
198F ALA* 2.9 9.7 + - - +
199F ALA* 2.7 35.0 + - - +
202F GLN* 5.1 0.2 + - - -
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Residues in contact with LEU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F MET* 3.6 27.6 - - + +
191F ILE* 4.4 18.4 - - + -
192F ASP 2.9 11.4 + - - +
193F ILE* 3.6 18.8 - - + +
195F GLY* 1.3 74.7 - - - +
197F GLN* 1.3 64.8 + - - +
199F ALA* 3.2 7.2 + - + +
200F TYR* 3.1 52.1 + - + +
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Residues in contact with GLN 197 (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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193F ILE 3.2 10.9 + - - +
194F MET* 3.2 13.4 + - - +
195F GLY 3.0 0.2 - - - -
196F LEU* 1.3 79.5 - - - +
198F ALA* 1.3 63.3 + - - +
200F TYR* 3.2 24.1 + - - +
201F ALA* 3.2 12.6 + - - +
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Residues in contact with ALA 198 (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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194F MET 3.1 7.6 + - - +
195F GLY* 2.9 11.7 + - - +
197F GLN* 1.3 78.8 - - - +
199F ALA* 1.3 64.7 + - - +
201F ALA* 2.8 10.0 + - - +
202F GLN* 2.8 41.3 + - + +
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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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182F GLU* 4.9 6.6 - - - +
184F MET* 4.0 23.3 - - + -
195F GLY 2.7 15.5 + - - +
196F LEU* 3.2 18.8 - - + +
198F ALA* 1.3 74.7 - - - +
200F TYR* 1.3 57.2 - - + +
202F GLN* 3.5 15.1 + - - +
203F LEU* 2.9 27.2 + - - +
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Residues in contact with TYR 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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196F LEU* 3.1 51.7 + - + +
197F GLN* 3.5 17.0 - - - +
198F ALA 3.1 0.2 - - - -
199F ALA* 1.3 72.3 - - - +
201F ALA* 1.3 57.4 + - - +
203F LEU* 2.9 22.5 + - + +
204F HIS* 2.8 34.8 + - - +
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Residues in contact with ALA 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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197F GLN* 3.2 9.8 + - - +
198F ALA* 2.8 12.9 + - - +
200F TYR* 1.3 79.0 - - - +
202F GLN* 1.3 64.9 + - + +
204F HIS* 3.0 19.2 + - - +
205F THR* 3.0 16.3 + - - +
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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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195F GLY 5.1 0.4 + - - -
198F ALA* 2.8 40.2 + - + +
199F ALA* 3.6 12.7 - - - +
201F ALA* 1.3 73.1 - - + +
203F LEU* 1.3 65.1 + - - +
205F THR* 3.0 25.5 + - - +
206F GLU* 3.0 17.6 + - + +
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Residues in contact with LEU 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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179F LYS* 4.1 15.5 - - + -
182F GLU* 3.4 39.7 + - + +
199F ALA 2.9 14.3 + - - +
200F TYR* 2.9 25.9 + - + +
202F GLN* 1.3 75.2 - - - +
204F HIS* 1.3 65.4 + - - +
206F GLU* 2.7 26.9 + - + +
207F GLN* 2.8 48.1 + - + +
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Residues in contact with HIS 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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200F TYR 2.8 14.5 + - - +
201F ALA* 3.2 14.1 + - - +
203F LEU* 1.3 73.7 - - - +
205F THR* 1.3 66.1 + - - +
207F GLN* 3.2 13.3 + - + +
208F GLU* 3.0 61.3 + - + +
6X 3DR 5.5 1.8 - - - -
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Residues in contact with THR 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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201F ALA 3.0 13.2 - - - +
202F GLN* 3.0 20.0 + - - +
204F HIS* 1.3 80.1 + - + +
206F GLU* 1.3 68.1 + - - +
208F GLU* 3.6 7.1 + - - +
209F ARG* 3.2 50.3 + - - +
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Residues in contact with GLU 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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179F LYS* 3.5 28.3 + - + -
182F GLU* 3.9 15.1 - - - +
202F GLN* 3.0 10.9 + - - +
203F LEU* 2.7 33.6 + - + +
205F THR* 1.3 80.6 + - - +
207F GLN* 1.3 61.0 - - - +
209F ARG* 3.3 9.7 - - - +
210F THR* 3.0 25.9 + - - -
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Residues in contact with GLN 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179F LYS* 5.0 10.6 - - + +
203F LEU* 2.8 57.0 + - + +
204F HIS* 3.7 11.5 - - + +
206F GLU* 1.3 70.0 - - - +
208F GLU* 1.3 69.6 + - - +
210F THR* 2.8 8.2 + - - -
211F TYR* 2.8 60.9 + - + -
326F PRO* 6.0 0.5 - - - +
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Residues in contact with GLU 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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204F HIS* 3.0 46.5 + - + +
205F THR* 3.9 6.6 - - - +
207F GLN* 1.3 77.3 - - - +
209F ARG* 1.3 56.3 + - - +
211F TYR* 4.8 1.1 - - - -
212F PHE* 2.9 57.8 + - + -
213F MET* 3.1 31.3 + - + +
222F SER* 4.6 0.7 + - - -
6X 3DR 3.6 34.3 + - - -
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Residues in contact with ARG 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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205F THR* 3.2 35.6 + - - +
206F GLU* 3.3 12.1 - - - +
207F GLN 2.8 0.4 + - - -
208F GLU* 1.3 80.0 + - - +
210F THR* 1.3 64.5 + - - +
213F MET* 2.9 60.7 + - + +
214F GLN* 3.3 7.3 + - - +
219F VAL* 3.8 29.4 - - + +
223F PHE* 5.3 9.5 - - - -
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Residues in contact with THR 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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175F PRO* 3.4 26.2 - - + +
177F GLU* 4.3 17.5 + - + +
178F THR* 4.1 20.9 - - + +
179F LYS 5.5 0.9 - - - +
206F GLU* 3.0 13.8 + - - +
207F GLN* 2.8 13.6 + - - -
209F ARG* 1.3 73.4 - - - +
211F TYR* 1.3 68.8 + - + +
214F GLN* 2.9 29.7 + - - +
20J GLY* 3.5 1.2 - - - -
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Residues in contact with TYR 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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174F LEU* 4.0 24.5 - - + -
175F PRO* 4.7 4.5 - - + -
178F THR* 3.5 34.1 - - + +
179F LYS 4.6 0.7 + - - -
207F GLN* 2.8 61.4 + - + +
208F GLU* 4.4 1.6 - - - -
210F THR* 1.3 80.5 - - + +
212F PHE* 1.3 79.3 + + + +
326F PRO* 3.8 15.0 - - + +
15J ARG* 5.2 0.2 + - - -
18J TYR* 3.7 14.7 - + + +
19J VAL 3.7 7.1 + - - -
20J GLY 2.7 22.6 + - - -
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Residues in contact with PHE 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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208F GLU* 2.9 44.8 + - + -
210F THR 3.5 0.2 - - - -
211F TYR* 1.3 94.5 - + + +
213F MET* 1.3 74.6 + - + +
214F GLN 3.7 0.3 + - - -
218F ASP* 3.9 4.2 - - - +
15J ARG* 4.4 11.0 - - - +
18J TYR* 4.0 9.4 - + + -
20J GLY 3.3 19.7 - - - +
21J GLY* 4.0 0.6 - - - +
1X 3DR 3.7 33.4 + - - +
6X 3DR 3.2 36.6 - - + -
7X 3DR 2.9 24.5 - - - +
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Residues in contact with MET 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F GLU* 3.1 50.3 + - + +
209F ARG* 2.9 41.3 + - - +
212F PHE* 1.3 95.5 - - + +
214F GLN* 1.3 61.1 + - - +
215F ARG 3.3 2.2 - - - -
218F ASP* 3.9 15.9 - - + +
219F VAL* 3.5 36.0 - - + +
222F SER* 3.2 36.3 - - - +
6X 3DR 4.9 1.6 - - + +
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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