Contacts of the helix formed by residues 201 - 216 (chain F) in PDB entry 6G2T
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 THR 201 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F ARG* 4.7 20.8 + - - +
62F GLY 6.1 0.4 - - - +
64F LEU 6.1 0.2 - - - +
189F MET* 5.4 0.6 - - - +
199F PHE 3.6 0.9 - - - -
200F THR* 1.3 88.7 + - - +
202F THR* 1.3 58.5 + - - +
203F ALA* 3.2 15.9 - - + +
204F GLU* 2.9 28.4 + - - +
205F ARG* 2.8 35.2 + - - +
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Residues in contact with THR 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F THR* 4.9 6.6 + - - -
66F LEU* 3.1 50.5 + - + +
68F TYR* 5.4 3.4 - - + -
200F THR 4.4 0.2 + - - -
201F THR* 1.3 77.1 - - - +
203F ALA* 1.3 63.6 + - - +
205F ARG* 3.1 36.4 + - + +
206F GLU* 3.3 15.2 + - + +
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Residues in contact with ALA 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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61F ARG* 3.1 62.4 - - + +
62F GLY* 4.4 8.1 - - - +
64F LEU 4.5 5.9 + - - +
66F LEU* 4.9 4.9 - - - +
201F THR* 3.2 14.2 - - + +
202F THR* 1.3 80.6 - - - +
204F GLU* 1.3 63.3 + - - +
206F GLU* 3.8 5.0 + - - +
207F ILE* 3.7 4.9 + - - +
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Residues in contact with GLU 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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198F SER 5.2 0.2 - - - +
199F PHE* 3.5 40.2 - - + -
200F THR* 3.4 7.4 + - - -
201F THR* 2.9 48.3 + - - +
203F ALA* 1.3 74.9 - - - +
205F ARG* 1.3 64.5 + - - +
206F GLU 3.2 2.5 - - - -
207F ILE* 3.1 31.1 + - + +
208F VAL* 3.4 10.7 + - - +
241F LEU* 5.9 2.9 - - + -
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Residues in contact with ARG 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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68F TYR* 3.7 29.7 + - - -
182F ARG* 3.2 52.0 + - - +
185F THR* 3.7 13.7 - - + +
186F ASP* 2.9 30.1 + - - -
189F MET* 4.1 28.1 - - + -
199F PHE* 5.3 1.6 - - - -
201F THR 2.8 15.8 + - - +
202F THR* 3.1 29.5 + - - +
204F GLU* 1.3 77.9 - - - +
206F GLU* 1.3 57.1 + - + +
208F VAL* 2.9 30.3 - - - +
209F ARG 3.6 1.2 + - - -
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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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33F ILE* 3.6 15.2 - - - +
58F GLN* 2.9 31.9 + - - +
61F ARG* 4.0 7.2 + - - +
66F LEU* 3.2 32.8 - - - +
68F TYR* 3.1 32.0 + - + +
185F THR* 5.8 0.2 - - - -
202F THR* 3.3 9.5 + - + +
203F ALA 4.0 6.7 - - - +
204F GLU 3.2 0.2 - - - -
205F ARG* 1.3 76.9 - - + +
207F ILE* 1.3 60.1 + - - +
209F ARG* 3.0 26.5 + - - +
210F ASP* 2.9 25.8 + - - +
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Residues in contact with ILE 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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61F ARG* 3.2 35.7 - - - +
199F PHE* 5.5 2.9 - - + -
203F ALA 3.7 3.4 - - - +
204F GLU* 3.1 33.8 + - + +
206F GLU* 1.3 77.5 - - - +
208F VAL* 1.3 59.5 + - - +
210F ASP* 3.1 12.9 + - + +
211F ILE* 3.0 23.4 + - + +
239F TYR* 4.0 15.3 - - + +
241F LEU* 3.5 32.5 - - + -
242F PRO* 4.3 18.8 - - + -
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Residues in contact with VAL 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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185F THR* 3.5 26.0 - - + +
188F LEU* 3.6 16.1 - - + +
189F MET* 4.4 14.8 - - + -
192F LEU* 4.1 13.2 - - + -
199F PHE* 3.4 38.8 - - + -
204F GLU 3.4 2.6 + - - +
205F ARG* 2.9 26.0 - - - +
207F ILE* 1.3 77.6 - - - +
209F ARG* 1.3 53.2 + - - +
211F ILE* 3.1 14.0 + - + +
212F LYS* 2.7 35.0 + - - +
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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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14F GLY* 5.3 5.9 + - - -
15F MET* 5.2 13.5 - - - +
31F PRO* 4.7 12.3 - - - +
58F GLN* 4.5 18.2 + - - +
68F TYR* 3.9 19.7 + - - -
156F ASP* 4.4 16.5 + - - -
182F ARG* 6.4 0.4 - - - +
185F THR* 4.1 13.5 - - + +
205F ARG 4.2 1.6 - - - +
206F GLU* 3.0 37.7 + - - +
208F VAL* 1.3 84.5 - - - +
210F ASP* 1.3 57.0 + - - +
212F LYS* 3.2 24.7 + - - +
213F GLU* 2.9 62.7 + - + +
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Residues in contact with ASP 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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206F GLU 2.9 11.3 + - - +
207F ILE* 3.1 17.9 + - + +
209F ARG* 1.3 77.6 - - - +
211F ILE* 1.3 62.4 + - - +
213F GLU* 3.4 23.3 + - - +
214F LYS* 2.8 27.9 + - - +
239F TYR* 3.5 17.7 + - - +
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Residues in contact with ILE 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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188F LEU* 4.9 8.7 - - + -
192F LEU* 5.4 4.7 - - + -
199F PHE* 5.2 4.9 - - + -
207F ILE* 3.0 24.7 + - + +
208F VAL* 3.1 23.6 - - + +
210F ASP* 1.3 77.9 - - - +
212F LYS* 1.3 55.5 + - - +
214F LYS* 4.3 0.4 - - - +
215F LEU* 2.8 63.1 + - + +
216F CYS 5.7 0.2 - - - +
239F TYR* 3.5 42.0 - - + -
241F LEU* 5.1 2.9 - - + -
247F ILE* 5.4 8.7 - - + -
249F ILE* 4.6 13.9 - - + -
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Residues in contact with LYS 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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156F ASP* 5.4 1.4 + - - -
181F GLY* 2.7 40.2 + - - -
184F LEU* 4.3 13.5 - - + -
185F THR* 2.8 19.6 + - - +
188F LEU* 3.9 18.8 - - + -
208F VAL 2.7 16.4 + - - +
209F ARG* 3.3 24.4 - - - +
211F ILE* 1.3 72.9 - - - +
213F GLU* 1.3 69.1 + - - +
214F LYS 3.3 0.5 + - - -
216F CYS* 2.7 43.2 + - - +
256F CYS* 5.2 4.3 - - - -
302F THR* 4.4 3.9 - - - +
305F TYR* 3.1 26.1 + - + +
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Residues in contact with GLU 213 (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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15F MET* 5.3 5.9 - - - +
209F ARG* 2.9 55.0 + - + +
210F ASP* 3.7 15.2 - - - +
211F ILE 3.3 0.8 - - - -
212F LYS* 1.3 82.2 - - - +
214F LYS* 1.3 60.1 + - + +
216F CYS 5.0 1.0 - - - +
304F MET* 5.4 6.8 - - - +
305F TYR* 4.5 17.1 - - + -
306F PRO* 5.7 2.3 - - - +
335F LYS* 5.3 11.2 + - - +
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Residues in contact with LYS 214 (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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210F ASP* 2.8 35.9 + - - +
211F ILE* 4.1 1.1 - - - +
212F LYS 3.3 0.2 - - - -
213F GLU* 1.3 81.0 - - + +
215F LEU* 1.3 76.3 + - + +
216F CYS 3.6 6.2 - - - +
237F LYS* 5.7 1.9 + - - -
239F TYR* 3.2 35.3 - - - -
306F PRO* 5.6 4.2 - - - +
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Residues in contact with LEU 215 (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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211F ILE* 2.8 41.2 + - + +
214F LYS* 1.3 86.3 - - + +
216F CYS* 1.3 60.6 + - - +
217F TYR* 3.9 3.8 + - - -
237F LYS* 3.6 32.3 - - + +
238F SER 5.0 4.0 - - - +
239F TYR* 3.4 41.3 - - + -
249F ILE* 4.7 11.4 - - + -
253F ARG* 3.4 46.2 + - - +
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Residues in contact with CYS 216 (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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188F LEU* 6.0 2.9 - - + -
211F ILE* 3.8 1.2 + - - +
212F LYS* 2.7 56.2 + - - +
213F GLU 5.0 0.7 - - - +
214F LYS 3.6 6.8 - - - +
215F LEU* 1.3 82.6 - - - +
217F TYR* 1.3 62.1 + - - +
253F ARG* 3.4 31.6 - - + +
256F CYS* 5.4 2.0 - - + -
257F PRO* 3.9 16.4 - - + -
305F TYR* 4.0 14.1 - - - +
306F PRO* 3.8 13.5 - - - +
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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
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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