Contacts of the helix formed by residues 196 - 214 (chain F) in PDB entry 5N9G
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 196 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183F PHE* 4.5 0.4 - - - -
195F GLU* 1.4 79.6 + - - +
197F LYS* 1.3 69.2 + - - +
198F GLU* 3.5 11.7 + - - +
199F LYS* 3.1 47.5 + - + +
200F MET* 3.1 23.4 + - - +
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Residues in contact with LYS 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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178F SER* 3.5 42.6 + - - +
183F PHE* 3.7 47.0 - - + +
195F GLU 3.5 3.6 + - - -
196F ASP* 1.3 76.0 + - - +
198F GLU* 1.3 62.1 + - + +
200F MET* 3.5 1.9 + - - +
201F LEU* 3.0 47.5 + - + +
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Residues in contact with GLU 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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196F ASP* 3.4 12.2 + - - +
197F LYS* 1.3 81.0 - - + +
199F LYS* 1.4 59.1 + - + +
201F LEU* 3.2 30.0 + - - +
202F SER* 2.9 32.8 + - - -
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Residues in contact with LYS 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 GLU* 3.9 14.4 - - - +
196F ASP* 3.1 36.9 + - + +
198F GLU* 1.4 74.1 - - - +
200F MET* 1.3 61.4 + - - +
202F SER* 3.7 5.4 + - - -
203F ARG* 3.2 24.1 + - - +
237F LEU* 3.9 22.5 - - + +
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Residues in contact with MET 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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177F CYS* 4.5 11.9 - - + +
180F PHE* 4.5 7.2 - - + -
182F LEU* 4.1 16.4 - - + -
183F PHE* 4.1 24.2 - - + -
195F GLU* 4.2 10.1 - - + -
196F ASP 3.1 17.9 + - - +
197F LYS* 3.9 3.1 - - - +
199F LYS* 1.3 74.1 - - - +
201F LEU* 1.4 61.4 + - + +
203F ARG* 3.5 0.4 + - - -
204F THR* 2.9 32.0 + - - +
230F THR* 3.3 22.4 - - - +
233F ALA* 3.8 4.2 - - + +
234F TRP* 3.7 51.6 - - + +
237F LEU* 3.8 8.9 - - + +
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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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173F VAL* 3.9 7.9 - - + +
174F LYS* 3.8 33.0 - - + +
177F CYS* 3.7 28.5 - - + -
178F SER* 4.6 5.8 - - - +
183F PHE* 6.2 0.9 - - + -
197F LYS* 3.0 36.9 + - + +
198F GLU* 3.2 31.2 + - - +
200F MET* 1.4 74.8 - - + +
202F SER* 1.4 53.9 + - - +
204F THR* 3.2 7.2 - - - +
205F MET* 2.9 36.1 + - - +
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Residues in contact with SER 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 GLU 2.9 17.7 + - - -
199F LYS* 3.9 6.1 - - - -
201F LEU* 1.4 74.6 - - - +
203F ARG* 1.3 59.0 + - - +
205F MET* 3.7 6.2 + - - +
206F GLN* 3.1 42.2 + - - +
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Residues in contact with ARG 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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199F LYS 3.2 17.6 + - - +
200F MET* 4.7 0.4 - - - -
201F LEU 3.2 0.2 - - - -
202F SER* 1.3 75.4 + - - +
204F THR* 1.3 59.9 + - - +
206F GLN* 2.9 13.0 + - - +
207F LEU* 2.8 34.1 + - + +
233F ALA* 3.7 20.4 - - + +
236F SER* 2.7 48.6 + - - -
237F LEU* 3.4 27.9 - - + +
297F ILE* 3.9 1.6 - - - +
298F GLY* 3.1 40.9 - - - +
301F LEU* 3.6 21.3 - - + -
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Residues in contact with THR 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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173F VAL* 3.8 5.4 - - + +
177F CYS* 3.7 22.7 - - + -
200F MET 2.9 29.8 + - - +
201F LEU* 3.2 18.8 - - - +
203F ARG* 1.3 73.9 - - - +
205F MET* 1.3 51.7 + - - +
207F LEU* 3.1 2.8 + - - +
208F VAL* 2.8 44.7 + - - +
226F ILE* 3.9 6.4 + - - +
229F ALA* 3.5 9.3 - - - +
230F THR* 3.2 36.3 + - - +
233F ALA* 3.5 5.8 - - - +
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Residues in contact with MET 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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169F LEU* 4.6 4.3 - - + -
170F ALA* 3.5 44.2 - - + +
173F VAL* 4.0 19.1 - - + -
174F LYS* 6.3 0.7 - - - -
201F LEU 2.9 18.5 + - - +
202F SER* 3.8 7.9 - - - +
204F THR* 1.3 77.9 - - - +
206F GLN* 1.4 57.1 + - + +
208F VAL* 3.3 15.2 + - + -
209F GLU* 2.9 57.8 + - + +
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Residues in contact with GLN 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 SER* 3.1 30.7 + - - +
203F ARG* 2.9 14.2 + - - +
205F MET* 1.4 73.4 - - + +
207F LEU* 1.3 60.4 + - - +
209F GLU* 3.5 14.2 + - - +
210F LEU* 3.0 27.0 + - - +
301F LEU* 3.6 43.9 - - + +
302F GLN* 5.3 0.5 - - - -
304F ARG* 3.8 20.5 + - - +
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Residues in contact with LEU 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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203F ARG* 2.8 22.9 + - + +
204F THR 3.1 6.0 + - - +
206F GLN* 1.3 76.9 - - - +
208F VAL* 1.4 55.4 + - - +
210F LEU* 3.1 7.5 + - + +
211F ALA* 2.9 28.6 + - - +
229F ALA* 3.7 18.4 - - + +
232F LEU* 3.9 29.6 - - + -
233F ALA* 3.8 31.2 - - - +
269F LEU* 3.9 17.5 - - + +
273F LEU* 4.2 17.5 - - + -
297F ILE* 4.1 12.6 - - + -
301F LEU* 3.8 20.4 - - + -
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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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169F LEU* 4.1 31.2 - - + -
173F VAL* 3.8 25.4 - - + -
204F THR* 2.8 33.1 + - - +
205F MET* 3.7 12.6 - - + +
207F LEU* 1.4 68.4 - - - +
209F GLU* 1.3 60.0 + - - +
211F ALA* 3.3 7.6 + - - +
212F ASN* 2.9 28.2 + - + +
217F VAL* 4.2 2.8 - - + +
225F VAL* 4.3 12.1 - - + +
226F ILE* 4.3 11.0 - - + -
229F ALA* 3.5 18.4 - - + -
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Residues in contact with GLU 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 MET* 2.9 47.1 + - + +
206F GLN* 3.6 13.8 - - - +
208F VAL* 1.3 73.9 - - - +
210F LEU* 1.4 57.1 + - - +
212F ASN* 3.1 9.1 + - - +
213F GLU* 2.9 39.0 + - - +
304F ARG* 2.9 36.3 + - - +
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Residues in contact with LEU 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 GLN 3.0 15.2 + - - +
207F LEU* 3.3 11.7 - - + +
209F GLU* 1.4 72.6 - - - +
211F ALA* 1.3 56.4 + - - +
213F GLU* 3.3 8.0 + - - +
214F THR* 2.7 38.5 + - + +
269F LEU* 4.3 8.3 - - + -
272F VAL* 4.0 7.9 - - + -
273F LEU* 3.6 33.9 - - + -
276F MET* 3.7 19.5 - - + -
301F LEU* 4.0 15.7 - - + -
304F ARG* 4.4 8.2 - - + +
308F VAL* 3.5 32.3 - - + -
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Residues in contact with ALA 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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207F LEU 2.9 12.3 + - - +
208F VAL* 3.6 8.3 - - - +
210F LEU* 1.3 75.6 - - - +
212F ASN* 1.3 58.2 + - - +
214F THR* 3.5 6.8 + - - -
215F TRP 3.3 4.0 + - - -
216F LEU* 2.8 52.2 + - + +
217F VAL* 3.9 2.7 - - + -
225F VAL* 3.6 27.1 - - + -
269F LEU* 4.1 9.3 - - + +
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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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169F LEU* 4.8 14.4 - - + +
208F VAL* 2.9 14.1 + - + +
209F GLU* 3.1 12.6 + - - +
211F ALA* 1.3 76.4 - - - +
213F GLU* 1.3 57.1 + - + +
214F THR 3.3 0.7 + - - -
215F TRP* 3.4 6.9 + - - -
217F VAL* 3.6 20.0 + - + +
218F THR* 4.8 0.5 + - - -
269G ARG* 2.7 33.9 + - - -
271G GLU* 3.3 27.0 - - - +
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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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209F GLU* 2.9 22.0 + - - +
210F LEU* 3.7 5.9 - - - +
212F ASN* 1.3 76.3 - - + +
214F THR* 1.4 61.5 + - + +
215F TRP 3.4 0.7 - - - -
304F ARG* 2.7 36.2 + - - +
305F GLN* 4.5 14.5 + - - +
308F VAL* 4.3 23.3 - - + +
357F LEU* 3.5 15.1 - - - +
269G ARG* 3.0 22.2 + - - +
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Residues in contact with THR 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 LEU* 2.7 32.3 + - + +
211F ALA* 3.5 7.6 + - - -
212F ASN 3.3 0.4 - - - -
213F GLU* 1.4 75.3 - - - +
215F TRP* 1.4 70.6 + - - +
216F LEU* 3.4 14.5 + - - +
272F VAL* 3.7 38.9 - - + +
308F VAL* 4.0 16.4 - - + -
312F PHE* 4.6 2.2 - - + -
357F LEU* 3.6 27.1 - - + +
358F LEU 4.5 5.2 - - - +
360F PRO* 5.1 0.2 - - - +
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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
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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