Contacts of the helix formed by residues 209 - 226 (chain L) in PDB entry 5GJQ
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 GLY 209 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K VAL* 3.6 19.9 - - - +
237K GLN* 3.6 8.1 + - - -
207L TYR 2.6 5.5 + - - -
208L ILE* 1.3 81.3 - - - +
210L GLU* 1.3 60.9 + - - -
211L SER 3.1 3.6 - - - -
212L ALA* 3.2 21.0 + - - +
213L ARG* 3.4 13.7 + - - +
256L THR* 6.0 0.9 - - - -
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Residues in contact with GLU 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L ILE 4.2 4.0 - - - +
205L ASP* 2.2 54.5 - - + +
206L LYS 4.4 0.9 - - - +
207L TYR* 2.8 39.2 + - + +
208L ILE 3.5 2.6 + - - -
209L GLY* 1.3 75.8 - - - +
211L SER* 1.3 58.6 + - - +
213L ARG* 2.5 38.2 + - - +
214L LEU* 3.8 21.6 + - + +
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Residues in contact with SER 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L ILE* 3.0 27.1 + - - +
204L VAL* 3.1 19.5 - - - +
205L ASP 4.0 2.1 + - - -
208L ILE 5.3 0.2 + - - -
209L GLY* 3.1 0.6 - - - -
210L GLU* 1.3 78.7 - - - +
212L ALA* 1.3 60.8 + - - +
213L ARG 3.5 0.2 - - - -
214L LEU 4.2 1.3 - - - -
215L ILE* 3.3 30.1 + - - +
253L ILE* 5.1 2.8 - - - +
256L THR* 3.2 35.9 - - - +
261M ILE* 5.8 0.5 - - - +
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Residues in contact with ALA 212 (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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233K SER 3.8 12.6 - - - +
234K GLU* 5.7 0.2 - - - -
236K VAL 5.3 2.2 - - - +
209L GLY* 3.2 18.8 + - - +
211L SER* 1.3 78.2 - - - +
213L ARG* 1.3 56.3 + - - +
215L ILE* 3.6 1.0 + - - +
216L ARG* 2.7 45.8 + - - +
256L THR* 4.3 3.5 + - - +
259L GLU* 3.3 32.7 - - + +
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Residues in contact with ARG 213 (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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238K LYS* 5.7 10.1 - - - +
116L ASP* 3.9 28.3 + - - -
209L GLY 3.4 11.7 + - - +
210L GLU* 2.5 33.8 + - - +
212L ALA* 1.3 77.5 - - - +
214L LEU* 1.3 69.3 + - - +
216L ARG* 3.2 9.3 + - + +
217L GLU* 2.8 47.9 + - + +
125M LYS* 5.1 11.3 - - - +
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Residues in contact with LEU 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L ASP* 6.3 1.6 - - + -
118L LEU* 4.7 19.1 - - + -
119L VAL* 4.7 9.4 - - + -
122L MET* 3.9 26.2 - - + -
202L SER 4.2 5.2 - - - +
203L ILE* 3.4 52.7 - - + +
205L ASP* 6.0 2.0 - - - +
210L GLU* 3.8 17.2 + - + +
211L SER 4.5 0.2 - - - +
212L ALA 3.5 0.2 - - - -
213L ARG* 1.3 87.4 - - - +
215L ILE* 1.3 63.2 + - - +
217L GLU* 3.5 6.3 + - + +
218L MET* 3.0 29.5 + - + +
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Residues in contact with ILE 215 (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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203L ILE* 4.4 8.3 - - + -
211L SER 3.3 21.3 + - - +
212L ALA 3.9 3.1 - - - +
213L ARG 3.2 0.2 - - - -
214L LEU* 1.3 76.7 - - - +
216L ARG* 1.3 65.2 - - - +
218L MET* 3.2 16.0 + - + -
219L PHE* 3.0 44.7 + - + -
238L ILE* 5.2 0.4 - - + -
256L THR* 3.2 28.9 - - + +
259L GLU* 3.9 9.9 - - + -
260L LEU* 2.6 56.3 - - + +
263L GLN* 4.0 7.4 - - - +
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Residues in contact with ARG 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K VAL* 4.7 8.1 - - - +
233K SER* 3.1 18.3 + - - -
234K GLU* 3.2 43.4 + - - +
237K GLN* 6.1 0.8 - - - +
212L ALA* 2.7 31.2 + - - +
213L ARG* 3.5 10.3 - - + +
215L ILE* 1.3 77.2 - - - +
217L GLU* 1.3 53.3 + - + +
219L PHE* 3.3 1.6 + - - +
220L ASN* 2.6 53.7 + - - +
259L GLU* 2.1 44.1 + - - +
262L ASN* 5.6 1.8 - - - +
263L GLN* 3.8 23.8 - - - +
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Residues in contact with GLU 217 (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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114L GLU* 3.8 31.6 - - - +
115L VAL* 4.3 7.8 - - - +
116L ASP* 4.2 16.8 - - + +
119L VAL* 4.3 16.7 - - + +
213L ARG* 2.8 39.0 + - + +
214L LEU* 3.7 7.4 - - + +
216L ARG* 1.3 72.0 - - - +
218L MET* 1.3 62.0 + - - +
220L ASN* 3.9 14.3 + - - +
221L TYR* 2.8 37.4 + - - +
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Residues in contact with MET 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L VAL* 5.5 6.1 - - + -
122L MET* 4.2 22.0 - - + -
196L LEU* 4.0 17.8 - - + +
198L VAL* 2.9 33.2 - - + -
203L ILE* 3.5 34.3 - - + -
214L LEU* 3.0 28.1 + - + +
215L ILE* 3.2 20.6 + - + +
217L GLU* 1.3 78.8 - - - +
219L PHE* 1.3 65.6 + - + +
221L TYR* 4.2 1.9 - - - +
222L ALA* 3.2 26.2 + - - +
230L ILE* 4.5 11.1 - - + +
232L MET* 5.1 8.5 - - + -
260L LEU* 5.5 0.2 - - + -
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Residues in contact with PHE 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215L ILE* 3.0 40.1 + - + +
216L ARG 4.1 0.7 - - - +
218L MET* 1.3 85.5 - - + +
220L ASN* 1.3 53.7 + - - +
222L ALA* 3.9 3.5 - - - +
223L ARG* 2.3 55.2 + - + +
230L ILE* 5.2 8.5 - - + -
232L MET* 4.4 15.9 - - + -
260L LEU* 4.7 9.2 - - + -
263L GLN* 3.0 35.7 - - + +
264L MET* 4.3 12.3 - - + -
270L LEU* 4.1 28.0 - - + -
273L VAL* 5.8 1.3 - - + -
275L MET* 3.3 36.6 - - + -
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Residues in contact with ASN 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L ARG* 4.6 20.1 - - - +
216L ARG* 2.6 41.6 + - - +
217L GLU* 3.8 15.3 + - - +
219L PHE* 1.3 69.7 - - - +
221L TYR* 1.3 67.3 + - - +
223L ARG* 3.0 19.4 + - - +
224L ASP* 2.8 30.8 + - - +
263L GLN* 5.4 3.3 + - - -
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Residues in contact with TYR 221 (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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115L VAL* 5.2 13.0 - - + -
119L VAL* 4.0 21.3 - - + -
120L TYR* 6.5 0.7 - + - -
123L SER* 3.6 16.6 + - - -
124L HIS* 3.4 23.5 + + - -
194L ASN* 2.6 27.5 + - - -
196L LEU* 3.2 32.1 - - + -
217L GLU* 2.8 24.7 + - - +
218L MET 4.2 0.7 - - - +
220L ASN* 1.3 73.1 - - - +
222L ALA* 1.3 67.5 + - - +
224L ASP* 3.4 3.7 - - - +
225L HIS* 2.4 75.0 + + + +
228L CYS* 4.1 1.3 - - - -
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Residues in contact with ALA 222 (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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196L LEU* 3.9 11.4 - - + -
218L MET 3.2 18.5 + - - +
219L PHE* 3.9 2.5 - - - +
220L ASN 3.1 0.4 - - - -
221L TYR* 1.3 88.3 - - + +
223L ARG* 1.3 60.3 + - - +
226L GLN 2.3 33.8 + - - -
228L CYS* 3.9 10.5 - - + -
230L ILE* 4.3 1.3 - - + -
273L VAL* 3.0 32.4 - - + +
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Residues in contact with ARG 223 (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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219L PHE* 2.3 54.4 + - + +
220L ASN* 3.2 20.0 + - - +
222L ALA* 1.3 65.6 - - - +
224L ASP* 1.3 63.3 + - - +
226L GLN* 2.5 34.3 + - - +
263L GLN* 3.9 31.3 + - - +
268L ASP* 3.3 50.6 + - - +
269L THR 4.7 3.0 - - - -
270L LEU* 3.5 34.8 - - + +
271L HIS 5.3 1.6 - - - +
273L VAL* 4.0 2.6 - - - +
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Residues in contact with ASP 224 (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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113L ARG* 3.6 23.2 + - - -
220L ASN* 2.8 17.2 + - - +
221L TYR* 3.7 2.7 - - - +
223L ARG* 1.3 85.5 - - - +
225L HIS* 1.3 65.0 + - - +
226L GLN* 3.1 9.1 + - - +
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Residues in contact with HIS 225 (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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124L HIS* 4.9 8.4 + + - -
194L ASN* 3.6 13.2 + - - -
221L TYR* 2.4 73.9 + + + +
222L ALA 3.2 0.2 - - - -
224L ASP* 1.3 70.0 - - - +
226L GLN* 1.3 67.6 + - - +
227L PRO* 3.2 11.3 - - - +
228L CYS* 3.3 15.4 - - - -
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Residues in contact with GLN 226 (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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222L ALA 2.3 18.5 + - - +
223L ARG* 2.5 34.8 + - - +
224L ASP 3.1 6.0 - - - +
225L HIS* 1.3 70.5 - - - +
227L PRO* 1.4 68.0 - - - +
271L HIS* 2.5 46.7 + - - +
272L ARG* 3.3 24.4 + - + +
273L VAL* 2.6 25.6 - - + -
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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