Contacts of the helix formed by residues 211 - 228 (chain F) in PDB entry 5MG3
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 LEU 211 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559D THR* 4.0 12.8 - - + -
157F ILE* 3.6 29.4 - - + -
161F VAL* 4.2 20.4 - - + -
173F VAL* 3.7 27.6 - - + -
177F LEU* 3.9 9.1 - - + +
207F ILE* 3.8 18.2 - - + -
208F GLY* 3.9 7.9 - - - -
210F SER* 1.3 77.2 - - - +
212F ASN* 1.3 56.4 + - - +
213F ASP* 2.7 13.5 + - - -
214F SER* 3.2 15.3 + - - -
215F ILE* 2.9 45.2 + - + +
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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
----------------------------------------------------------
519D ASP* 3.3 20.4 + - - +
523D LEU* 4.6 14.5 - - + +
552D SER* 5.4 0.2 - - - -
556D ALA* 4.9 17.4 - - + +
208F GLY 3.2 20.8 + - - +
209F TYR* 4.0 3.4 - - - +
210F SER 2.9 18.9 + - - -
211F LEU* 1.3 77.8 - - - +
213F ASP* 1.4 59.8 + - - +
215F ILE* 3.5 13.4 - - + +
216F VAL* 3.4 30.3 + - - +
251F THR* 3.7 15.1 - - - +
252F SER* 3.0 22.1 + - - -
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Residues in contact with ASP 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F SER* 3.4 18.9 + - - -
211F LEU* 2.7 27.7 + - - -
212F ASN* 1.4 73.6 + - - +
214F SER* 1.3 76.9 + - - +
215F ILE 3.2 0.2 - - - -
216F VAL* 3.1 23.7 - - - +
217F VAL* 3.3 13.0 - - - +
248F THR* 3.6 36.1 - - + +
251F THR* 4.7 8.8 - - + +
252F SER* 5.0 3.3 + - - -
284F GLY* 3.5 26.7 - - - +
285F THR* 4.4 2.1 + - + +
289F ILE* 4.6 2.7 - - + -
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Residues in contact with SER 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LEU* 5.1 1.3 - - - +
173F VAL* 4.0 29.7 - - - +
177F LEU* 4.4 8.5 - - - +
211F LEU* 3.2 27.8 + - - -
213F ASP* 1.3 88.5 + - - +
215F ILE* 1.3 56.2 + - - +
217F VAL* 3.6 1.7 + - - +
218F SER* 3.0 32.2 + - - -
289F ILE* 3.8 28.2 + - - +
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Residues in contact with ILE 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D LEU* 6.4 0.2 - - + -
552D SER* 4.3 15.5 - - - +
555D ASP* 3.8 38.6 - - + +
556D ALA* 4.8 3.6 - - + +
559D THR* 4.1 23.6 - - + +
160F TYR* 6.0 1.8 - - + -
161F VAL* 5.4 7.6 - - + -
165F PHE* 3.8 19.1 - - + -
208F GLY* 5.6 1.1 - - - +
211F LEU* 2.9 41.3 + - + +
212F ASN* 3.5 14.6 - - + +
213F ASP 3.2 0.4 - - - -
214F SER* 1.3 77.3 - - - +
216F VAL* 1.4 56.4 + - - +
218F SER* 4.4 0.2 - - - -
219F ASP* 2.9 31.9 + - - +
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Residues in contact with VAL 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D LEU* 4.0 8.1 - - + -
552D SER* 3.5 22.2 - - - +
212F ASN 3.4 13.6 + - - +
213F ASP* 3.1 26.5 - - - +
215F ILE* 1.4 73.1 - - - +
217F VAL* 1.3 59.7 + - - +
219F ASP* 3.8 2.4 - - - +
220F ARG* 3.0 30.5 + - - +
244F THR* 3.8 19.0 - - + +
247F ARG* 3.3 48.1 + - + +
248F THR* 4.1 6.1 - - + -
251F THR* 5.8 1.6 - - + +
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Residues in contact with VAL 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F ASP 3.3 15.9 - - - +
214F SER 3.6 5.3 + - - +
215F ILE 3.5 0.6 - - - -
216F VAL* 1.3 73.3 - - - +
218F SER* 1.3 59.5 + - - +
220F ARG* 3.1 4.0 + - - +
221F ILE* 2.8 38.0 + - + +
240F SER 4.2 13.0 - - - +
241F LEU* 3.7 30.3 - - + -
244F THR* 4.0 19.1 - - + -
248F THR* 3.7 20.4 - - + -
289F ILE* 4.1 17.0 - - + -
290F TYR* 4.0 8.7 - - + +
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Residues in contact with SER 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F PHE* 3.2 38.5 - - - +
169F LEU* 3.7 30.2 - - - +
214F SER 3.0 20.3 + - - -
215F ILE 3.9 1.6 - - - -
217F VAL* 1.3 75.4 - - - +
219F ASP* 1.4 57.8 + - - +
221F ILE* 3.7 7.6 - - - +
222F ARG* 2.9 33.4 + - - +
289F ILE* 5.4 0.4 - - - +
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Residues in contact with ASP 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527D ARG* 5.8 3.1 + - - -
551D SER* 2.6 32.6 + - - -
552D SER* 3.7 12.5 + - - +
555D ASP* 4.4 1.2 - - - +
164F ARG* 4.2 9.1 + - - -
165F PHE* 3.7 23.2 - - + -
215F ILE 2.9 22.8 + - - +
216F VAL* 3.8 6.5 - - - +
218F SER* 1.4 70.7 - - - +
220F ARG* 1.4 55.7 + - - +
222F ARG* 3.4 3.0 + - - +
223F GLU* 2.9 33.4 + - - +
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Residues in contact with ARG 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527D ARG* 5.3 5.2 - - - +
531D GLU* 2.6 45.6 + - - +
534D ASN* 4.2 15.1 + - - +
536D ARG* 3.2 14.2 - - - +
216F VAL 3.0 19.3 + - - +
217F VAL 3.1 3.6 + - - +
219F ASP* 1.4 74.1 - - - +
221F ILE* 1.3 50.3 + - - +
223F GLU* 3.3 12.9 + - - +
224F ASN* 2.8 87.4 + - - +
227F LYS* 5.1 8.5 - - - +
240F SER* 4.9 4.3 - - - +
243F GLN* 3.5 33.6 - - + +
244F THR* 4.3 17.9 - - + +
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Residues in contact with ILE 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F LEU* 5.1 12.1 - - + -
217F VAL* 2.8 36.6 + - + +
218F SER* 3.7 9.6 - - - +
220F ARG* 1.3 71.5 - - - +
222F ARG* 1.4 72.1 + - - +
224F ASN* 3.9 1.7 - - - +
225F PHE* 3.0 31.5 + - - +
237F PHE* 3.8 50.5 - - + +
240F SER* 3.3 26.2 + - - +
241F LEU* 4.2 0.2 - - + -
289F ILE* 6.1 0.2 - - + -
293F SER* 4.0 19.3 - - - +
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Residues in contact with ARG 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F ARG 5.1 0.4 - - - +
165F PHE* 3.8 44.7 + - + +
166F GLU* 3.4 41.4 + - - +
169F LEU* 6.1 1.0 - - - +
218F SER* 2.9 24.3 + - - +
219F ASP* 3.7 4.9 - - - +
221F ILE* 1.4 81.5 - - - +
223F GLU* 1.3 62.6 + - - +
225F PHE* 3.1 39.8 + - - +
226F ARG* 3.0 59.1 + - - +
237F PHE* 3.9 20.6 - - - -
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Residues in contact with GLU 223 (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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527D ARG* 5.0 7.1 + - - -
536D ARG* 2.7 45.9 + - - -
547D ARG* 5.1 8.8 + - - -
548D GLY* 6.2 0.2 - - - -
219F ASP* 2.9 25.0 + - - +
220F ARG* 3.6 14.3 - - - +
222F ARG* 1.3 73.1 - - - +
224F ASN* 1.4 62.7 + - - +
226F ARG* 3.5 10.5 + - - +
227F LYS* 3.4 26.8 + - + +
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Residues in contact with ASN 224 (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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220F ARG* 2.8 62.0 + - - +
221F ILE* 4.1 3.4 - - - +
223F GLU* 1.4 74.5 - - - +
225F PHE* 1.4 60.9 + - - +
227F LYS* 3.5 21.8 - - - +
228F ILE* 3.4 26.6 - - + +
236F ILE* 3.5 24.7 - - + +
240F SER* 2.8 25.2 + - - +
243F GLN* 3.5 14.3 + - - -
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Residues in contact with PHE 225 (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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221F ILE 3.0 19.7 + - - +
222F ARG* 3.1 37.0 + - - +
224F ASN* 1.4 74.1 - - - +
226F ARG* 1.3 70.5 + - + +
228F ILE* 3.4 26.7 + - + +
233F PRO* 3.7 40.4 - - + -
236F ILE* 5.1 1.5 - - - +
237F PHE* 4.2 13.0 - + + -
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Residues in contact with ARG 226 (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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164F ARG* 5.4 11.1 + - - +
165F PHE* 5.6 1.0 + - - -
222F ARG* 3.0 52.7 + - - +
223F GLU* 3.5 8.6 + - - +
225F PHE* 1.3 85.4 - - + +
227F LYS* 1.4 60.7 + - - +
228F ILE 3.7 4.7 + - - +
229F ARG* 4.5 4.7 + - - -
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Residues in contact with LYS 227 (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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220F ARG* 5.1 5.6 - - - +
223F GLU* 3.4 16.5 + - + +
224F ASN* 3.5 32.2 + - - +
226F ARG* 1.4 72.7 - - - +
228F ILE* 1.3 73.2 + - + +
229F ARG* 2.9 34.4 + - - +
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Residues in contact with ILE 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F ASN 3.4 15.7 - - - +
225F PHE* 3.4 26.7 - - + +
226F ARG 3.4 5.6 - - - +
227F LYS* 1.3 93.0 - - + +
229F ARG* 1.3 64.2 + - - +
231F GLY* 4.0 19.5 - - - +
232F THR 3.6 26.9 - - - +
233F PRO* 4.3 8.7 - - + -
236F ILE* 4.5 22.7 - - + -
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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