Contacts of the helix formed by residues 222 - 233 (chain F) in PDB entry 2NYM
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 GLN 222 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204F ASP 3.9 1.2 + - - -
205F ASP* 5.7 0.6 - - - +
207F GLY* 4.7 2.4 - - - -
221F GLY* 1.3 72.1 - - - +
223F ASP* 1.3 67.6 + - - +
225F SER* 3.0 1.9 + - - -
226F GLU* 3.0 50.2 + - + +
252F HIS* 3.0 40.7 + - + -
253F ASP* 4.4 16.0 + - - +
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Residues in contact with ASP 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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207F GLY* 3.3 12.0 - - - -
208F GLY* 2.8 42.4 + - - -
221F GLY 3.7 1.6 - - - -
222F GLN* 1.3 76.7 + - - +
224F ILE* 1.3 75.5 + - - +
226F GLU* 3.4 10.1 + - - +
227F THR* 3.0 25.7 + - - -
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Residues in contact with ILE 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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170F LEU* 4.6 6.8 - - + +
208F GLY* 3.4 3.6 - - - -
209F TRP* 2.7 84.8 - - + +
220F PHE* 3.7 18.2 - - + -
221F GLY 3.0 7.2 + - - +
223F ASP* 1.3 89.3 - - - +
225F SER* 1.3 63.4 + - - +
227F THR* 3.8 5.9 - - - -
228F PHE* 3.3 19.1 + - + +
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Residues in contact with SER 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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170F LEU* 3.8 22.2 - - - +
220F PHE* 3.9 1.2 - - - -
221F GLY 2.9 5.1 + - - -
222F GLN 3.3 5.4 - - - -
224F ILE* 1.3 73.5 - - - +
226F GLU* 1.3 67.8 + - - +
227F THR 2.9 3.7 + - - -
228F PHE* 3.0 14.1 + - - +
229F ASN* 3.1 18.2 + - - -
237F VAL* 5.6 1.2 - - - +
252F HIS* 2.5 44.9 + - - -
255F ASN* 4.5 8.5 - - - -
256F VAL* 4.6 6.8 - - - +
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Residues in contact with GLU 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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222F GLN* 3.0 45.1 + - + +
223F ASP* 3.8 9.0 - - - +
225F SER* 1.3 77.8 - - - +
227F THR* 1.3 61.8 + - - +
229F ASN* 3.5 4.0 - - - +
230F HIS* 3.1 24.0 + - - +
253F ASP* 4.8 5.7 - - - +
255F ASN* 3.6 30.7 + - - +
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Residues in contact with THR 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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223F ASP 3.0 16.2 + - - -
224F ILE* 3.8 6.6 - - - -
225F SER 2.9 1.8 + - - -
226F GLU* 1.3 74.8 - - - +
228F PHE* 1.3 68.7 + - - +
229F ASN 3.0 2.1 + - - -
230F HIS* 3.0 8.1 + - + +
231F ALA* 2.8 26.4 + - + +
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Residues in contact with PHE 228 (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 PHE* 3.6 32.5 - + - -
170F LEU* 3.1 35.7 - - + -
171F SER 6.3 0.2 - - - -
174F ILE* 4.4 24.5 - - + -
175F ASP* 3.3 33.7 - - - -
176F THR 4.5 0.7 - - - -
177F LEU* 4.3 10.8 - - + -
180F ILE* 4.9 0.9 - - + -
198F LEU* 6.4 0.4 - - + -
224F ILE* 3.3 10.7 + - + +
225F SER* 3.0 8.6 + - - +
227F THR* 1.3 77.8 - - - +
229F ASN* 1.3 63.8 + - - +
231F ALA* 3.2 19.2 - - - +
232F ASN* 3.2 23.9 + - - +
234F LEU* 3.8 16.3 - - + +
237F VAL* 4.6 5.8 - - + -
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Residues in contact with ASN 229 (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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225F SER* 3.1 16.8 + - - -
226F GLU 3.5 7.9 - - - +
227F THR 3.0 0.2 - - - -
228F PHE* 1.3 76.6 - - - +
230F HIS* 1.3 65.0 + - - +
231F ALA 3.0 5.3 + - - -
233F GLY* 3.1 4.7 + - - -
234F LEU* 2.7 65.1 + - - +
235F THR 4.8 0.4 - - - -
236F LEU 3.8 5.5 + - - -
237F VAL* 3.5 19.1 - - - +
255F ASN* 2.7 45.1 + - - +
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Residues in contact with HIS 230 (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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226F GLU 3.1 12.4 + - - +
227F THR* 3.0 8.6 + - + +
229F ASN* 1.3 78.5 - - - +
231F ALA* 1.3 64.4 + - - +
233F GLY* 4.1 5.2 + - - -
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Residues in contact with ALA 231 (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 ASP 4.4 7.4 - - - +
176F THR* 5.9 2.2 - - + -
227F THR* 2.8 15.6 + - + +
228F PHE* 3.2 14.8 - - - +
229F ASN 3.0 1.2 - - - -
230F HIS* 1.3 83.0 - - - +
232F ASN* 1.3 69.5 + - - +
233F GLY 3.2 2.7 + - - -
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Residues in contact with ASN 232 (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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161F GLY 5.2 1.0 - - - +
175F ASP 3.5 18.8 + - - -
176F THR* 3.1 11.4 - - - -
177F LEU* 2.7 52.0 + - + +
228F PHE* 3.2 31.7 + - - -
231F ALA* 1.3 76.1 - - - +
233F GLY* 1.3 59.2 + - - +
234F LEU* 4.2 12.0 - - + +
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Residues in contact with GLY 233 (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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161F GLY 3.8 13.0 - - - +
162F GLN* 4.4 6.4 - - - +
229F ASN 3.1 6.1 + - - -
230F HIS 4.6 4.0 - - - -
231F ALA 3.2 4.4 + - - -
232F ASN* 1.3 81.3 - - - +
234F LEU* 1.3 60.6 - - - +
235F THR 3.8 2.1 + - - -
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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