Contacts of the helix formed by residues 207 - 217 (chain X) in PDB entry 2AE0
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 SER 207 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99X THR* 6.0 6.0 - - - +
205X ASP 3.4 4.3 + - - -
206X MET* 1.3 82.6 - - - +
208X MET* 1.3 72.1 + - - +
209X GLN* 3.4 9.9 + - - +
210X ALA* 3.2 19.8 + - - +
211X ILE* 3.1 24.4 + - - +
323X TRP 4.4 3.6 + - - -
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Residues in contact with MET 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157X PHE* 5.1 3.8 - - - -
158X ILE* 4.4 26.3 - - + +
161X VAL* 4.1 31.4 - - + -
206X MET* 5.9 1.6 - - + -
207X SER* 1.3 76.8 - - - +
209X GLN* 1.3 57.9 + - + +
211X ILE* 3.2 22.3 + - + +
212X ARG* 2.9 27.4 + - - +
1002X ACY 3.7 30.5 - - + +
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Residues in contact with GLN 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X GLY 3.7 19.5 - - - +
101X TYR* 5.1 3.8 - - + -
102X TYR* 3.3 18.5 - - - -
207X SER* 3.2 9.0 + - - +
208X MET* 1.3 80.8 - - + +
210X ALA* 1.3 57.0 + - - +
212X ARG* 3.0 37.5 + - - +
213X HIS* 2.9 23.7 + - - +
318X GLY 3.9 9.5 + - - -
321X ALA* 3.7 13.3 - - - +
322X GLY 2.9 31.9 + - - +
323X TRP* 3.6 14.0 - - - +
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Residues in contact with ALA 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201X VAL* 4.1 25.3 - - + +
205X ASP 3.3 25.8 - - - +
206X MET* 4.2 1.8 - - - -
207X SER* 3.2 17.5 + - - +
209X GLN* 1.3 74.5 - - - +
211X ILE* 1.3 64.4 + - - +
213X HIS* 3.5 3.3 + - - +
214X TRP* 3.1 22.0 + - - +
323X TRP* 3.6 22.8 + - + +
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Residues in contact with ILE 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X MET* 3.5 31.0 - - + +
157X PHE* 4.4 8.7 - - + -
158X ILE* 5.2 3.4 - - + -
191X ILE* 4.3 16.4 - - + -
192X GLY* 3.9 15.9 - - - +
195X LEU* 3.8 19.1 - - + -
206X MET* 3.8 13.0 - - - -
207X SER 3.1 9.9 + - - +
208X MET* 3.2 30.5 + - + +
210X ALA* 1.3 73.0 - - - +
212X ARG* 1.3 65.4 + - - +
214X TRP* 3.3 3.8 + - - +
215X GLY 3.2 17.2 + - - -
1002X ACY 3.9 22.7 - - - +
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Residues in contact with ARG 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X TYR* 3.1 26.7 + - - -
104X PRO* 3.6 26.1 - - - +
154X MET* 4.2 6.9 - - + +
155X ASP* 2.9 32.0 + - - +
158X ILE* 3.5 41.3 - - + +
208X MET 2.9 13.6 + - - +
209X GLN* 3.0 39.9 + - - +
211X ILE* 1.3 78.8 - - - +
213X HIS* 1.3 61.3 + - - +
215X GLY* 3.2 3.6 + - - -
216X GLU* 3.1 42.0 + - + +
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Residues in contact with HIS 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209X GLN 2.9 12.2 + - - +
210X ALA 3.9 4.0 - - - +
211X ILE 3.3 0.2 - - - -
212X ARG* 1.3 74.2 - - - +
214X TRP* 1.3 66.2 + - - +
216X GLU* 3.2 18.1 + - + +
217X THR* 2.8 52.2 + - + +
281X ASN* 5.0 3.8 - - - -
323X TRP* 3.2 77.5 + + + -
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Residues in contact with TRP 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X MET* 4.4 2.5 - - + -
195X LEU* 3.5 31.4 - - + +
198X ARG* 5.4 6.7 - - - -
200X GLU* 3.2 44.1 + - + -
201X VAL* 4.2 9.6 - - + -
210X ALA 3.1 15.1 + - - +
211X ILE 3.5 9.2 - - - +
212X ARG 3.3 0.2 - - - -
213X HIS* 1.3 77.1 - - - +
215X GLY* 1.3 68.1 + - - +
217X THR* 3.2 8.2 + - - -
218X HIS* 2.6 67.8 + + + -
222X GLU* 3.7 29.2 - - + -
223X VAL* 4.1 11.0 - - + -
226X LEU* 3.5 29.4 - - + -
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Residues in contact with GLY 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154X MET* 3.9 16.2 - - - -
211X ILE 3.2 7.9 + - - -
212X ARG 3.2 4.2 + - - -
213X HIS 3.2 0.2 - - - -
214X TRP* 1.3 83.9 - - - +
216X GLU* 1.3 56.5 + - - +
218X HIS 3.0 24.4 + - - +
223X VAL* 3.7 26.3 - - - +
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Residues in contact with GLU 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212X ARG* 3.1 35.6 + - + +
213X HIS* 3.2 23.6 + - - +
215X GLY* 1.3 76.0 - - - +
217X THR* 1.3 62.7 + - + +
218X HIS 3.3 3.4 + - - +
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Residues in contact with THR 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213X HIS* 2.8 44.9 + - + +
214X TRP* 3.2 10.0 + - - -
215X GLY 3.2 0.2 - - - -
216X GLU* 1.3 78.2 - - + +
218X HIS* 1.3 75.8 + - - +
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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