Contacts of the helix formed by residues 190 - 198 (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 190 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188X TYR* 5.5 0.6 - - - -
189X ARG* 1.3 71.7 - - - +
191X ILE* 1.3 63.8 + - - +
192X GLY* 3.4 4.0 + - - -
193X LYS* 3.1 35.4 + - - +
194X VAL* 3.4 23.2 + - - +
1002X ACY 3.4 15.1 + - - -
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Residues in contact with ILE 191 (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* 3.5 35.2 - - + -
190X SER* 1.3 71.7 - - - +
192X GLY* 1.3 65.5 + - - +
194X VAL* 3.1 6.1 + - + +
195X LEU* 3.0 23.2 + - + +
211X ILE* 4.3 17.0 - - + -
226X LEU* 3.3 52.9 - - + +
227X LEU* 4.1 10.3 - - + +
229X GLN* 4.4 6.3 - - + -
230X ASN* 3.8 26.7 - - + +
1002X ACY 3.0 13.6 + - - +
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Residues in contact with GLY 192 (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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190X SER* 3.9 2.7 - - - -
191X ILE* 1.3 79.2 - - - +
193X LYS* 1.3 56.3 + - - +
195X LEU 3.3 1.0 + - - -
196X ILE* 2.9 35.7 + - - +
206X MET* 3.4 32.0 - - - +
211X ILE* 3.9 5.3 - - - +
1002X ACY 3.2 14.0 + - - -
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Residues in contact with LYS 193 (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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190X SER* 3.1 28.5 + - - +
191X ILE 3.2 0.2 - - - -
192X GLY* 1.3 73.1 - - - +
194X VAL* 1.3 61.1 - - + +
196X ILE* 3.3 11.2 + - + +
197X ASP* 2.9 61.5 + - - +
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Residues in contact with VAL 194 (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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189X ARG* 6.0 2.5 - - + -
190X SER 3.4 15.7 + - - +
191X ILE* 3.1 11.5 + - + +
193X LYS* 1.3 78.3 - - + +
195X LEU* 1.3 58.1 + - - +
197X ASP* 3.3 7.1 + - - +
198X ARG* 3.0 58.8 + - + +
226X LEU* 3.7 19.5 - - + -
229X GLN* 4.3 22.4 - - + +
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Residues in contact with LEU 195 (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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191X ILE* 3.0 16.5 + - + +
192X GLY 3.6 7.2 - - - +
194X VAL* 1.3 75.8 - - - +
196X ILE* 1.3 60.6 + - - +
198X ARG* 3.5 5.2 + - - -
199X GLY 3.4 2.1 + - - -
200X GLU* 3.1 35.6 + - + +
201X VAL* 3.4 19.5 + - + -
206X MET* 3.9 8.1 - - + -
211X ILE* 3.8 35.4 - - + -
214X TRP* 3.5 44.6 - - + +
226X LEU* 3.9 27.8 - - + -
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Residues in contact with ILE 196 (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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192X GLY 2.9 23.3 + - - +
193X LYS* 3.6 9.4 - - + +
194X VAL 3.2 0.2 - - - -
195X LEU* 1.3 78.5 - - - +
197X ASP* 1.3 69.7 + - - +
199X GLY* 3.2 13.7 + - - -
201X VAL 3.6 18.3 - - - +
203X LYS* 3.7 52.7 + - + +
206X MET* 3.8 30.5 - - + -
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Residues in contact with ASP 197 (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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193X LYS* 2.9 52.9 + - - +
194X VAL* 3.8 6.9 - - - +
196X ILE* 1.3 85.0 - - - +
198X ARG* 1.3 61.2 + - + +
199X GLY 3.2 1.2 + - - -
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Residues in contact with ARG 198 (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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194X VAL* 3.0 35.6 + - + +
195X LEU* 4.0 4.0 - - - +
196X ILE 3.2 0.4 - - - -
197X ASP* 1.3 77.7 - - + +
199X GLY* 1.3 61.1 + - - +
200X GLU* 3.4 28.2 + - + +
214X TRP* 5.4 7.5 - - - -
225X GLU* 3.2 36.8 + - - -
226X LEU* 4.1 17.0 - - - +
229X GLN* 4.0 18.0 + - - +
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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