Contacts of the helix formed by residues 202 - 210 (chain F) in PDB entry 2AJQ
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 202 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F GLY 3.4 13.2 - - - -
54F GLY* 5.0 1.6 - - - -
55F LEU* 4.6 0.4 - - - -
201F VAL* 1.3 79.9 - - - +
203F TYR* 1.3 65.7 + - - -
204F THR* 3.3 4.5 - - - -
205F THR* 3.2 8.5 + - - -
206F PHE* 3.1 19.5 + - - +
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Residues in contact with TYR 203 (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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50F VAL 5.7 0.9 - - - -
53F GLY* 3.0 33.9 + - - +
54F GLY 4.0 2.9 - - - +
55F LEU* 3.3 32.3 - - + +
86F GLU* 3.4 50.3 + - + +
87F ASN* 3.6 19.7 - - - -
202F GLY* 1.3 71.9 - - - -
204F THR* 1.3 87.7 + - + +
206F PHE* 3.3 1.5 + - - +
207F TRP* 3.0 34.0 + + - -
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Residues in contact with THR 204 (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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202F GLY* 4.9 2.6 - - - -
203F TYR* 1.3 111.5 - - + +
205F THR* 1.3 62.3 + - - +
207F TRP* 4.2 3.9 - - - +
208F SER* 3.0 29.5 + - - -
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Residues in contact with THR 205 (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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196F ILE* 4.5 7.6 - - + -
198F PHE* 4.5 0.2 - - - -
201F VAL* 4.0 26.7 - - + -
202F GLY* 3.2 11.4 + - - -
204F THR* 1.3 80.2 + - - +
206F PHE* 1.3 61.8 + - - +
208F SER* 4.0 5.8 - - - -
209F GLU* 2.9 48.1 + - + +
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Residues in contact with PHE 206 (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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1F MET* 4.1 6.7 - - + -
55F LEU* 3.5 29.2 - - + -
89F ILE* 3.4 35.2 - - + -
94F LEU* 5.2 1.1 - - + -
182F LEU* 5.8 0.2 - - + -
186F LEU* 4.3 7.4 - - + -
192F PHE* 3.9 21.3 - + - -
198F PHE* 3.7 45.7 - + + -
201F VAL* 4.2 4.2 - - + +
202F GLY 3.1 8.1 + - - +
203F TYR* 3.3 7.6 + - - +
205F THR* 1.3 80.0 - - - +
207F TRP* 1.3 87.8 + + - +
210F SER* 2.6 33.8 + - - -
214F VAL* 4.5 8.5 - - + -
218F HIS* 5.7 0.2 - + - -
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Residues in contact with TRP 207 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55F LEU* 4.9 1.1 - - + -
85F ARG* 4.3 17.5 - - - -
86F GLU* 2.8 34.1 + - + +
88F CYS 3.5 26.2 - - - -
89F ILE* 4.4 4.5 - - + -
203F TYR* 3.0 31.7 + + - +
204F THR* 4.3 3.1 - - - +
206F PHE* 1.3 108.3 - + - +
208F SER* 1.3 63.4 + - - +
210F SER* 3.4 17.4 + - - +
211F LEU 5.2 0.9 - - - +
212F GLU* 5.9 0.7 - - - -
214F VAL* 4.0 10.3 - - + -
215F ASP* 4.0 40.9 - - + +
218F HIS* 3.8 35.2 - + + -
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Residues in contact with SER 208 (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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204F THR 3.0 21.5 + - - -
205F THR* 3.6 7.2 - - - -
207F TRP* 1.3 79.2 - - - +
209F GLU* 1.3 83.0 + - - +
210F SER 3.7 4.0 + - - +
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Residues in contact with GLU 209 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193F PRO* 3.4 22.5 - - - +
196F ILE* 4.1 24.6 - - + +
198F PHE* 4.0 17.7 - - + -
205F THR* 2.9 35.7 + - + +
208F SER* 1.3 97.4 + - - +
210F SER* 1.3 64.5 + - - +
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Residues in contact with SER 210 (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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191F TYR 3.6 14.4 - - - -
192F PHE* 3.7 23.5 - - - -
193F PRO* 4.4 0.7 - - - -
198F PHE* 4.0 4.2 - - - -
206F PHE* 2.6 26.2 + - - -
207F TRP* 3.4 15.2 + - - +
208F SER 3.5 4.2 - - - +
209F GLU* 1.3 81.1 - - - +
211F LEU* 1.3 68.0 + - - +
212F GLU* 3.5 1.9 + - - -
214F VAL* 3.9 17.1 - - - +
215F ASP 5.3 0.3 + - - -
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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