Contacts of the helix formed by residues 202 - 213 (chain F) in PDB entry 1PQ3
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 ASP 202 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149F ASN* 2.9 16.6 + - - +
155F SER* 5.6 5.4 + - - -
200F ASP* 4.2 6.9 + - - +
201F VAL* 1.3 75.1 - - - +
203F PRO* 1.3 76.7 - - + +
204F PRO* 3.2 11.7 - - + -
205F GLU* 2.9 27.4 + - + +
206F HIS* 3.0 10.9 + - - +
556F S2C 2.5 34.6 + - - -
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Residues in contact with PRO 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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83C ASN* 3.7 44.6 - - + +
85C LEU* 5.3 5.4 - - + -
152C LEU* 3.7 22.9 - - + +
329E GLY* 5.7 3.1 - - - +
201F VAL 3.9 2.7 - - - +
202F ASP* 1.3 84.5 - - + +
204F PRO* 1.3 70.8 - - + +
206F HIS* 3.3 8.6 + - + +
207F PHE* 3.0 22.3 + - - +
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Residues in contact with PRO 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 3.8 35.9 - - + +
149F ASN* 4.0 4.9 - - - +
153F THR* 3.8 39.0 - - + +
202F ASP* 3.3 11.7 - - + -
203F PRO* 1.3 96.6 - - + +
205F GLU* 1.3 63.4 + - - +
207F PHE* 3.2 6.2 + - + +
208F ILE* 3.0 28.6 + - - +
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Residues in contact with GLU 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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145F HIS* 5.4 0.7 - - - +
146F ALA* 3.6 7.9 + - + +
147F ASP* 3.1 13.8 + - - -
148F ILE* 2.8 45.0 + - + +
149F ASN* 3.6 30.7 + - - +
161F GLY 4.1 0.3 - - - +
200F ASP 4.5 2.4 - - - +
201F VAL* 3.5 14.5 - - + -
202F ASP* 2.9 35.4 + - + +
204F PRO* 1.3 76.1 - - - +
206F HIS* 1.3 58.4 - - - +
208F ILE* 3.0 6.8 + - - +
209F LEU* 2.9 33.1 + - - +
556F S2C 4.0 6.3 + - - +
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Residues in contact with HIS 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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328E GLU* 3.2 28.4 + - + +
329E GLY* 3.1 36.3 + - - +
201F VAL* 3.6 10.2 - - + +
202F ASP 3.0 11.4 + - - +
203F PRO* 3.5 12.6 - - + +
204F PRO 3.3 0.2 - - - -
205F GLU* 1.3 74.5 - - - +
207F PHE* 1.3 63.1 + - - +
209F LEU* 3.4 7.1 + - + +
210F LYS* 3.0 61.4 + - + +
216F TYR* 4.4 5.4 - + - -
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Residues in contact with PHE 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 4.2 22.7 - - + -
173C ASP* 3.4 27.4 - - - -
174C LYS* 4.0 28.3 - - + -
176C PRO* 5.8 0.9 - - + -
174F LYS* 5.9 3.6 - - - -
203F PRO 3.0 12.7 + - - +
204F PRO* 3.3 11.4 - - + +
205F GLU 3.2 0.2 - - - -
206F HIS* 1.3 78.3 + - - +
208F ILE* 1.3 64.6 + - + +
210F LYS* 3.9 3.9 - - - +
211F ASN* 2.8 61.1 + - - +
212F TYR* 6.1 1.6 - + - -
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Residues in contact with ILE 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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148F ILE* 3.5 47.6 - - + +
149F ASN* 5.2 0.2 - - - -
150F THR* 4.1 21.8 - - + +
153F THR* 5.1 8.5 - - + +
171F LEU* 4.0 13.5 - - + -
204F PRO 3.0 21.5 + - - +
205F GLU* 3.0 8.5 + - - +
207F PHE* 1.3 82.4 - - + +
209F LEU* 1.3 67.7 + - - +
211F ASN* 3.2 3.7 + - - -
212F TYR* 2.9 43.4 + - + +
214F ILE* 4.5 1.3 - - + -
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Residues in contact with LEU 209 (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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328E GLU 5.9 0.2 - - - +
146F ALA* 4.2 9.4 - - + -
148F ILE* 4.1 13.2 - - + -
195F TYR* 3.7 28.9 - - + -
198F LEU* 4.2 23.6 - - + -
201F VAL* 4.3 13.9 - - + -
205F GLU 2.9 22.4 + - - +
206F HIS* 3.8 8.7 - - + +
208F ILE* 1.3 71.6 - - - +
210F LYS* 1.3 63.9 + - + +
213F ASP* 3.0 19.8 + - - -
214F ILE* 3.0 36.3 + - + +
216F TYR* 4.2 25.8 - - + -
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Residues in contact with LYS 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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328E GLU* 4.4 6.3 + - - -
206F HIS* 3.0 45.9 + - + +
207F PHE* 3.9 3.8 - - - +
209F LEU* 1.3 77.1 - - + +
211F ASN* 1.3 63.4 + - - +
213F ASP* 3.3 20.3 + - - +
216F TYR* 3.5 29.5 + - + +
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Residues in contact with ASN 211 (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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173C ASP* 5.4 5.1 + - - -
174F LYS* 4.4 8.0 + - - -
207F PHE* 2.8 47.1 + - + +
208F ILE* 3.7 3.6 - - - +
210F LYS* 1.3 79.0 - - - +
212F TYR* 1.3 82.7 + - + +
213F ASP* 3.4 1.4 + - - +
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Residues in contact with TYR 212 (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 GLU* 3.3 49.0 + - + -
171F LEU* 3.6 23.5 - - + +
174F LYS* 2.9 38.9 + - + +
190F SER* 3.5 21.3 + - - +
207F PHE* 6.1 1.1 - + - -
208F ILE* 2.9 38.5 + - + +
211F ASN* 1.3 97.2 - - + +
213F ASP* 1.3 71.4 + - - +
214F ILE* 3.2 15.1 + - + -
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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
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190F SER 4.8 2.3 - - - +
191F ALA* 5.6 2.3 - - - +
209F LEU 3.0 8.1 + - - -
210F LYS* 3.3 15.6 + - - +
211F ASN 3.4 1.8 - - - +
212F TYR* 1.3 80.2 - - - +
214F ILE* 1.3 63.7 + - - +
215F GLN* 3.2 24.3 + - - +
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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