Contacts of the strand formed by residues 202 - 209 (chain F) in PDB entry 1R8Y
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 ILE 202 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F ARG* 5.9 1.3 - - - +
186F ALA 3.6 22.0 - - - +
187F PRO 4.7 0.9 - - - +
188F PRO* 3.7 40.2 - - + +
189F GLY 5.2 0.7 - - - +
200F LYS* 5.4 1.8 - - + -
201F ASP* 1.3 90.8 + - - +
203F THR* 1.3 72.6 + - - +
204F THR* 4.1 3.9 + - - +
218F LEU* 4.2 20.9 - - + -
219F ASP 3.7 1.8 - - - +
220F TYR* 3.4 40.8 - - + +
210G ASN* 4.3 5.7 + - - +
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Residues in contact with THR 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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202F ILE* 1.3 77.5 + - - +
204F THR* 1.3 59.5 + - - +
205F SER* 4.5 2.5 - - - +
217F THR 3.6 1.4 - - - +
218F LEU* 3.6 5.0 - - - -
219F ASP* 3.2 49.2 + - - +
209G VAL* 3.8 20.9 - - + -
210G ASN* 3.3 26.6 + - - +
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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
----------------------------------------------------------
180F ILE* 4.5 2.5 - - + -
184F GLY 3.3 25.0 - - - +
185F CYS* 3.4 5.3 - - - +
186F ALA* 2.6 37.0 + - + +
202F ILE* 4.1 2.8 + - - +
203F THR* 1.3 72.0 - - - +
205F SER* 1.3 62.0 + - - +
206F VAL* 4.4 8.3 - - + -
216F VAL* 4.0 14.1 - - + -
217F THR 3.9 2.0 - - - -
218F LEU* 3.8 15.6 - - + +
208G THR 3.7 1.6 - - - +
209G VAL* 3.7 1.6 - - - +
210G ASN* 3.0 33.8 + - - -
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Residues in contact with SER 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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5E TYR* 4.9 4.2 + - - -
203F THR* 4.2 1.0 + - - +
204F THR* 1.3 76.8 + - - +
206F VAL* 1.3 63.6 + - - +
207F LEU 3.9 0.7 + - - -
215F MET 3.8 0.7 - - - +
216F VAL* 3.4 2.1 - - - -
217F THR* 2.8 53.3 + - - -
219F ASP* 4.0 14.7 + - - -
239F ARG* 4.8 3.9 + - - -
207G LEU* 4.2 13.7 - - - -
208G THR 3.4 3.4 - - - -
209G VAL* 4.1 25.1 - - - +
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Residues in contact with VAL 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F ILE* 5.2 1.3 - - + -
181F LEU* 3.8 27.1 - - + -
184F GLY* 4.5 17.3 - - - +
204F THR* 4.4 12.6 - - + -
205F SER* 1.3 75.8 - - - +
207F LEU* 1.3 63.6 + - - +
208F THR* 3.9 18.3 + - - +
213F ALA* 5.1 1.8 - - + -
215F MET 3.4 8.1 - - - +
216F VAL* 4.2 13.7 - - + -
206G VAL 3.5 3.5 - - - +
207G LEU* 3.6 3.8 - - - +
208G THR* 2.8 46.0 + - + +
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Residues in contact with LEU 207 (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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5E TYR* 5.0 7.0 - - + +
205F SER 3.9 0.8 + - - -
206F VAL* 1.3 73.8 - - - +
208F THR* 1.3 63.4 + - - +
209F VAL* 4.0 11.2 - - + -
213F ALA* 3.8 0.9 - - - -
214F HIS* 2.9 44.5 + - + -
215F MET* 2.8 38.2 + - + +
205G SER* 4.0 14.6 - - - -
206G VAL 3.5 17.5 - - - +
207G LEU* 4.3 12.3 - - + -
5H TYR* 3.7 40.6 - - + +
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Residues in contact with THR 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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206F VAL* 3.9 13.1 + - - +
207F LEU* 1.3 75.0 + - - +
209F VAL* 1.3 59.0 + - - +
210F ASN 3.9 0.2 + - - -
211F ASN* 3.4 44.2 + - - +
212F LYS 3.7 6.3 - - - +
213F ALA* 3.9 9.5 - - - +
184G GLY* 5.0 1.3 - - - +
204G THR 3.4 2.3 - - - +
205G SER* 3.2 1.4 - - - -
206G VAL* 2.7 53.1 + - + +
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Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F LEU* 4.0 9.1 + - + -
208F THR* 1.3 70.9 - - - +
210F ASN* 1.3 67.0 + - + +
211F ASN 3.4 1.6 - - - -
212F LYS* 2.8 37.6 + - - +
214F HIS* 4.1 30.9 - - + +
203G THR* 3.7 28.0 - - + -
204G THR 3.4 4.0 - - - +
205G SER* 3.9 17.3 - - - +
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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