Contacts of the strand formed by residues 201 - 205 (chain F) in PDB entry 5IJ7
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 LEU 201 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175F HIS* 4.4 0.2 - - - -
193F LEU* 4.1 11.2 - - + -
194F SER 3.3 7.4 - - - +
195F VAL* 3.4 31.4 - - + -
200F ALA* 1.3 77.9 - - - +
202F ARG* 1.3 66.0 + - - +
214F ILE* 3.5 1.9 - - - +
215F PHE* 2.8 61.9 + - + +
221F HIS* 4.0 10.3 - - + -
225F VAL* 4.0 14.8 - - + -
228F ALA* 3.8 7.6 - - + -
237F ILE* 4.8 2.7 - - + -
239F SER* 3.7 34.3 - - - +
249F TRP* 4.1 10.3 - - + +
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Residues in contact with ARG 202 (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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174F GLY* 3.0 34.6 + - - -
175F HIS* 3.6 23.3 + - + +
176F GLY 5.1 0.4 - - - +
192F LEU 3.4 1.9 - - - +
193F LEU* 3.3 8.9 - - - +
194F SER* 2.8 48.7 + - - +
198F ASP* 4.8 4.8 + - - -
200F ALA* 5.4 1.4 - - + +
201F LEU* 1.3 78.6 - - - +
203F LEU* 1.3 58.9 + - - +
204F TRP* 3.5 26.6 - - - +
211F LEU* 3.6 30.6 - - + +
213F ALA 3.6 2.0 - - - -
214F ILE* 4.2 21.6 - - + +
215F PHE* 4.9 0.2 - - - -
569T ASP 4.6 1.8 + - - -
570T THR* 2.9 38.1 + - - +
571T CYS* 4.6 2.2 - - - +
572T LEU* 4.7 0.8 - - - +
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Residues in contact with LEU 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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191F LEU* 4.0 18.8 - - + -
192F LEU 3.5 9.0 - - - +
193F LEU* 4.5 4.5 - - + +
202F ARG* 1.3 70.7 - - - +
204F TRP* 1.3 56.5 + - - +
211F LEU* 3.4 5.3 - - - +
212F VAL* 2.8 45.7 + - + -
213F ALA 3.0 14.2 + - - +
215F PHE* 3.8 20.7 - - + -
230F TYR* 3.2 31.2 - - + +
237F ILE* 5.3 0.9 - - + -
251F ILE* 4.8 7.4 - - + -
256F MET* 3.6 29.4 - - + -
260F ILE* 4.5 14.1 - - + -
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Residues in contact with TRP 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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158F ILE* 3.4 22.4 - - + +
172F TYR* 3.9 42.4 - + + -
173F VAL 4.2 5.2 - - - -
174F GLY* 4.6 0.4 - - - -
175F HIS* 4.6 9.0 - - - -
190F ASN 3.3 2.4 - - - +
191F LEU* 3.4 7.1 - - - +
192F LEU* 2.8 43.0 + - + +
194F SER* 2.9 26.5 + - - -
202F ARG* 3.5 44.4 - - + +
203F LEU* 1.3 74.0 - - - +
205F ASN* 1.3 59.5 + - - +
206F ILE* 3.7 20.6 - - + -
209F ASP 5.7 1.1 - - - -
210F THR 3.4 10.3 - - - -
211F LEU* 4.0 28.5 - - + -
212F VAL* 4.2 3.6 - - - -
572T LEU* 4.1 20.9 - - + -
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Residues in contact with ASN 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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172F TYR* 4.5 0.5 + - - -
190F ASN* 3.4 5.0 - - - +
191F LEU* 4.1 9.0 - - + +
204F TRP* 1.3 71.4 - - - +
206F ILE* 1.3 58.5 + - - +
207F GLN* 3.1 22.0 + - - +
208F THR* 3.1 16.5 + - - -
209F ASP* 3.0 23.9 + - - -
210F THR* 2.8 30.9 + - - +
212F VAL* 3.9 5.8 - - + +
263F SER* 2.8 24.1 + - - +
264F TYR* 3.5 35.5 - - - -
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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