Contacts of the strand formed by residues 263 - 271 (chain F) in PDB entry 3IT8
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 TYR 263 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F ASP* 2.5 36.8 + - + +
206F SER* 2.8 21.5 + - - -
207F PHE* 2.8 34.4 + - + -
208F TYR* 3.8 9.6 - + - -
210F PRO* 3.8 27.6 - - + -
254F ILE* 3.9 16.2 - - + -
255F LYS 3.7 4.3 - - - -
256F LYS* 3.7 45.0 + - + +
257F ASP* 3.4 4.7 - - - -
261F ASN 3.3 18.4 - - - -
262F THR* 1.3 81.7 + - - +
264F SER* 1.3 61.3 + - - +
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Residues in contact with SER 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F VAL 3.4 8.1 - - - -
205F ASN* 3.8 10.2 + - - +
206F SER 3.0 13.5 + - - -
207F PHE* 3.7 3.1 - - - -
253F ASN 3.7 0.5 - - - +
254F ILE* 3.1 5.7 - - - +
255F LYS* 3.0 37.1 + - - +
257F ASP* 2.7 28.6 + - - +
258F LYS* 5.3 0.9 + - - -
263F TYR* 1.3 70.2 - - - +
265F LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 265 (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 CYS 5.1 0.4 - - - +
203F THR* 3.4 3.1 - - - -
204F VAL* 2.8 46.4 + - + +
205F ASN* 5.2 0.5 - - - +
207F PHE* 3.7 15.7 - - + -
212F VAL* 3.5 31.9 - - + +
214F THR* 5.1 6.3 - - - +
252F TRP* 4.3 20.9 - - + -
253F ASN 3.2 26.7 - - - +
254F ILE* 4.0 10.5 - - + -
264F SER* 1.3 77.8 - - - +
266F THR* 1.3 91.1 + - - +
267F ASP* 4.2 8.5 - - + +
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Residues in contact with THR 266 (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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201F GLU* 3.8 31.7 + - + +
202F CYS 3.5 3.8 - - - -
203F THR* 4.2 8.4 - - + +
253F ASN* 3.1 38.6 + - + +
265F LEU* 1.3 84.0 + - - +
267F ASP* 1.3 63.2 + - - +
268F LEU* 4.1 3.9 + - + +
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Residues in contact with ASP 267 (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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201F GLU* 3.4 1.7 - - - -
202F CYS* 2.7 49.2 + - + +
214F THR* 2.9 27.4 - - + +
216F TRP* 2.7 32.1 + - - -
239F ARG* 3.4 31.2 + - - -
252F TRP* 3.8 8.8 - - - -
253F ASN 5.9 0.7 + - - -
265F LEU* 4.2 10.9 - - + +
266F THR* 1.3 76.5 - - - +
268F LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 268 (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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193F LEU* 4.1 22.9 - - + -
199F THR* 3.8 24.7 - - + +
200F LEU 3.3 15.7 - - - +
201F GLU* 3.4 31.4 - - + +
239F ARG* 4.7 6.8 + - - -
266F THR* 4.1 4.9 + - + -
267F ASP* 1.3 78.9 + - - +
269F VAL* 1.3 73.0 + - - +
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Residues in contact with VAL 269 (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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199F THR* 3.2 9.1 + - - -
200F LEU* 2.7 39.8 + - + +
216F TRP* 3.0 54.5 - - + +
237F TRP* 5.3 8.5 - - + -
239F ARG* 5.3 6.1 - - - -
267F ASP* 4.4 0.4 - - - +
268F LEU* 1.3 81.9 - - - +
270F ARG* 1.3 70.2 + - - +
271F THR* 3.2 6.6 + - - +
275F MET* 5.3 1.1 - - + -
279F PRO* 4.7 13.5 - - + -
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Residues in contact with ARG 270 (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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193F LEU* 6.1 6.4 - - + +
195F ASP* 3.2 22.8 + - - -
196F GLY* 2.9 38.0 - - - +
197F ASN* 3.5 17.0 + - - +
198F MET 4.3 6.3 - - - -
199F THR* 4.6 4.5 - - - +
269F VAL* 1.3 78.5 - - - +
271F THR* 1.3 52.5 + - - +
272F THR* 2.6 43.9 + - - +
275F MET* 4.4 3.6 - - - +
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Residues in contact with THR 271 (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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197F ASN* 2.5 32.3 + - - +
198F MET* 2.9 46.3 + - + +
200F LEU* 3.6 34.0 + - + +
269F VAL* 3.2 3.6 + - - +
270F ARG* 1.3 67.0 - - - +
272F THR* 1.3 54.2 + - - +
275F MET* 3.8 29.6 - - + -
278F GLN* 5.3 4.0 - - + -
279F PRO* 4.8 4.4 - - + +
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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