Contacts of the strand formed by residues 234 - 241 (chain F) in PDB entry 4U8T
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 ARG 234 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F LEU* 6.0 3.8 - - - +
228F SER* 3.1 17.2 + - - -
229F VAL 4.1 0.2 + - - -
232F SER* 3.0 43.1 + - - +
233F GLY* 1.3 81.6 - - - +
235F PHE* 1.3 71.8 + - - +
236F CYS* 5.5 3.7 - - + +
273F ASP* 3.0 38.2 + - - -
274F VAL 3.1 19.7 - - - +
275F HIS* 3.9 20.2 + - + -
276F ASN* 3.5 7.7 + - - +
321F GLN* 4.7 10.1 + - - -
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Residues in contact with PHE 235 (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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182F VAL* 4.0 20.9 - - + -
184F LYS* 5.1 3.1 - - - -
226F LEU* 3.7 36.6 - - + -
227F PHE 3.3 17.5 - - - +
228F SER* 3.6 17.5 - - - -
234F ARG* 1.3 80.8 - - - +
236F CYS* 1.3 60.5 + - - +
237F GLY 3.8 0.7 - - - -
272F ARG 3.6 1.0 - - - +
273F ASP* 3.4 2.1 - - - -
274F VAL 2.8 35.1 + - - +
276F ASN* 3.8 14.6 - - - -
279F LEU* 3.9 19.5 - - + -
292F VAL* 3.9 22.0 - - + -
293F THR* 4.1 20.0 - - + -
295F SER* 5.6 0.2 - - - -
309F ILE* 6.4 0.7 - - + -
313F PHE* 3.9 19.7 - + + -
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Residues in contact with CYS 236 (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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188F LEU* 5.1 2.9 - - + -
191F VAL* 4.1 15.9 - - - -
227F PHE* 3.0 23.9 + - - -
228F SER* 4.6 2.7 - - - +
229F VAL* 4.7 16.8 - - + +
234F ARG* 5.5 4.3 - - + +
235F PHE* 1.3 74.7 - - - +
237F GLY* 1.3 60.0 + - - +
272F ARG 3.1 26.6 + - - +
273F ASP* 3.7 17.2 - - - +
323F PHE* 3.5 36.9 + - + -
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Residues in contact with GLY 237 (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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226F LEU* 3.9 1.2 - - - -
227F PHE 3.0 24.1 + - - +
236F CYS* 1.3 82.6 - - - +
238F VAL* 1.3 67.9 + - - +
268F TRP* 4.0 11.7 - - - -
270F VAL 3.1 15.3 - - - -
272F ARG 3.6 1.9 + - - -
313F PHE* 3.7 15.0 - - - -
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Residues in contact with VAL 238 (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 ILE* 5.8 0.7 - - + -
224F TYR* 4.3 15.9 - - + -
225F LEU 3.4 4.0 - - - +
226F LEU* 3.7 30.1 - - + -
237F GLY* 1.3 79.2 - - - +
239F ALA* 1.3 69.1 + - - +
268F TRP* 3.7 5.1 - - - -
269F ILE* 2.8 29.6 + - + -
270F VAL* 2.8 29.4 + - + +
310F LEU* 4.1 15.7 - - + -
313F PHE* 3.9 31.6 - - + -
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Residues in contact with ALA 239 (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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224F TYR* 3.5 4.7 - - - +
225F LEU* 2.8 33.9 + - + +
227F PHE* 4.0 18.1 - - + -
238F VAL* 1.3 76.3 - - - +
240F GLU* 1.3 67.9 + - - +
266F VAL* 4.4 8.7 - - + -
267F ARG 3.4 13.7 - - - +
268F TRP* 3.8 24.7 - - + -
269F ILE* 4.2 1.3 - - - +
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Residues in contact with GLU 240 (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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222F LYS* 3.7 32.5 + - + +
223F ILE 3.5 8.1 - - - +
224F TYR* 3.7 23.2 + - + -
225F LEU* 4.7 1.1 - - - -
239F ALA* 1.3 75.2 - - - +
241F MSE 1.3 67.0 + - - +
242F SER* 6.0 0.3 - - - -
266F VAL* 3.1 10.9 - - - +
267F ARG* 2.9 51.0 + - + +
269F ILE* 3.2 34.9 - - + +
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Residues in contact with MSE 241 (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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210F LEU* 3.8 31.6 - - + +
214F TYR* 3.2 51.5 - - + -
222F LYS* 4.8 12.3 + - - +
223F ILE* 3.2 47.8 + - + +
225F LEU* 3.9 12.8 - - + -
240F GLU* 1.3 79.4 - - - +
242F SER* 1.3 60.1 + - - +
243F SER 4.2 6.7 - - - +
264F PHE* 3.7 28.5 - - + -
265F LYS 3.7 4.3 - - - -
266F VAL* 4.3 1.1 - - - -
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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