Contacts of the strand formed by residues 223 - 229 (chain B) 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 ILE 223 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG* 3.3 10.8 - - + +
181B PHE* 3.8 23.6 - - + -
210B LEU 4.2 1.3 - - - +
213B ALA* 3.5 21.1 - - + +
214B TYR* 3.4 40.5 - - + +
217B LEU* 3.6 19.3 - - + +
222B LYS* 1.3 75.0 - - - +
224B TYR* 1.3 63.6 + - - +
225B LEU* 3.9 4.9 + - + -
240B GLU* 3.4 4.9 - - - +
241B MSE 3.2 60.3 + - + +
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Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 4.5 11.0 - - + +
173B HIS 3.6 8.7 + - - -
174B VAL* 3.6 26.0 - - + +
175B PRO* 3.1 24.6 - - - +
178B SER* 3.9 12.6 - - - -
179B ARG 3.0 9.6 + - - -
180B PHE* 3.4 33.7 - + + -
181B PHE 3.0 25.8 + - - +
222B LYS* 3.8 18.7 + - + +
223B ILE* 1.3 76.5 - - - +
225B LEU* 1.3 64.7 + - - +
226B LEU* 4.2 4.4 - - + +
238B VAL* 4.3 15.0 - - + -
239B ALA 3.6 1.6 - - - -
240B GLU* 3.8 27.2 + - + -
269B ILE* 3.9 14.1 - - + -
310B LEU* 4.7 7.0 - - + -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PHE* 3.5 13.5 - - + -
183B ILE* 3.9 21.8 - - + -
200B TRP* 5.0 1.1 - - + -
210B LEU* 4.3 2.0 - - + -
223B ILE* 3.9 9.9 - - + +
224B TYR* 1.3 82.3 - - - +
226B LEU* 1.3 62.3 + - - +
227B PHE* 3.7 24.6 + - + -
238B VAL* 3.2 7.4 - - - +
239B ALA 2.7 40.5 + - - +
241B MSE 3.5 37.5 - - + +
264B PHE* 4.2 7.2 - - + -
266B VAL* 4.2 26.0 - - + -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B PHE* 5.4 5.2 - - + -
181B PHE 2.8 18.3 + - - +
182B VAL* 4.6 1.1 - - - -
183B ILE 2.9 23.0 + - - +
224B TYR* 5.1 6.5 - - + +
225B LEU* 1.3 74.8 - - - +
227B PHE* 1.3 63.3 + - - +
235B PHE* 3.6 28.0 - - + -
237B GLY 3.7 3.8 - - - +
238B VAL* 3.7 29.4 - - + -
292B VAL* 5.5 0.2 - - + -
301B ILE* 3.6 26.7 - - + -
306B SER* 5.0 6.1 - - - +
309B ILE* 4.1 28.3 - - + -
310B LEU* 4.1 13.7 - - + -
313B PHE* 4.6 4.3 - - + -
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ILE* 3.4 30.1 - - + -
185B SER* 5.4 1.1 - - - -
191B VAL* 4.3 15.7 - - + -
194B SER* 4.4 2.0 - - - -
200B TRP* 3.7 44.6 - + + -
225B LEU* 3.8 32.8 - - + -
226B LEU* 1.3 72.1 - - - +
228B SER* 1.3 60.6 + - - +
235B PHE* 3.3 7.2 - - - +
236B CYS* 2.8 37.3 + - - -
237B GLY 2.8 15.3 + - - +
239B ALA* 4.1 10.3 - - + -
266B VAL* 5.5 0.7 - - + -
268B TRP* 3.5 42.2 - + + -
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ILE 2.8 6.4 + - - -
184B LYS* 2.8 39.7 + - - +
185B SER* 3.2 22.0 + - - -
191B VAL* 5.8 0.7 - - - -
227B PHE* 1.3 77.2 - - - +
229B VAL* 1.3 61.7 + - - +
234B ARG 2.9 23.6 + - - -
235B PHE* 3.7 26.9 - - - +
236B CYS* 4.6 2.2 - - - +
276B ASN* 5.2 0.7 + - - -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B LYS* 3.6 7.0 + - - -
185B SER 3.3 11.7 - - - +
186B SER 4.5 2.2 - - - +
187B SER* 4.1 5.6 - - - +
188B LEU* 4.0 38.4 - - + +
191B VAL* 3.9 27.1 - - + -
228B SER* 1.3 75.1 + - - +
230B ASN* 1.3 76.7 + - - +
231B ALA 3.3 0.5 + - - -
232B SER* 2.7 39.8 + - - -
233B GLY 4.7 0.2 + - - -
234B ARG 4.2 0.2 + - - -
236B CYS* 4.4 9.0 - - - -
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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