Contacts of the helix formed by residues 224 - 233 (chain B) in PDB entry 1T8U
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 GLU 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ASP 5.7 0.5 - - - +
222B THR* 3.7 9.3 - - - +
223B ARG* 1.3 89.5 + - + +
225B ALA* 1.3 65.7 + - - +
226B PRO* 3.4 0.7 - - - -
227B ALA* 3.3 9.4 + - + +
228B ARG* 3.0 66.2 + - + +
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Residues in contact with ALA 225 (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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188B PHE* 4.6 14.6 - - + -
219B TYR* 3.4 24.5 - - + +
222B THR* 3.1 24.5 + - + +
224B GLU* 1.3 76.5 - - - +
226B PRO* 1.3 66.8 - - + +
228B ARG* 3.2 5.2 + - - -
229B ILE* 2.8 35.4 + - + +
298B TRP* 3.7 11.9 - - + -
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Residues in contact with PRO 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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222B THR 3.4 10.3 - - - +
223B ARG 3.5 11.0 - - - +
224B GLU 3.6 0.7 - - - -
225B ALA* 1.3 94.1 - - + +
227B ALA* 1.3 61.6 + - - +
230B SER* 3.1 25.3 + - - -
297B HIS* 3.9 17.3 - - + +
298B TRP* 3.4 48.5 - - + +
301B HIS* 3.5 24.9 - - + +
302B PHE* 3.4 6.7 - - + -
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Residues in contact with ALA 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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223B ARG 5.4 0.8 + - - +
224B GLU* 3.3 12.3 + - + +
226B PRO* 1.3 79.1 - - - +
228B ARG* 1.3 60.3 + - + +
230B SER* 3.4 3.2 + - - -
231B ALA* 2.9 28.6 + - - +
301B HIS* 3.8 28.8 - - + +
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Residues in contact with ARG 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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188B PHE* 3.0 50.3 + - + -
189B ASP* 4.5 8.5 + - - +
192B TYR* 3.3 62.3 + - + +
224B GLU* 3.0 57.6 + - + +
225B ALA 3.7 2.2 - - - +
227B ALA* 1.3 75.7 - - + +
229B ILE* 1.3 66.0 + - - +
231B ALA* 3.1 5.7 + - - +
232B MET* 3.1 17.8 + - - +
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Residues in contact with ILE 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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156B ILE* 4.3 10.5 - - + -
158B ILE* 4.2 16.4 - - + -
188B PHE* 3.6 38.8 - - + -
219B TYR* 4.3 6.5 - - + -
225B ALA* 2.8 20.7 + - + +
228B ARG* 1.3 71.4 - - - +
230B SER* 1.3 62.8 + - - +
232B MET* 3.2 7.6 + - + +
233B SER 3.1 20.1 + - - +
236B THR* 3.8 26.6 + - + +
238B LEU* 4.2 3.1 - - + -
298B TRP* 3.7 27.4 - - + -
302B PHE* 3.8 19.7 - - + -
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Residues in contact with SER 230 (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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226B PRO 3.1 20.1 + - - -
227B ALA* 3.5 6.1 - - - -
229B ILE* 1.3 77.8 - - - +
231B ALA* 1.3 62.2 + - - +
233B SER* 3.3 4.2 + - - -
234B LYS* 3.2 31.4 + - - +
301B HIS* 3.9 21.7 + - - +
302B PHE* 3.6 17.6 - - - -
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Residues in contact with ALA 231 (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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192B TYR* 4.7 7.9 - - - +
196B LEU* 5.4 1.3 - - - +
227B ALA 2.9 16.5 + - - +
228B ARG* 3.1 9.1 + - - +
230B SER* 1.3 73.1 - - - +
232B MET* 1.3 66.9 + - - +
233B SER* 4.5 0.3 - - - -
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Residues in contact with MET 232 (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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152B LEU* 3.7 37.1 - - + +
153B PRO* 3.8 25.6 - - + +
156B ILE* 4.5 1.3 - - + -
188B PHE* 3.8 23.8 - - + -
196B LEU* 3.9 25.9 - - + +
199B TYR* 3.9 16.6 - - - -
228B ARG 3.1 11.4 + - - +
229B ILE* 3.2 12.3 + - + +
231B ALA* 1.3 80.8 - - - +
233B SER* 1.3 64.9 + - - +
236B THR* 3.6 28.3 - - + +
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 6.3 0.4 - - - -
229B ILE 3.1 7.8 + - - +
230B SER* 3.3 7.0 + - - +
231B ALA 4.5 0.4 - - - -
232B MET* 1.3 91.4 - - - +
234B LYS* 1.3 62.9 + - - +
235B ASP* 3.4 18.7 + - - +
236B THR* 2.7 35.4 + - - -
302B PHE* 4.3 0.9 - - - -
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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