Contacts of the helix formed by residues 222 - 233 (chain B) in PDB entry 1IS0
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 SER 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B PHE* 3.7 15.9 - - - +
220B PHE* 3.4 9.2 + - - +
221B SER* 1.3 85.3 + - - +
223B LEU* 1.3 63.2 + - - +
224B GLN* 3.0 22.8 - - - +
225B GLN* 3.0 25.4 + - - +
226B LEU* 3.2 17.5 + - - +
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Residues in contact with LEU 223 (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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148B TRP* 3.8 14.6 - - + -
149B TYR* 4.5 9.0 - - + -
174B VAL* 4.4 12.6 - - + -
184B TYR* 3.9 40.2 - - + -
204B ILE* 4.1 28.5 - - + -
212B PHE* 4.0 34.1 - - + -
222B SER* 1.3 72.2 - - - +
224B GLN* 1.3 69.9 + - - +
226B LEU* 3.2 7.7 + - + +
227B VAL* 3.0 33.0 + - + +
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Residues in contact with GLN 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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146B GLU* 5.3 5.4 - - - +
148B TRP* 3.7 27.4 - - + +
222B SER* 3.0 21.9 - - - +
223B LEU* 1.3 97.5 - - - +
225B GLN* 1.3 54.4 + - - +
227B VAL* 3.3 3.5 + - - +
228B ALA* 3.0 28.6 + - - +
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Residues in contact with GLN 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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219B GLN 5.3 0.7 - - - +
220B PHE* 3.6 18.2 - - + +
221B SER* 2.8 47.1 + - - +
222B SER* 3.0 19.0 + - - +
224B GLN* 1.3 73.4 - - - +
226B LEU* 1.3 61.3 + - - +
228B ALA* 3.7 7.4 - - + +
229B TYR* 3.0 29.1 + - + +
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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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186B LEU* 4.2 18.8 - - + -
204B ILE* 3.7 43.3 - - + -
212B PHE* 4.6 6.5 - - + -
213B TYR* 4.7 2.7 - - - +
214B ILE* 4.2 11.2 - - + -
220B PHE* 3.6 37.2 - - + -
222B SER 3.2 11.6 + - - +
223B LEU* 3.2 11.9 + - + +
225B GLN* 1.3 76.2 - - - +
227B VAL* 1.3 73.6 + - + +
229B TYR* 3.4 1.6 + - - +
230B TYR* 3.1 39.6 + - + -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP* 3.9 29.6 - - + +
172B PHE* 3.5 34.8 - - + -
174B VAL* 3.8 28.9 - - + -
186B LEU* 5.0 0.4 - - + -
223B LEU 3.0 19.9 + - - +
224B GLN 3.7 5.2 - - - +
225B GLN 3.3 0.2 - - - -
226B LEU* 1.3 81.3 - - + +
228B ALA* 1.3 60.0 + - - +
230B TYR 3.6 0.2 + - - -
231B SER* 2.6 36.3 + - - +
241B LEU* 3.7 7.6 - - + +
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Residues in contact with ALA 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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224B GLN 3.0 16.8 + - - +
225B GLN* 3.7 9.4 - - + +
227B VAL* 1.3 77.0 - - - +
229B TYR* 1.3 63.1 + - - +
231B SER* 3.1 9.3 + - - -
232B LYS* 3.0 27.6 + - + +
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Residues in contact with TYR 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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218B THR* 3.7 20.1 + - + +
220B PHE* 3.3 37.5 - + + -
225B GLN* 3.0 11.7 + - + +
226B LEU 3.5 2.9 - - - +
228B ALA* 1.3 76.6 - - - +
230B TYR* 1.3 78.1 + + - +
232B LYS* 3.0 26.5 + - + +
233B HIS* 3.1 45.3 + + - -
235B ASP* 2.7 34.5 + - + -
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Residues in contact with TYR 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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186B LEU* 4.8 0.9 - - + -
214B ILE* 3.9 22.8 - - + +
215B THR* 4.3 4.0 + - - -
218B THR* 3.9 22.3 + - - +
220B PHE* 3.6 22.5 - + - -
226B LEU* 3.1 32.3 + - + +
229B TYR* 1.3 97.4 - + - +
231B SER* 1.3 57.4 + - - +
232B LYS 3.3 0.2 - - - -
233B HIS 3.4 13.3 - - - +
234B ALA* 3.3 27.5 - - - -
235B ASP* 4.2 5.1 + - + -
237B LEU* 4.0 13.5 - - + -
240B ARG* 3.8 5.7 - - - -
241B LEU* 2.9 44.5 + - + -
355D ILE* 3.8 27.4 - - + +
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Residues in contact with SER 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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172B PHE* 4.4 4.3 - - - -
227B VAL* 2.6 28.9 + - - +
228B ALA* 3.1 9.4 + - - -
230B TYR* 1.3 77.5 - - - +
232B LYS* 1.3 61.1 + - - +
240B ARG* 2.9 32.3 + - - -
241B LEU* 3.4 26.3 + - - +
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Residues in contact with LYS 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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228B ALA* 3.0 15.4 + - + +
229B TYR* 3.0 16.2 + - + +
231B SER* 1.3 80.2 - - - +
233B HIS* 1.3 88.2 + - + +
240B ARG* 4.5 6.0 - - - +
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Residues in contact with HIS 233 (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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229B TYR* 3.2 56.2 + + - +
230B TYR* 3.4 14.8 - - - -
231B SER 3.5 0.8 - - - -
232B LYS* 1.3 111.5 + - - +
234B ALA* 1.3 64.2 + - - +
235B ASP* 4.2 11.0 - - + +
240B ARG* 4.6 4.5 - - - -
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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