Contacts of the helix formed by residues 226 - 238 (chain B) in PDB entry 4IRP
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 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B TYR* 5.4 8.3 - - - -
196B TYR* 3.3 31.1 + - - -
221B PHE* 3.9 9.3 - - - -
225B GLY* 1.3 78.9 + - - -
227B GLU* 1.3 66.4 + - - +
228B ASP 3.1 3.6 - - - +
229B ASP* 3.0 40.9 + - + +
230B GLU* 3.1 12.1 + - - +
233B ARG* 5.2 1.8 + - - +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASN* 4.8 2.3 - - - +
141B ARG* 3.2 33.2 + - - +
142B ALA* 2.8 42.3 + - + +
217B MET* 3.9 5.7 - - + +
218B SER* 5.6 1.3 + - - -
221B PHE* 3.4 43.8 - - + +
223B GLY* 3.9 17.7 + - - -
224B TRP 4.5 1.7 - - - +
225B GLY 3.9 2.6 + - - -
226B ARG* 1.3 73.8 - - - +
228B ASP* 1.3 64.8 + - - +
230B GLU* 3.6 5.0 + - - +
231B PHE* 3.1 19.8 + - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 2.5 42.3 + - - -
196B TYR* 5.9 0.7 - - - +
199B TYR* 5.5 2.4 - - + -
200B VAL* 3.6 25.6 - - + +
201B GLY* 3.9 19.9 - - - +
217B MET* 3.7 8.0 - - - +
226B ARG* 3.1 1.6 - - + -
227B GLU* 1.3 76.6 - - - +
229B ASP* 1.3 63.0 + - - +
231B PHE* 2.9 20.5 + - - +
232B TYR 2.9 11.4 + - - -
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Residues in contact with ASP 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B TYR* 3.1 26.2 + - - -
198B THR* 4.2 11.8 - - - +
200B VAL* 4.5 1.4 - - - +
226B ARG* 3.0 48.8 + - + +
228B ASP* 1.3 77.2 - - - +
230B GLU* 1.3 65.9 + - - +
232B TYR* 3.3 10.1 + - - +
233B ARG* 3.1 44.5 + - - +
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Residues in contact with GLU 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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218B SER* 3.9 15.3 + - - -
220B ARG* 5.1 1.6 - - - +
221B PHE* 3.7 28.9 - - + -
226B ARG 3.1 5.4 + - - +
227B GLU 3.8 6.6 - - - +
229B ASP* 1.3 77.1 - - - +
231B PHE* 1.3 63.6 + - - +
233B ARG* 3.3 28.1 + - + +
234B ARG* 2.8 61.6 + - - +
283B ARG 3.9 19.5 + - - +
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B VAL* 5.3 1.3 - - + -
204B LEU* 3.8 22.2 - - + -
206B LEU* 3.6 30.1 - - + -
211B TYR* 3.9 13.9 - + - -
214B CYS* 3.9 15.9 - - + -
216B GLY 3.4 32.3 - - - -
217B MET* 3.7 30.3 - - + -
227B GLU 3.1 13.1 + - - +
228B ASP* 2.9 10.6 + - - +
230B GLU* 1.3 77.9 + - - +
232B TYR* 1.3 68.2 + - - +
234B ARG* 3.0 8.9 + - - +
235B ILE* 2.9 51.7 + - + +
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Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LYS 6.0 0.2 - - - -
198B THR* 4.0 34.7 - - + +
200B VAL* 3.6 28.9 - - + +
228B ASP 2.9 6.7 + - - -
229B ASP* 3.3 8.7 + - - +
231B PHE* 1.3 76.5 - - - +
233B ARG* 1.3 71.7 + - + +
235B ILE* 3.1 14.1 + - + +
236B LYS* 3.1 58.7 + - + +
242B LEU* 4.0 35.0 - - + -
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Residues in contact with ARG 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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221B PHE* 5.5 2.0 - - - -
226B ARG* 5.2 1.6 + - - +
229B ASP* 3.1 39.9 + - - +
230B GLU* 3.7 33.8 - - + +
231B PHE 3.1 0.2 - - - -
232B TYR* 1.3 82.9 - - + +
234B ARG* 1.3 60.8 + - - +
236B LYS* 4.0 4.4 - - - +
237B GLY* 2.8 27.9 + - - -
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Residues in contact with ARG 234 (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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214B CYS* 3.5 25.4 + - + +
215B ASN* 3.0 16.6 + - - +
216B GLY 3.0 29.9 + - - -
217B MET* 3.9 2.3 - - - +
218B SER* 3.8 19.6 - - - +
220B ARG* 4.9 0.4 - - - +
230B GLU* 2.8 39.5 + - - +
231B PHE* 3.0 14.5 + - + +
233B ARG* 1.3 76.3 - - - +
235B ILE* 1.3 65.2 + - - +
237B GLY* 3.7 1.6 - - - -
238B ALA* 3.0 25.5 + - - +
283B ARG 3.3 21.7 + - - -
285B GLY 2.7 30.3 + - - -
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Residues in contact with ILE 235 (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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182B PRO* 3.9 31.9 - - + -
200B VAL* 4.8 2.0 - - + -
204B LEU* 4.4 8.1 - - + -
214B CYS* 3.9 17.3 - - - -
231B PHE* 2.9 49.2 + - + +
232B TYR* 3.1 15.9 + - + +
234B ARG* 1.3 75.2 - - - +
236B LYS* 1.3 67.7 + - + +
238B ALA* 3.2 6.8 + - - +
240B LEU* 3.1 50.3 + - + +
242B LEU* 4.6 18.4 - - + +
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Residues in contact with LYS 236 (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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232B TYR* 3.1 55.5 + - + +
233B ARG* 4.0 5.4 - - - +
235B ILE* 1.3 76.4 - - + +
237B GLY* 1.3 57.1 + - - +
238B ALA 3.0 4.5 - - - -
239B GLY* 2.9 21.5 + - - -
240B LEU 2.7 27.3 + - - +
241B GLN* 3.9 10.7 - - - +
242B LEU* 4.6 4.5 - - + +
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Residues in contact with GLY 237 (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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233B ARG 2.8 21.5 + - - -
234B ARG* 3.7 2.5 - - - -
236B LYS* 1.3 72.4 - - - +
238B ALA* 1.3 58.0 + - - +
239B GLY 3.1 1.6 + - - -
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Residues in contact with ALA 238 (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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213B LEU* 3.8 35.8 - - + +
214B CYS* 4.3 16.6 - - - -
234B ARG 3.0 16.7 + - - +
235B ILE 3.5 6.7 - - - +
236B LYS 3.0 1.8 + - - -
237B GLY* 1.3 78.0 - - - +
239B GLY* 1.3 60.0 + - - +
240B LEU* 3.3 7.4 + - + +
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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