Contacts of the helix formed by residues 232 - 245 (chain B) in PDB entry 4IZ5
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 HIS 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B ARG* 3.7 15.7 + - - +
230B GLY 4.3 0.3 - - - -
231B LYS* 1.3 99.9 + - + +
233B TYR* 1.3 67.4 + - - +
234B LEU* 3.6 2.5 - - + +
235B ASP* 3.8 14.1 - - + +
236B GLN* 3.1 23.4 + - - +
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Residues in contact with TYR 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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191B ARG* 3.4 28.1 - - - +
199B MET* 2.7 52.2 + - + +
200B LEU* 4.3 8.3 - - - +
232B HIS* 1.3 76.7 - - - +
234B LEU* 1.3 83.9 + - + +
236B GLN* 3.2 14.4 + - - +
237B LEU* 3.4 27.0 + - + +
260B ALA* 5.9 0.9 - - - +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B HIS* 4.7 1.6 - - + +
233B TYR* 1.3 100.6 - - + +
235B ASP* 1.3 59.7 + - - +
237B LEU* 3.5 8.5 + - + +
238B ASN* 3.2 30.4 + - - +
263B TYR* 3.3 41.2 + - + +
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Residues in contact with ASP 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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229B PRO 4.8 0.3 - - - +
230B GLY* 3.3 4.2 - - - -
231B LYS* 2.7 32.5 + - + +
232B HIS* 3.8 22.9 - - + +
233B TYR 3.2 0.2 - - - -
234B LEU* 1.3 77.4 - - - +
236B GLN* 1.3 60.8 + - - +
238B ASN* 3.3 9.9 + - - +
239B HIS* 3.0 44.5 + - - -
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Residues in contact with GLN 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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191B ARG* 2.8 38.6 + - + +
192B TRP* 3.6 9.0 + - - +
194B ARG 4.7 2.0 + - - -
199B MET* 3.6 24.0 - - + +
212B TRP* 6.0 0.2 - - - +
228B PHE* 2.9 43.5 + - - +
230B GLY* 3.1 19.6 + - - +
232B HIS 3.1 18.1 + - - +
233B TYR 3.2 5.8 + - - +
235B ASP* 1.3 75.3 - - - +
237B LEU* 1.3 64.4 + - - +
239B HIS* 3.3 3.9 + - - +
240B ILE* 3.2 31.1 + - - +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PRO* 4.9 3.1 - - + +
199B MET* 4.1 22.0 - - + -
200B LEU* 3.6 30.7 - - + -
233B TYR* 3.4 54.0 + - + +
234B LEU* 3.6 10.8 - - - +
235B ASP 3.3 0.4 - - - -
236B GLN* 1.3 77.4 - - - +
238B ASN* 1.3 66.2 + - - +
240B ILE* 3.1 21.0 + - + +
241B LEU* 3.2 19.6 + - + +
263B TYR* 4.9 11.4 - - + -
264B LEU* 4.5 18.4 - - + -
296B PHE* 6.5 0.2 - - + -
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Residues in contact with ASN 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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234B LEU* 3.2 17.3 + - - +
235B ASP* 3.6 16.2 - - - +
236B GLN 3.3 0.2 - - - -
237B LEU* 1.3 76.4 - - - +
239B HIS* 1.3 58.8 + - + +
241B LEU* 3.7 3.3 + - - +
242B GLY* 3.0 26.0 + - - -
263B TYR* 4.1 8.4 + - - -
267B LEU* 3.7 30.1 - - - +
270B LYS* 3.6 20.9 + - - +
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Residues in contact with HIS 239 (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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225B ARG* 5.4 4.7 - - - -
227B ILE 4.7 1.6 + - - -
228B PHE* 3.5 17.4 - - + -
229B PRO* 3.2 42.0 + - + +
230B GLY* 4.2 5.6 - - - -
235B ASP* 3.0 46.5 + - - +
236B GLN* 3.6 11.4 - - - +
237B LEU 3.2 0.2 - - - -
238B ASN* 1.3 79.0 - - + +
240B ILE* 1.3 62.3 + - - +
242B GLY* 3.4 4.4 + - - +
243B ILE* 3.3 30.4 - - - +
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Residues in contact with ILE 240 (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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194B ARG 4.4 1.6 - - - +
196B PRO* 4.3 19.3 - - + -
199B MET* 3.8 26.2 - - + -
212B TRP* 3.9 22.2 - - + -
228B PHE* 3.7 26.9 - - + -
236B GLN* 3.4 20.9 - - - +
237B LEU* 3.1 11.5 + - + +
239B HIS* 1.3 76.6 - - - +
241B LEU* 1.3 64.8 + - + +
243B ILE* 3.3 1.9 + - - -
244B LEU* 2.8 53.3 + - + +
296B PHE* 4.8 3.1 - - + -
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Residues in contact with LEU 241 (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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237B LEU 3.2 15.3 + - - +
238B ASN* 4.3 3.8 - - - +
240B ILE* 1.3 76.8 - - + +
242B GLY* 1.3 61.2 + - - +
243B ILE 3.2 0.9 - - - -
244B LEU* 4.9 1.1 - - + -
245B GLY* 3.1 34.0 + - - +
246B SER* 4.8 5.6 - - - +
247B PRO* 3.7 31.4 - - + -
264B LEU* 4.2 20.2 - - + +
267B LEU* 4.1 28.9 - - + -
268B PRO 6.1 0.2 - - - +
270B LYS* 3.3 28.9 - - + +
271B ASN 4.6 0.2 - - - +
296B PHE* 4.4 24.9 - - + -
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Residues in contact with GLY 242 (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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238B ASN 3.0 18.4 + - - -
239B HIS* 3.8 3.6 - - - -
240B ILE 3.2 0.8 - - - -
241B LEU* 1.3 77.4 - - - +
243B ILE* 1.3 65.0 + - - +
245B GLY 4.7 0.4 - - - -
270B LYS* 4.3 14.7 - - - +
271B ASN 4.1 5.2 - - - +
273B VAL* 3.8 16.1 - - - +
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Residues in contact with ILE 243 (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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227B ILE* 4.4 17.7 - - + +
228B PHE* 3.9 19.1 - - + -
239B HIS* 3.3 20.2 - - - +
240B ILE 3.3 1.6 + - - -
242B GLY* 1.3 83.8 - - - +
244B LEU* 1.3 61.8 + - - +
245B GLY 3.3 2.0 - - - -
272B LYS* 3.8 1.6 + - - +
273B VAL* 3.0 37.7 + - + +
275B TRP* 4.0 26.4 - - + -
278B LEU* 3.7 34.1 - - + -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TRP* 3.6 28.0 - - + -
228B PHE* 4.6 7.0 - - + -
240B ILE* 2.8 30.1 + - + +
241B LEU* 4.9 1.6 - - + -
243B ILE* 1.3 74.1 - - - +
245B GLY* 1.3 65.8 + - - +
246B SER 5.0 0.2 - - - +
272B LYS* 3.6 34.6 + - - +
275B TRP* 3.7 28.3 - - + -
291B ASP* 5.8 0.2 - - - +
294B LEU* 3.2 29.2 - - + +
296B PHE* 4.2 20.0 - - + +
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Residues in contact with GLY 245 (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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241B LEU* 3.1 29.2 + - - +
243B ILE 3.3 4.0 + - - -
244B LEU* 1.3 85.4 - - - +
246B SER* 1.3 68.3 + - - +
247B PRO* 3.5 2.6 - - - +
270B LYS 3.3 11.7 - - - -
271B ASN 3.6 1.1 + - - -
272B LYS* 3.6 17.0 - - - +
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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