Contacts of the helix formed by residues 226 - 239 (chain B) in PDB entry 4CRU
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 ALA 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B PRO* 4.2 1.2 - - - +
225B SER* 1.3 73.0 + - - +
227B ARG* 1.3 58.4 + - - +
229B LEU* 3.4 8.2 + - - +
230B LYS* 2.9 28.8 + - - +
265B VAL* 5.6 11.9 - - + +
269B ASP* 4.6 12.6 - - + +
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Residues in contact with ARG 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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176B GLU* 2.9 40.8 + - - +
177B LEU* 3.0 27.7 - - - +
180B THR* 3.8 22.4 + - + +
225B SER* 3.8 1.1 - - - +
226B ALA* 1.3 78.2 - - - +
228B LEU* 1.3 66.4 + - - +
230B LYS* 3.4 9.4 + - - +
231B HIS* 3.2 33.3 + - + +
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Residues in contact with LEU 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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176B GLU* 5.0 6.1 - - + +
179B LYS* 3.8 37.0 - - + +
180B THR* 3.7 18.4 - - - +
183B THR* 3.5 27.1 - - - +
216B MET* 3.7 18.2 - - + -
219B GLN* 5.9 1.3 - - - +
220B LEU* 4.0 23.6 - - + -
225B SER* 3.4 19.7 + - - +
226B ALA 3.3 0.4 - - - -
227B ARG* 1.3 80.1 - - - +
229B LEU* 1.3 65.1 + - - +
231B HIS* 3.1 4.5 + - + +
232B VAL* 3.0 26.4 + - + +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 5.7 1.1 - - + -
220B LEU* 3.8 25.2 - - + +
225B SER 2.9 20.0 + - - +
226B ALA* 3.7 7.4 - - - +
228B LEU* 1.3 75.8 - - - +
230B LYS* 1.3 64.1 + - - +
232B VAL* 3.2 5.4 + - + +
233B VAL* 2.9 45.5 + - + +
257B LEU* 4.7 4.0 - - + -
262B PHE* 3.9 44.9 - - + -
265B VAL* 4.0 13.0 - - + -
266B LEU* 3.9 27.6 - - + -
272B THR* 4.7 0.2 - - + -
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Residues in contact with LYS 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 ALA 2.9 15.1 + - - +
227B ARG* 3.4 13.7 - - - +
228B LEU 3.1 0.2 - - - -
229B LEU* 1.3 77.2 - - - +
231B HIS* 1.3 66.2 + - + +
233B VAL* 3.5 2.6 + - - +
234B ARG* 3.0 26.5 + - - +
269B ASP* 4.1 8.9 + - - +
271B THR* 4.0 20.4 + - - +
272B THR* 3.2 29.6 - - - +
275B TRP* 3.6 31.7 - - + -
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Residues in contact with HIS 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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180B THR* 3.7 33.9 - - + +
183B THR* 3.5 21.5 - - + -
184B PHE* 3.8 30.4 - + + +
187B GLN* 2.7 30.3 + - - +
227B ARG* 3.2 20.9 + - - +
228B LEU* 3.1 6.3 + - - +
230B LYS* 1.3 84.3 - - + +
232B VAL* 1.3 65.9 + - - +
234B ARG* 3.3 2.1 + - - +
235B CYS* 3.0 28.1 + - - -
275B TRP* 6.1 0.2 - - - -
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Residues in contact with VAL 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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183B THR* 4.3 9.2 - - + -
213B LEU* 4.3 13.0 - - + +
216B MET* 3.9 32.5 - - + -
217B VAL* 3.8 17.7 - - + -
220B LEU* 4.2 14.4 - - + -
228B LEU 3.0 20.0 + - - +
229B LEU* 3.6 8.3 - - + +
231B HIS* 1.3 77.4 - - - +
233B VAL* 1.3 65.6 + - + +
235B CYS* 3.2 4.2 + - - +
236B TYR* 3.0 45.8 + - + -
257B LEU* 5.4 0.7 - - + -
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 2.9 37.2 + - + +
230B LYS 3.8 3.8 - - - +
232B VAL* 1.3 78.6 - - + +
234B ARG* 1.3 62.1 + - - +
236B TYR* 3.2 8.6 + - - +
237B LEU* 2.9 21.0 + - - +
257B LEU* 4.4 16.6 - - + -
266B LEU* 5.9 0.9 - - + -
272B THR* 3.9 18.4 - - + +
275B TRP* 3.8 13.9 - - + +
276B LEU* 3.7 42.8 - - + +
279B LEU* 4.9 3.4 - - + +
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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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187B GLN* 3.6 39.5 - - + +
191B LEU* 3.3 26.5 - - + +
230B LYS 3.0 15.0 + - - +
231B HIS 3.3 0.6 + - - +
233B VAL* 1.3 76.8 - - - +
235B CYS* 1.3 57.2 + - - +
237B LEU* 3.4 21.4 + - - +
238B ARG* 2.9 51.3 + - + +
241B ASP* 5.5 2.2 + - - -
275B TRP* 3.7 46.0 - - + +
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Residues in contact with CYS 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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183B THR* 4.0 15.7 - - - -
186B LEU* 4.3 8.7 - - - -
187B GLN* 3.8 34.5 - - - +
190B LEU* 3.8 20.4 - - + +
213B LEU* 4.2 16.2 - - + -
231B HIS 3.0 19.5 + - - -
232B VAL 3.2 8.3 + - - +
234B ARG* 1.3 78.0 - - - +
236B TYR* 1.3 62.5 + - - +
238B ARG* 3.3 3.5 + - - +
239B LEU* 3.0 29.5 + - - +
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Residues in contact with TYR 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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210B ALA* 3.9 8.6 + - + -
213B LEU* 3.3 28.5 - - + +
214B GLY* 3.1 31.7 + - - -
217B VAL* 3.9 2.2 - - + -
232B VAL* 3.0 35.6 + - + -
233B VAL* 3.7 5.4 - - - +
235B CYS* 1.3 77.1 - - - +
237B LEU* 1.3 63.1 + - - +
239B LEU* 3.2 8.4 + - + +
240B SER* 3.1 17.5 + - - -
249B LEU* 3.7 25.7 - - + +
252B CYS* 5.8 0.7 - - - -
253B LEU* 3.7 22.0 - - + -
254B PRO* 3.4 16.9 - - + +
257B LEU* 3.6 24.0 - - + -
279B LEU* 3.6 25.3 - - + +
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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
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233B VAL 2.9 16.9 + - - +
234B ARG* 3.7 24.2 - - - +
236B TYR* 1.3 74.9 - - - +
238B ARG* 1.3 62.2 + - - +
240B SER* 2.7 23.6 + - - -
241B ASP* 3.6 8.4 + - - +
275B TRP* 3.9 43.5 - - + +
278B GLN* 3.7 14.1 - - + -
279B LEU* 3.6 34.0 - - + +
282B ASN* 3.7 18.4 - - - +
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Residues in contact with ARG 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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190B LEU* 2.8 40.6 + - + +
191B LEU* 3.1 36.1 + - + +
192B ASP 3.7 0.4 + - - -
193B ASP* 2.8 38.6 + - - +
196B LEU* 3.5 23.5 - - + +
234B ARG* 2.9 30.6 + - + +
235B CYS* 3.8 4.0 - - - +
237B LEU* 1.3 74.1 - - - +
239B LEU* 1.3 66.5 + - - +
241B ASP* 2.9 53.0 + - - +
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Residues in contact with LEU 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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190B LEU* 3.7 27.8 - - + -
196B LEU* 4.0 3.4 - - + -
199B ILE* 4.1 10.1 - - + -
200B CYS* 4.0 22.9 - - - -
206B PHE* 4.2 19.7 - - + -
209B VAL* 4.3 9.9 - - + -
210B ALA* 5.4 2.0 - - - +
213B LEU* 3.9 25.8 - - + -
235B CYS 3.0 21.3 + - - +
236B TYR* 3.2 13.9 + - + +
238B ARG* 1.3 76.2 - - - +
240B SER* 1.3 57.0 + - - +
242B ASN* 3.0 18.5 + - - +
245B ALA* 3.1 21.0 - - + +
249B LEU* 4.0 10.5 - - + -
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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