Contacts of the helix formed by residues 230 - 245 (chain B) in PDB entry 5UFL
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 ASN 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B GLU 4.5 7.0 + - - +
224B LYS* 3.1 35.0 + - - +
225B LEU 4.0 3.1 - - - +
227B HIS 3.4 2.1 + - - +
229B ARG* 1.3 115.6 - - - +
231B ILE* 1.3 64.9 + - - +
232B HIS 3.2 3.4 - - - -
233B GLN* 3.2 28.3 + - + +
234B THR* 3.6 9.4 + - - -
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Residues in contact with ILE 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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225B LEU 3.5 18.4 + - - +
226B PHE* 3.8 28.3 - - + -
227B HIS 3.1 20.5 + - - +
228B ALA* 4.2 10.3 - - - -
229B ARG 4.4 2.0 - - - +
230B ASN* 1.3 73.8 - - - +
232B HIS* 1.3 68.6 + - + +
234B THR* 3.0 9.7 + - + -
235B PHE* 2.9 60.9 + - + -
261B LEU* 5.6 0.7 - - + -
267B ILE* 4.5 11.4 - - + -
270B TYR* 4.1 19.5 - - + +
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Residues in contact with HIS 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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229B ARG 4.6 8.7 + - - +
231B ILE* 1.3 82.7 - - + +
233B GLN* 1.3 74.6 + - + +
236B GLN* 3.1 46.6 + - - +
274B TYR* 3.4 27.1 - + - -
275B GLU* 3.5 34.1 - - - +
276B HIS* 4.0 20.7 + + - -
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Residues in contact with GLN 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 ARG 4.3 2.6 - - - +
230B ASN* 3.2 23.7 + - - +
232B HIS* 1.3 92.9 + - - +
234B THR* 1.3 61.1 + - - +
236B GLN* 3.4 12.0 + - - +
237B LEU* 2.9 30.5 + - - +
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Residues in contact with THR 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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209B LEU* 4.4 8.7 - - + -
225B LEU* 2.8 46.0 + - + +
226B PHE* 4.1 24.0 - - + -
230B ASN 3.6 5.2 + - - -
231B ILE* 3.0 13.1 + - + -
233B GLN* 1.3 79.0 - - - +
235B PHE* 1.3 56.1 + - + +
237B LEU* 3.5 7.3 + - + +
238B ILE* 3.0 51.3 + - + +
261B LEU* 5.1 0.4 - - + -
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Residues in contact with PHE 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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231B ILE* 2.9 48.6 + - + +
234B THR* 1.3 75.0 - - - +
236B GLN* 1.3 59.6 + - - +
238B ILE* 3.9 6.7 - - + -
239B PHE* 2.9 40.5 + + + -
258B LEU* 4.8 15.7 - - + -
261B LEU* 4.9 3.4 - - + -
267B ILE* 3.6 37.2 - - + -
270B TYR* 3.9 7.0 - - + -
271B LEU* 3.7 43.5 - - + -
274B TYR* 3.7 42.6 - + + -
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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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232B HIS* 3.1 38.3 + - - +
233B GLN* 3.6 12.1 - - - +
235B PHE* 1.3 74.9 - - - +
237B LEU* 1.3 57.8 + - - +
239B PHE* 4.4 2.3 - - - +
240B ASN* 3.1 30.0 + - + +
274B TYR* 3.3 19.1 + - - +
276B HIS* 5.2 5.4 + - + -
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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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197B LEU* 4.1 30.5 - - + +
202B LEU* 5.3 3.4 - - + -
205B VAL* 3.9 29.2 - - + -
209B LEU* 4.1 17.0 - - + -
225B LEU* 6.0 1.1 - - + -
233B GLN 2.9 17.9 + - - +
234B THR* 3.7 7.9 - - - +
236B GLN* 1.3 75.6 - - - +
238B ILE* 1.3 64.2 + - - +
240B ASN* 3.4 13.8 + - - +
241B ILE* 3.0 39.0 + - + +
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Residues in contact with ILE 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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209B LEU* 3.6 21.3 - - + -
234B THR* 3.0 35.8 + - + +
235B PHE* 3.9 7.9 - - + +
237B LEU* 1.3 75.4 - - - +
239B PHE* 1.3 59.2 + - + +
241B ILE* 3.3 7.9 + - - +
242B LEU* 3.0 23.7 + - + +
254B SER* 3.4 20.0 + - - +
257B LEU* 4.0 12.1 - - + -
258B LEU* 4.1 38.6 - - + -
261B LEU* 3.7 29.6 - - + -
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Residues in contact with PHE 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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235B PHE* 2.9 32.7 + + + +
236B GLN* 4.4 2.7 - - - +
238B ILE* 1.3 74.2 - - + +
240B ASN* 1.3 63.5 + - - +
242B LEU* 3.9 8.3 - - + -
243B ILE* 3.1 34.8 + - + +
258B LEU* 3.8 29.6 - - + -
271B LEU* 3.7 31.2 - - + -
274B TYR* 4.1 6.5 - + - -
277B PHE* 4.1 14.1 - + - -
280B CYS* 3.7 44.2 - - + -
281B LEU* 5.8 0.2 - - - -
284B VAL* 4.3 20.6 - - + -
306B PHE* 4.2 14.8 - + - -
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Residues in contact with ASN 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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202B LEU* 4.1 25.2 - - - +
236B GLN* 3.1 22.3 + - + +
237B LEU* 3.5 12.7 + - - +
239B PHE* 1.3 73.7 - - - +
241B ILE* 1.3 57.8 + - - +
243B ILE* 5.5 0.2 - - - -
244B ASN* 2.8 65.0 + - - +
245B GLY 3.6 0.5 + - - -
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Residues in contact with ILE 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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202B LEU* 4.1 34.1 - - + +
205B VAL* 3.8 25.6 - - + -
206B VAL* 3.9 40.4 - - + +
209B LEU* 4.8 5.8 - - + -
237B LEU* 3.0 29.1 + - + +
238B ILE* 3.6 10.3 - - + +
240B ASN* 1.3 75.8 - - + +
242B LEU* 1.3 59.9 + - - +
245B GLY* 2.9 24.3 + - - -
246B ASP 5.1 0.3 - - - +
250B THR* 4.0 19.7 + - - -
254B SER* 4.0 9.9 - - - +
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Residues in contact with LEU 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 ILE 3.0 12.5 + - - +
239B PHE* 3.9 14.8 - - + +
240B ASN 3.2 0.2 - - - -
241B ILE* 1.3 79.1 - - - +
243B ILE* 1.3 62.1 + - + +
245B GLY 4.7 0.7 + - - -
246B ASP 5.3 1.0 - - - +
251B ARG* 3.1 40.0 + - - +
254B SER* 3.3 26.5 - - - +
255B VAL* 4.2 17.0 - - + +
258B LEU* 4.4 12.3 - - + -
284B VAL* 4.5 13.0 - - + -
287B LEU* 3.5 23.8 - - + -
299B VAL* 5.1 2.5 - - + -
302B LEU* 3.4 32.3 - - + -
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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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239B PHE* 3.1 28.2 + - + +
242B LEU* 1.3 80.7 - - + +
244B ASN* 1.3 77.7 + - - +
245B GLY 3.6 2.4 + - - +
251B ARG* 4.7 8.7 + - - -
280B CYS* 4.1 13.9 - - - +
283B GLN* 3.5 53.4 - - + +
284B VAL* 4.4 15.0 - - + -
287B LEU* 4.5 18.9 - - + +
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Residues in contact with ASN 244 (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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202B LEU* 4.2 8.1 - - + +
240B ASN* 2.8 42.1 + - - +
243B ILE* 1.3 89.6 - - - +
245B GLY* 1.3 67.2 + - - +
283B GLN* 5.1 3.4 + - - +
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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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202B LEU* 3.6 21.7 - - - +
240B ASN 3.6 2.0 + - - -
241B ILE 2.9 21.5 + - - -
242B LEU 4.6 0.6 - - - -
243B ILE 3.6 2.9 - - - +
244B ASN* 1.3 82.7 - - - +
246B ASP* 1.3 66.6 + - - +
247B GLY* 3.7 1.4 + - - -
250B THR* 4.0 1.6 - - - -
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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