Contacts of the helix formed by residues 230 - 244 (chain B) in PDB entry 1UES
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 LYS 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ASN* 3.7 28.3 - - - +
225B GLU 4.2 2.7 - - - +
226B PHE* 2.9 41.2 + - + +
229B GLY* 1.3 87.7 - - - +
231B HIS* 1.3 66.6 + - - +
232B LEU 3.5 0.9 - - - -
233B LYS* 3.7 4.2 - - + +
234B THR* 3.0 29.6 + - - +
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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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160A GLU* 3.6 10.8 - - - -
164A TYR* 2.7 33.4 + + - -
169A ASN* 3.5 25.7 - - + +
226B PHE 2.8 30.2 + - - -
227B HIS* 3.3 19.7 - - + +
230B LYS* 1.3 73.7 - - - +
232B LEU* 1.3 65.3 + - - +
234B THR* 3.2 8.1 + - - -
235B TYR* 3.1 38.6 + - + -
274B HIS* 5.3 0.2 - - - +
361B HIS* 3.3 37.5 + + + +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.4 20.9 - - + -
206B ILE* 4.0 6.5 - - + +
227B HIS 3.0 13.9 + - - +
228B HIS* 3.3 28.5 + - + +
230B LYS 3.5 0.2 - - - -
231B HIS* 1.3 75.0 - - - +
233B LYS* 1.3 64.5 + - - +
235B TYR* 3.0 11.1 + - + -
236B VAL* 2.9 30.9 + - + +
271B THR* 4.0 24.2 - - + +
274B HIS* 3.7 33.4 - - + -
275B ASN* 3.8 17.5 - - - +
278B PHE* 4.2 4.7 - - + -
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.7 27.3 - - + +
228B HIS 3.5 4.2 + - - -
229B GLY 3.3 25.4 - - - +
230B LYS* 3.5 4.9 + - - +
231B HIS 3.3 0.4 - - - -
232B LEU* 1.3 77.2 - - - +
234B THR* 1.3 58.7 + - - +
236B VAL* 3.2 3.6 + - - +
237B ASP* 2.7 72.8 + - - +
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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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169A ASN* 5.4 2.9 + - - -
230B LYS* 3.0 19.4 + - - +
231B HIS* 3.5 7.2 - - - -
233B LYS* 1.3 74.3 - - - +
235B TYR* 1.3 70.5 + - + +
237B ASP* 3.9 6.1 - - - +
238B ASN* 2.9 50.2 + - - +
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Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 4.1 15.8 - + - -
231B HIS* 3.1 35.0 + - + -
232B LEU* 3.0 13.1 + - + +
234B THR* 1.3 80.4 - - + +
236B VAL* 1.3 57.3 + - - +
238B ASN* 3.7 3.3 - - - +
239B LEU* 2.9 30.3 + - - +
266B ASN 4.9 0.2 - - - -
267B ASN* 3.4 25.1 - - - +
270B GLN* 3.0 43.2 + - + -
271B THR* 3.7 15.5 - - - +
274B HIS* 3.5 29.8 - + - -
359B TRP* 3.7 21.8 - - - -
361B HIS* 4.4 5.0 - + - -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B HIS* 3.5 27.3 - - + +
204B GLU* 3.6 29.2 - - - +
205B LEU* 4.1 7.2 - - + +
206B ILE 5.7 0.2 - - - +
232B LEU* 2.9 27.7 + - + +
233B LYS* 3.6 9.4 - - - +
235B TYR* 1.3 76.0 - - - +
237B ASP* 1.3 68.8 + - - +
239B LEU* 3.2 6.9 + - - +
240B ASN* 3.0 27.0 + - - +
271B THR* 4.0 23.8 - - + -
275B ASN* 5.8 0.2 - - - +
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Residues in contact with ASP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LYS* 2.7 59.3 + - - +
234B THR* 4.1 5.5 - - - +
236B VAL* 1.3 80.5 - - - +
238B ASN* 1.3 63.1 + - - +
240B ASN* 3.4 2.4 + - - +
241B LYS* 2.8 56.3 + - - +
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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 THR* 2.9 42.3 + - - +
235B TYR* 3.7 1.0 - - - +
237B ASP* 1.3 76.3 - - - +
239B LEU* 1.3 66.6 + - - +
241B LYS* 3.3 6.9 + - - +
242B LEU* 3.0 31.2 + - + +
267B ASN* 3.3 30.9 + - - +
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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
----------------------------------------------------------
203B HIS* 3.5 36.3 - - + +
235B TYR 2.9 18.3 + - - +
236B VAL* 3.2 6.5 + - - +
238B ASN* 1.3 77.4 - - - +
240B ASN* 1.3 62.0 + - - +
242B LEU* 3.0 4.5 + - - -
243B ILE* 3.0 33.8 + - + +
253B LEU* 4.2 10.1 - - + -
256B ILE* 4.6 5.6 - - + -
264B ILE* 4.2 20.0 - - + +
267B ASN* 4.0 8.7 - - + +
268B ALA* 3.9 35.9 - - + +
271B THR* 4.0 12.8 - - + +
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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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201B MET 4.9 0.2 - - - -
202B THR* 2.9 28.3 + - + +
203B HIS* 2.7 51.6 + - - -
236B VAL* 3.0 26.1 + - - +
237B ASP* 3.7 6.1 + - - +
239B LEU* 1.3 76.8 - - - +
241B LYS* 1.3 74.0 - - + +
243B ILE* 2.9 28.9 - - - +
244B ILE* 4.4 3.6 - - - +
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Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASP* 2.8 50.7 + - - +
238B ASN* 3.7 8.7 - - - +
239B LEU 3.2 0.2 - - - -
240B ASN* 1.3 92.3 - - + +
242B LEU* 1.3 64.6 + - + +
244B ILE* 4.3 15.2 - - - +
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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 ASN* 3.0 21.0 + - + +
239B LEU* 3.0 4.7 + - - +
241B LYS* 1.3 81.4 - - + +
243B ILE* 1.3 66.8 + - - +
244B ILE 3.2 10.1 + - - +
246B THR* 3.7 8.3 + - - +
263B GLY* 3.9 21.1 - - - +
264B ILE* 4.1 26.3 - - + +
267B ASN* 3.6 24.7 - - + +
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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
----------------------------------------------------------
201B MET* 3.0 36.8 - - + +
202B THR* 3.8 8.1 - - - +
203B HIS* 4.8 0.2 - - - +
239B LEU* 3.0 29.6 + - + +
240B ASN 2.9 20.2 - - - +
242B LEU* 1.3 71.7 - - - +
244B ILE* 1.3 93.3 + - + +
246B THR* 2.9 20.5 + - - -
248B PHE 4.4 4.9 - - - +
249B GLU* 3.0 43.6 - - + +
256B ILE* 4.5 5.6 - - + -
264B ILE* 5.3 5.6 - - + -
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Residues in contact with ILE 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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240B ASN 4.4 6.1 - - - +
241B LYS* 4.3 11.5 - - - +
242B LEU* 3.2 8.7 - - - +
243B ILE* 1.3 96.1 - - + +
245B GLY* 1.3 64.1 + - - +
246B THR* 3.8 0.9 + - - +
249B GLU* 3.2 13.0 - - - +
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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