Contacts of the helix formed by residues 227 - 239 (chain B) in PDB entry 1ULH
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 CYS 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A GLN 3.1 11.9 - - - +
209A LYS* 3.1 37.0 - - - +
211A VAL 3.1 7.6 - - - +
212A THR* 3.7 6.0 - - + +
155B LEU* 4.4 6.3 - - - -
225B SER 3.8 1.4 + - - -
226B ASP* 1.3 77.7 - - - +
228B ILE* 1.3 63.0 + - - +
229B GLY* 3.9 2.5 - - - -
230B LYS* 3.2 52.5 + - - +
231B ILE* 3.3 10.7 + - - +
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Residues in contact with ILE 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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207A ILE* 4.7 0.9 - - + +
208A GLN* 3.4 24.9 - - - +
211A VAL* 2.7 31.0 + - + +
212A THR 3.8 9.6 - - - +
213A PHE 4.2 1.1 - - - +
216A VAL* 3.5 30.3 - - + -
231A ILE* 3.7 18.2 - - + +
232A SER* 3.6 33.3 + - - +
234A PRO* 5.2 2.7 - - + -
235A ALA* 3.9 14.1 - - + +
272A MET* 6.1 0.7 - - - -
227B CYS* 1.3 69.1 - - - +
229B GLY* 1.3 68.4 + - - +
231B ILE* 3.1 20.8 + - - +
232B SER* 3.1 15.4 + - - -
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Residues in contact with GLY 229 (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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208A GLN* 3.1 43.7 + - - +
155B LEU* 3.4 25.8 - - - +
227B CYS 3.2 0.2 - - - -
228B ILE* 1.3 80.3 - - - +
230B LYS* 1.3 55.1 + - - +
232B SER* 3.7 1.8 + - - -
233B PHE* 3.1 21.8 + - - +
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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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155B LEU* 4.0 11.2 - - + -
156B TRP* 3.6 79.3 + - + +
222B PHE* 3.3 23.9 - - + -
226B ASP* 4.3 26.6 + - + +
227B CYS* 3.2 28.4 + - - +
228B ILE 3.1 0.6 - - - -
229B GLY* 1.3 75.2 - - - +
231B ILE* 1.3 66.8 + - + +
232B SER 3.2 0.2 - - - -
233B PHE* 3.3 9.2 + - - +
234B PRO* 3.5 1.4 - - - +
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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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213A PHE* 4.9 3.1 - - + -
228A ILE* 3.5 26.5 - - + +
231A ILE* 3.7 20.9 - - + -
213B PHE* 3.3 46.0 - - + -
216B VAL* 4.0 6.9 - - + +
222B PHE* 3.9 22.2 - - + -
223B THR 4.2 1.1 - - - +
226B ASP* 3.7 30.1 - - + +
227B CYS 3.3 12.8 - - - +
228B ILE* 3.1 12.5 + - - +
230B LYS* 1.3 78.4 - - - +
232B SER* 1.3 58.3 + - - +
234B PRO* 3.6 8.8 - - - +
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLN* 3.9 6.9 + - - -
228A ILE* 3.9 21.0 - - - +
232A SER* 3.3 27.5 + - - -
208B GLN* 4.3 14.9 + - - +
228B ILE 3.1 12.5 + - - -
229B GLY 3.7 3.6 + - - -
231B ILE* 1.3 78.7 - - - +
233B PHE* 1.3 64.1 + - - +
234B PRO* 3.0 5.6 - - - -
235B ALA* 3.1 19.4 + - - +
236B ILE* 4.3 5.2 + - - +
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Residues in contact with PHE 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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149B THR* 3.8 17.5 - - + -
151B ASP* 3.7 18.2 - - - -
152B GLU* 3.4 43.3 - - + -
155B LEU* 4.6 5.2 - - + -
156B TRP* 3.7 26.5 - + + -
190B ASP* 4.4 0.2 - - - -
222B PHE* 6.0 0.2 - + - -
229B GLY 3.1 19.4 + - - +
230B LYS 3.3 6.7 + - - +
232B SER* 1.3 75.0 - - - +
234B PRO* 1.3 71.9 - - + +
236B ILE* 2.9 41.2 + - + +
237B GLN* 3.6 28.6 + - + -
269B TYR* 3.9 16.2 - + - -
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Residues in contact with PRO 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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228A ILE* 5.0 2.9 - - + -
216B VAL* 3.8 20.6 - - + -
220B PHE* 4.0 14.8 - - + -
222B PHE* 3.8 13.0 - - + -
230B LYS 3.5 13.5 - - - +
231B ILE 3.6 6.5 - - - +
232B SER 3.3 5.4 - - - -
233B PHE* 1.3 90.1 - - + +
235B ALA* 1.3 60.8 + - - +
237B GLN* 3.2 4.2 + - - +
238B ALA* 3.0 22.3 + - - +
269B TYR* 4.3 16.4 - - + -
272B MET* 3.7 27.9 - - + +
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Residues in contact with ALA 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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228A ILE* 4.3 6.3 - - + +
204B VAL* 3.8 16.5 - - + +
207B ILE* 3.8 26.1 - - + +
208B GLN* 3.7 32.5 - - + +
232B SER 3.1 9.4 + - - +
233B PHE 3.0 0.4 + - - -
234B PRO* 1.3 78.1 - - - +
236B ILE* 1.3 58.0 + - - +
238B ALA* 3.2 1.6 + - - +
239B ALA* 3.0 29.8 + - - +
272B MET* 4.6 0.2 - - - +
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Residues in contact with ILE 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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201A TYR* 3.0 30.5 - - + +
208A GLN* 5.8 2.0 - - - +
147B GLN* 2.9 25.9 + - - +
151B ASP* 3.6 8.5 - - - +
190B ASP* 3.4 29.8 - - - +
194B MET* 3.7 10.1 - - + -
200B PHE* 3.8 12.4 - - + -
204B VAL* 3.8 21.1 - - + -
232B SER 4.7 3.6 - - - +
233B PHE* 2.9 32.2 + - + +
235B ALA* 1.3 75.0 - - - +
237B GLN* 1.3 61.0 + - - +
239B ALA* 4.0 4.5 - - - -
240B PRO* 3.5 5.7 - - - +
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Residues in contact with GLN 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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112B TYR* 2.6 34.7 + - - +
147B GLN* 3.5 9.4 - - - +
149B THR* 4.7 8.5 - - - +
152B GLU* 4.7 4.9 + - - -
233B PHE* 3.6 23.2 + - + -
234B PRO 3.2 3.3 + - - +
236B ILE* 1.3 78.0 - - - +
238B ALA* 1.3 64.7 + - - +
239B ALA 3.3 0.2 - - - -
240B PRO* 3.2 1.4 - - - +
266B GLN* 2.9 25.0 + - - +
269B TYR* 3.2 50.3 + - + -
270B PHE* 3.6 21.3 - - + -
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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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207B ILE* 3.9 17.7 - - + -
234B PRO 3.0 16.7 + - - +
235B ALA 3.2 5.4 + - - +
237B GLN* 1.3 81.9 - - - +
239B ALA* 1.3 59.3 + - - +
241B SER* 2.8 28.5 + - - -
242B PHE* 3.7 4.7 - - - -
269B TYR 4.9 1.3 - - - +
270B PHE* 5.1 1.1 - - - -
272B MET* 3.9 11.9 - - + -
273B THR* 3.1 29.6 - - + +
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Residues in contact with ALA 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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200B PHE* 3.7 20.9 - - + -
203B ASN* 4.4 8.0 + - + -
204B VAL* 4.0 16.2 - - + -
207B ILE* 3.6 16.4 - - + +
235B ALA 3.0 16.2 + - - +
236B ILE 4.1 1.8 - - - +
238B ALA* 1.3 72.2 - - - +
240B PRO* 1.4 63.3 - - + +
241B SER 2.9 10.5 + - - -
242B PHE* 3.2 12.0 + - - -
245B SER* 3.0 19.4 + - - -
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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