Contacts of the helix formed by residues 231 - 246 (chain B) in PDB entry 1ORZ
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 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B MET* 3.9 11.5 - - - +
220B MET* 5.4 2.5 - - + -
223B THR* 3.8 24.7 - - + +
229B GLY 4.8 4.9 + - - -
230B LEU* 1.3 75.8 - - - +
232B PRO* 1.3 68.0 - - - +
233B GLY 4.4 1.6 - - - +
234B LEU* 2.7 32.3 - - + +
235B ALA* 3.5 8.0 + - - +
123C THR* 5.3 3.1 - - + +
124C LEU* 5.0 15.0 - - + +
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Residues in contact with PRO 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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165B CYS* 4.8 8.5 - - + -
182B PRO* 3.6 34.8 - - + +
183B ALA* 5.3 0.2 - - - -
186B MET* 3.1 37.5 - - + -
222B CYS* 3.8 22.0 - - + +
223B THR* 4.5 2.0 - - - +
226B CYS* 5.4 1.6 - - + -
230B LEU* 3.2 11.2 - - + +
231B ASN* 1.3 89.2 - - - +
233B GLY* 1.3 59.6 + - - +
235B ALA* 3.1 2.3 + - + +
236B ILE* 2.8 36.8 + - + +
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Residues in contact with GLY 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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216B CYS* 5.4 4.0 - - - -
218B THR* 6.3 2.5 - - - -
220B MET* 4.2 19.3 - - - -
222B CYS* 3.9 9.2 - - - -
223B THR* 4.2 1.8 + - - -
231B ASN* 3.2 1.8 - - - +
232B PRO* 1.3 79.2 - - - +
234B LEU* 1.3 62.3 + - - +
236B ILE* 3.2 14.0 + - - +
237B ALA* 3.0 21.1 + - - +
240B LYS* 5.8 0.2 + - - -
123C THR* 3.7 5.6 - - - +
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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
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189B TYR* 5.2 4.0 - - + +
231B ASN* 2.7 27.2 + - - +
232B PRO 3.2 0.2 - - - -
233B GLY* 1.3 75.3 - - - +
235B ALA* 1.3 65.7 + - - +
237B ALA* 2.9 18.8 + - + +
238B GLU* 3.0 39.8 + - + +
123C THR* 2.8 48.6 - - + +
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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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156B LEU* 4.7 0.9 - - + -
185B LEU 4.8 0.7 - - - +
186B MET* 4.1 23.6 - - + -
189B TYR* 3.8 29.6 - - + -
231B ASN 3.5 10.4 + - - +
232B PRO 3.1 8.6 + - - +
234B LEU* 1.3 85.2 - - - +
236B ILE* 1.3 61.5 + - + +
238B GLU* 3.2 8.1 + - - +
239B ILE* 3.1 26.7 + - - +
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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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179B TYR* 3.8 7.4 - - - +
182B PRO* 4.7 8.5 - - + -
185B LEU* 3.5 41.5 - - + -
213B LEU* 4.5 5.8 - - + +
216B CYS* 3.6 30.3 - - + -
222B CYS* 5.7 1.6 - - - -
232B PRO* 2.8 30.0 + - + +
233B GLY* 3.4 9.0 - - - +
235B ALA* 1.3 75.8 - - - +
237B ALA* 1.3 61.9 + - - +
239B ILE* 3.2 10.7 + - + +
240B LYS* 3.0 47.8 + - + +
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Residues in contact with ALA 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 GLY 3.0 11.1 + - - +
234B LEU* 2.9 23.1 + - + +
236B ILE* 1.3 77.6 - - - +
238B GLU* 1.3 62.6 + - - +
240B LYS* 3.2 19.6 + - + +
241B LYS* 3.1 26.5 + - + +
116C TRP 5.4 4.9 - - - +
117C ASP* 5.3 11.5 - - - +
123C THR* 4.7 5.2 - - + +
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Residues in contact with GLU 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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152B LYS* 5.8 2.0 - - - -
189B TYR* 3.2 39.4 + - + +
234B LEU* 3.0 42.1 + - + +
235B ALA 3.2 2.0 + - - +
237B ALA* 1.3 74.1 - - - +
239B ILE* 1.3 66.2 + - - +
241B LYS* 3.0 16.5 + - - +
242B SER* 3.0 25.3 + - - +
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Residues in contact with ILE 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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185B LEU* 3.6 42.0 - - + +
188B ALA* 4.8 3.1 - - + -
189B TYR* 4.1 6.3 - - + +
192B LEU* 3.7 32.3 - - + -
207B LEU* 4.4 6.7 - - + -
213B LEU* 2.9 40.2 - - + -
235B ALA 3.1 17.0 + - - +
236B ILE* 3.2 10.3 + - - +
238B GLU* 1.3 75.2 - - - +
240B LYS* 1.3 63.0 + - - +
242B SER* 3.1 5.3 + - - +
243B LEU* 2.9 32.8 + - + +
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Residues in contact with LYS 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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213B LEU* 4.9 2.9 - - + -
214B TYR* 3.2 26.2 - - + -
216B CYS* 3.8 11.5 + - - -
218B THR* 3.9 16.0 + - - -
233B GLY 5.8 0.2 + - - -
236B ILE* 3.0 40.7 + - + +
237B ALA* 3.4 15.5 - - + +
238B GLU 3.2 0.2 - - - -
239B ILE* 1.3 75.8 - - - +
241B LYS* 1.3 59.1 + - + +
243B LEU* 3.2 1.8 + - - -
244B ALA 3.0 3.1 + - - -
113C HIS* 5.5 0.2 - - - -
117C ASP* 4.5 13.8 + - + +
30D ASN* 3.1 55.1 + - + +
38D TRP* 2.6 35.9 + - + -
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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
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237B ALA* 3.1 16.5 + - + +
238B GLU* 3.0 20.1 + - - +
240B LYS* 1.3 77.1 - - - +
242B SER* 1.3 60.4 + - - +
244B ALA* 2.8 22.8 + - + +
245B PHE* 2.9 11.1 + - - +
117C ASP 4.3 8.1 - - - +
118C THR 3.7 11.5 + - - -
32D LEU* 2.9 54.8 - - + +
38D TRP* 4.0 3.8 - - - -
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TYR* 6.0 1.0 - - - -
192B LEU* 5.1 9.6 - - - +
204B LYS* 3.9 26.6 + - - -
238B GLU* 3.0 14.2 + - - +
239B ILE* 3.1 10.5 + - - -
241B LYS* 1.3 77.1 - - - +
243B LEU* 1.3 59.2 + - - +
245B PHE* 2.9 30.3 + - - +
246B ALA 3.0 5.7 + - - -
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Residues in contact with LEU 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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204B LYS* 3.6 35.9 - - + +
207B LEU* 4.1 4.7 - - + -
213B LEU* 2.9 31.4 - - + -
214B TYR* 2.8 22.4 - - + +
239B ILE* 2.9 14.6 - - + +
240B LYS 3.2 7.9 - - - +
242B SER* 1.3 76.2 - - - +
244B ALA* 1.3 64.3 + - - +
246B ALA* 3.0 22.1 + - + +
37D HIS 3.8 7.8 - - - +
38D TRP* 3.4 5.7 - - - +
39D TYR* 2.9 42.3 - - + +
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Residues in contact with ALA 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 LYS 3.0 5.1 + - - -
241B LYS* 2.8 14.7 + - + +
243B LEU* 1.3 76.7 - - - +
245B PHE* 1.3 59.4 + - - +
246B ALA* 3.2 7.8 + - - +
32D LEU* 5.1 1.1 - - + -
36D TYR* 3.9 22.7 - - + +
37D HIS 4.4 0.3 - - - +
38D TRP* 2.9 52.9 - - + +
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Residues in contact with PHE 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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204B LYS* 4.5 11.7 - - - +
241B LYS 2.9 7.5 + - - +
242B SER* 2.9 20.1 + - - +
244B ALA* 1.3 75.1 - - - +
246B ALA* 1.4 66.3 + - - +
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Residues in contact with ALA 246 (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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204B LYS* 3.9 24.2 - - + +
208B ASN* 5.8 5.2 - - - +
242B SER 3.0 5.6 + - - +
243B LEU* 3.0 19.0 + - - +
244B ALA 3.5 5.2 - - - +
245B PHE* 1.4 83.0 - - - +
36D TYR* 5.4 0.2 - - - +
37D HIS* 2.8 38.6 + - - +
39D TYR* 5.3 5.4 - - + +
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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