Contacts of the helix formed by residues 223 - 242 (chain B) in PDB entry 2NTZ
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 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B MSE 4.8 0.4 + - - -
221B GLY 4.0 0.4 - - - -
222B ASN* 1.3 81.3 - - - +
224B ASN* 1.3 91.4 + - + +
225B LEU* 3.5 4.9 - - + +
226B GLU* 2.9 38.0 + - + +
227B PHE* 3.6 5.8 + - - -
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Residues in contact with ASN 224 (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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194B GLU* 3.3 19.3 + - - +
222B ASN 4.9 1.4 + - - -
223B LYS* 1.3 91.8 + - + +
225B LEU* 1.3 63.7 + - + +
227B PHE* 2.5 47.3 + - - +
228B ASP* 2.9 13.6 + - - +
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Residues in contact with LEU 225 (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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223B LYS* 3.2 6.6 + - + +
224B ASN* 1.3 83.6 - - + +
226B GLU* 1.3 59.7 + - + +
228B ASP* 3.4 14.2 + - + +
229B GLN* 2.8 30.9 + - - +
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Residues in contact with GLU 226 (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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220B MSE 3.5 40.3 - - + +
221B GLY* 4.8 3.6 - - - -
223B LYS* 2.9 28.1 + - + +
224B ASN 2.9 1.6 + - - -
225B LEU* 1.3 74.4 - - + +
227B PHE* 1.3 65.3 + - + +
229B GLN* 2.8 23.7 - - - +
230B LEU* 3.0 7.3 + - - +
267B LEU* 5.8 0.7 - - - +
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Residues in contact with PHE 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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192B PRO* 3.8 33.9 - - + -
194B GLU* 3.0 41.7 - - + +
195B LEU* 4.9 15.0 - - + -
217B GLY* 4.4 10.1 - - - -
220B MSE 4.1 24.9 - - + -
222B ASN* 3.3 44.6 - - - -
223B LYS 3.9 1.6 - - - -
224B ASN* 2.5 27.9 + - - +
226B GLU* 1.3 68.9 - - + +
228B ASP* 1.3 58.6 + - - +
229B GLN 2.8 3.1 - - - -
230B LEU* 2.4 34.4 + - + +
231B ILE* 2.7 16.0 + - + -
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLU* 4.6 9.9 - - - +
224B ASN* 2.9 20.6 + - - +
225B LEU* 3.6 19.5 - - + +
227B PHE* 1.3 75.3 - - - +
229B GLN* 1.3 62.7 + - - +
231B ILE* 3.7 17.1 - - - +
232B GLN* 3.2 35.0 + - + +
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Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU 2.8 14.7 + - - +
226B GLU* 2.8 20.0 - - - +
227B PHE 2.7 3.4 + - - -
228B ASP* 1.3 76.3 - - - +
230B LEU* 1.3 59.0 + - - +
232B GLN* 3.6 7.5 + - - +
233B ASN* 3.1 50.7 + - - +
267B LEU* 4.9 10.3 - - + +
277B VAL* 4.4 23.8 - - + +
278B VAL 4.5 15.7 + - - +
279B THR* 6.0 2.4 - - - +
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Residues in contact with LEU 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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195B LEU* 4.1 24.0 - - + -
198B LEU* 5.0 2.9 - - + -
216B VAL* 4.9 1.3 - - + -
220B MSE 3.3 36.3 - - + -
226B GLU 3.0 9.5 + - - +
227B PHE* 2.4 23.7 + - + +
229B GLN* 1.3 66.5 - - - +
231B ILE* 1.3 61.0 + - - +
232B GLN 2.8 2.1 + - - -
233B ASN* 2.8 9.5 + - - +
234B ILE* 2.6 40.5 + - + +
260B ILE* 4.3 22.9 - - + +
263B GLU* 3.6 35.9 - - + +
264B ALA* 4.1 4.3 - - + +
267B LEU* 4.7 3.3 - - + +
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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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194B GLU* 3.6 39.7 - - + +
195B LEU* 4.7 6.5 - - + -
198B LEU* 4.1 27.1 - - + -
227B PHE 2.7 16.6 + - - +
228B ASP* 3.7 24.2 - - - +
230B LEU* 1.3 73.1 - - - +
232B GLN* 1.3 62.4 + - + +
234B ILE* 2.9 18.5 - - - +
235B SER* 3.0 22.9 + - - +
238B ILE* 4.2 2.2 - - + +
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Residues in contact with GLN 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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228B ASP* 3.2 22.0 + - - +
229B GLN* 4.1 9.4 + - - +
230B LEU 2.8 3.6 + - - -
231B ILE* 1.3 77.5 - - + +
233B ASN* 1.3 54.1 + - - +
234B ILE 2.7 15.4 + - - -
235B SER* 3.2 15.6 + - - -
236B PRO* 3.5 10.9 - - - +
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Residues in contact with ASN 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 GLN* 3.1 34.6 + - - +
230B LEU 2.8 11.6 + - - +
232B GLN* 1.3 71.6 - - - +
234B ILE* 1.3 62.8 + - - +
236B PRO* 4.9 1.1 - - - -
237B GLU* 3.5 4.7 - - - +
263B GLU* 3.0 36.8 + - - +
267B LEU* 4.4 11.3 - - - +
278B VAL* 5.9 5.7 - - - +
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Residues in contact with ILE 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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198B LEU* 5.6 0.9 - - + -
230B LEU* 2.6 46.0 - - + +
231B ILE* 2.9 19.5 - - - +
232B GLN 2.9 0.2 - - - -
233B ASN* 1.3 82.4 - - - +
235B SER* 1.3 58.2 - - - +
236B PRO* 3.1 2.9 - - - -
237B GLU* 2.5 50.9 + - + +
238B ILE* 3.2 25.1 + - + -
259B LEU* 5.2 20.6 - - + +
260B ILE* 6.3 2.5 - - + -
262B LYS* 6.1 1.3 - - + -
263B GLU* 3.4 29.2 - - + +
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 3.0 27.2 + - - +
232B GLN* 3.7 14.1 - - - -
234B ILE* 1.3 76.1 - - - +
236B PRO* 1.3 68.2 - - - +
238B ILE* 3.1 23.1 + - - +
239B ASN* 3.1 25.2 + - - +
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Residues in contact with PRO 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 GLN 3.5 9.4 - - - +
233B ASN 4.9 0.4 - - - -
234B ILE* 2.8 5.4 - - - +
235B SER* 1.3 97.0 - - - +
237B GLU* 1.3 66.7 + - - +
239B ASN* 3.7 6.3 + - + +
240B ASP* 2.8 27.1 + - - +
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Residues in contact with GLU 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 ASN 3.5 5.6 - - - +
234B ILE* 2.5 46.2 + - - +
236B PRO* 1.3 91.7 - - - +
238B ILE* 1.3 55.6 + - - +
240B ASP* 3.5 13.0 - - + +
241B ILE* 2.7 43.4 + - + +
259B LEU* 4.4 17.5 - - + -
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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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198B LEU* 4.3 42.6 - - + +
231B ILE* 4.2 4.0 - - + +
234B ILE* 3.2 37.4 + - + +
235B SER* 3.3 15.7 - - - +
237B GLU* 1.3 78.4 - - - +
239B ASN* 1.3 61.6 + - - +
241B ILE* 3.8 6.9 - - - +
242B LEU* 3.0 47.6 + - + +
256B ILE* 5.1 20.0 - - + +
259B LEU* 5.1 7.9 - - + -
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Residues in contact with ASN 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 SER* 3.1 22.8 + - - +
236B PRO* 4.1 5.6 - - + +
238B ILE* 1.3 80.3 - - - +
240B ASP* 1.3 68.9 + - - +
242B LEU* 3.4 15.7 + - - +
243B SER* 3.3 18.4 + - - -
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Residues in contact with ASP 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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236B PRO 2.8 21.6 + - - +
237B GLU* 3.3 15.7 - - - +
238B ILE 3.2 0.2 - - - -
239B ASN* 1.3 76.3 - - - +
241B ILE* 1.3 68.6 + - - +
243B SER* 2.2 36.7 + - - -
244B ILE* 3.5 8.5 + - - +
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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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237B GLU* 2.7 26.2 + - + +
238B ILE* 3.8 4.5 - - - +
240B ASP* 1.3 77.0 - - - +
242B LEU* 1.3 54.2 + - - +
243B SER 2.7 15.2 + - - -
244B ILE* 2.8 28.7 + - + +
247B MSE 3.8 27.5 - - + +
252B VAL* 4.0 27.8 - - + +
255B LYS* 4.1 20.6 - - + +
256B ILE* 4.8 7.2 - - + -
259B LEU* 3.9 26.2 - - + -
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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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198B LEU 5.1 0.7 - - - +
200B PRO* 3.4 39.7 - - + -
238B ILE* 3.0 39.4 + - + +
239B ASN* 3.7 15.3 - - - +
240B ASP 3.3 0.6 - - - -
241B ILE* 1.3 73.6 - - - +
243B SER* 1.3 57.0 + - - +
244B ILE 4.2 3.5 - - - +
249B GLU* 5.0 3.4 - - - +
252B VAL* 3.9 23.3 - - + -
256B ILE* 4.6 2.5 - - + -
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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