Contacts of the helix formed by residues 219 - 234 (chain B) in PDB entry 1Z6T
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 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B LEU* 3.7 13.8 - - - +
217B PRO 3.6 0.4 - - - -
218B LEU* 1.3 77.1 + - - +
220B ILE* 1.3 65.6 + - - +
221B GLU* 3.2 14.6 + - - +
222B GLU* 2.7 46.3 + - - +
223B ALA* 3.0 22.3 + - - +
520B ALA* 5.6 3.6 - - + -
557B ARG* 4.1 14.1 - - - +
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Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LYS* 3.6 55.6 - - + +
195B LEU* 4.4 5.2 - - + -
196B LEU* 4.1 9.4 - - + +
199B LEU* 4.5 12.5 - - + +
219B ASN* 1.3 75.0 - - - +
221B GLU* 1.3 60.6 + - - +
223B ALA* 3.3 6.7 + - - +
224B LYS* 2.8 29.5 + - + +
249B TRP* 4.1 13.2 - - + -
253B ALA* 4.1 25.1 - - + -
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Residues in contact with GLU 221 (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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219B ASN* 3.2 14.6 + - - +
220B ILE* 1.3 80.2 - - - +
222B GLU* 1.3 57.9 + - + +
224B LYS* 3.3 8.1 + - - +
225B ASP* 3.0 29.3 + - - +
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Residues in contact with GLU 222 (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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215B ARG* 3.1 22.5 + - - -
217B PRO* 3.8 9.1 - - + +
218B LEU* 2.9 23.3 + - - +
219B ASN* 2.7 29.9 + - - +
221B GLU* 1.3 77.4 - - + +
223B ALA* 1.3 56.4 + - - +
225B ASP* 3.5 6.2 + - - +
226B ARG* 2.8 31.6 + - - +
557B ARG* 2.7 33.4 + - - -
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Residues in contact with ALA 223 (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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196B LEU* 4.4 4.3 - - + -
199B LEU* 3.8 34.4 - - + +
203B CYS* 4.1 4.0 - - - -
217B PRO* 3.4 26.8 - - + +
219B ASN 3.0 17.5 + - - +
220B ILE* 3.6 4.9 - - - +
222B GLU* 1.3 73.6 - - - +
224B LYS* 1.3 61.5 + - - +
226B ARG* 4.0 1.4 - - - +
227B LEU* 2.9 31.6 + - - +
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Residues in contact with LYS 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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199B LEU* 5.2 1.2 - - - +
220B ILE* 2.8 20.4 + - + +
221B GLU* 3.6 6.7 - - - +
223B ALA* 1.3 76.7 - - - +
225B ASP* 1.3 57.3 + - - +
227B LEU* 3.3 3.6 + - - +
228B ARG* 3.0 24.4 + - - +
252B LYS* 2.7 34.7 + - - +
253B ALA* 3.4 26.0 - - + +
255B ASP* 3.6 25.9 + - - +
256B SER* 3.5 13.3 + - - +
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Residues in contact with ASP 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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221B GLU* 3.0 16.1 + - + +
222B GLU* 3.8 6.5 - - - +
224B LYS* 1.3 74.9 - - - +
226B ARG* 1.3 63.8 + - - +
228B ARG* 3.3 33.6 + - - +
229B ILE* 3.2 34.1 + - - +
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Residues in contact with ARG 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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203B CYS* 4.1 14.2 - - - +
207B ASP* 5.5 1.8 - - - -
212B PHE* 5.2 3.8 - - - -
213B SER* 3.6 37.5 + - - +
215B ARG* 2.6 44.1 + - - +
216B LEU* 4.0 3.8 + - - +
217B PRO* 3.6 29.5 - - + +
222B GLU* 2.8 21.4 + - - +
223B ALA* 4.0 4.3 - - - +
225B ASP* 1.3 70.7 + - - +
227B LEU* 1.3 65.6 + - - +
229B ILE* 3.3 9.0 + - + +
230B LEU* 3.0 45.9 + - + +
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Residues in contact with LEU 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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199B LEU* 4.8 5.4 - - + -
202B LEU* 3.8 16.6 - - + -
203B CYS* 4.3 11.6 - - - -
206B LEU* 3.4 32.3 - - + -
223B ALA 2.9 18.6 + - - +
224B LYS 3.5 4.7 - - - +
226B ARG* 1.3 76.7 - - - +
228B ARG* 1.3 62.7 + - - +
230B LEU* 3.4 2.0 + - - +
231B MET* 3.0 40.1 + - + +
240B LEU* 4.3 8.3 - - + -
253B ALA 4.4 5.2 - - - +
254B PHE* 3.6 45.3 - - + +
256B SER* 4.9 5.8 - - - +
258B CYS* 5.5 1.6 - - - -
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Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LYS 3.0 13.8 + - - +
225B ASP* 3.4 27.6 + - - +
227B LEU* 1.3 76.9 - - - +
229B ILE* 1.3 91.1 + - - +
231B MET* 4.1 2.5 - - - +
232B LEU* 3.2 48.9 + - + +
256B SER* 3.7 36.3 - - - +
257B GLN* 3.9 16.4 - - - +
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Residues in contact with ILE 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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212B PHE* 4.0 29.6 - - + -
225B ASP* 3.2 24.5 + - - +
226B ARG* 3.9 9.9 - - + +
227B LEU 3.3 0.4 - - - -
228B ARG* 1.3 105.5 - - - +
230B LEU* 1.3 54.9 + - + +
232B LEU* 3.2 5.9 + - + +
233B ARG* 2.7 48.5 + - + +
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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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203B CYS* 3.7 32.8 - - + +
206B LEU* 4.1 24.5 - - + +
207B ASP* 3.8 22.2 - - + -
212B PHE* 3.8 32.8 - - + -
226B ARG* 3.0 40.3 + - + +
227B LEU* 4.0 3.4 - - - +
229B ILE* 1.3 77.3 - - + +
231B MET* 1.3 56.9 + - - +
233B ARG* 5.1 0.4 - - - -
234B LYS* 2.8 36.8 + - + +
235B HIS* 3.1 11.0 + - + -
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Residues in contact with MET 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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183B HIS* 5.4 2.9 - - + -
206B LEU* 3.9 24.9 - - - -
227B LEU* 3.0 28.9 + - + +
228B ARG* 4.1 3.6 - - - +
230B LEU* 1.3 76.0 - - - +
232B LEU* 1.3 57.3 + - - +
235B HIS* 3.0 38.7 - - + +
236B PRO* 3.1 6.2 - - - +
238B SER* 3.4 33.0 - - - +
239B LEU 5.0 1.1 - - - +
240B LEU* 4.2 29.4 - - + +
256B SER 5.4 1.1 - - - +
257B GLN 6.0 0.2 - - - +
258B CYS* 3.6 34.1 - - + -
259B GLN 5.7 0.2 - - - +
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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
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228B ARG* 3.2 40.0 + - + +
229B ILE* 3.6 4.5 - - + +
231B MET* 1.3 81.0 - - - +
233B ARG* 1.3 76.9 + - + +
236B PRO* 3.8 18.9 - - + +
568D LEU 4.7 2.9 - - - +
572D GLU* 6.0 3.8 - - - +
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Residues in contact with ARG 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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212B PHE* 3.6 33.9 - - + -
229B ILE* 2.7 35.3 + - + +
232B LEU* 1.3 91.0 - - + +
234B LYS* 1.3 60.3 + - - +
236B PRO* 4.4 0.7 - - - -
568D LEU 5.3 1.7 + - - -
569D CYS* 2.9 60.6 + - - +
570D GLU 3.8 8.1 + - - -
571D PRO* 3.0 41.3 - - - +
572D GLU* 5.2 7.0 - - - +
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Residues in contact with LYS 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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206B LEU 3.5 15.9 - - - +
207B ASP* 2.8 37.1 + - - +
208B GLN 3.8 2.2 - - - +
209B ASP* 2.8 31.6 + - - +
211B SER* 3.1 12.7 + - - +
212B PHE* 3.6 27.4 - - + -
230B LEU* 2.8 22.9 + - + +
233B ARG* 1.3 73.0 - - - +
235B HIS* 1.3 82.5 + - + +
236B PRO* 3.2 6.3 - - - -
565D GLN* 5.1 1.2 + - - -
569D CYS* 3.4 20.8 - - + +
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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