Contacts of the helix formed by residues 212 - 226 (chain B) in PDB entry 1Z6Z
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 ASP 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B LYS* 3.9 46.1 + - + +
210B SER* 3.4 1.1 - - - +
211B VAL* 1.3 78.4 - - - +
213B PRO* 1.4 69.5 - - - +
214B ASP* 3.4 19.0 + - - +
215B MET* 3.1 30.7 + - + +
216B ARG* 3.1 27.2 + - - +
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Residues in contact with PRO 213 (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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211B VAL 3.3 10.3 - - - +
212B ASP* 1.4 88.8 - - - +
214B ASP* 1.3 62.4 + - - +
216B ARG* 3.8 28.6 - - + +
217B LYS* 3.0 27.7 + - - +
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Residues in contact with ASP 214 (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 ASP* 3.2 17.9 + - - +
213B PRO* 1.3 78.9 - - - +
215B MET* 1.3 60.6 + - - +
217B LYS* 4.0 4.8 - - - +
218B GLY* 3.0 23.9 + - - -
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Residues in contact with MET 215 (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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161B PHE* 4.5 25.8 - - + -
162B LYS* 5.4 4.0 - - + +
164B TRP* 4.1 34.3 - - + +
210B SER* 4.2 9.4 - - - +
212B ASP* 3.1 27.7 + - + +
214B ASP* 1.3 78.5 - - - +
216B ARG* 1.3 66.4 + - - +
218B GLY* 3.1 6.4 + - - -
219B LEU* 2.9 53.2 + - + +
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Residues in contact with ARG 216 (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 ARG 3.7 18.6 - - - +
208B GLU* 3.7 24.2 - - - +
209B THR 4.6 0.2 - - - -
210B SER* 2.7 51.3 + - - +
211B VAL* 3.3 17.8 + - - +
212B ASP 3.1 8.0 + - - +
213B PRO* 3.8 29.3 - - - +
214B ASP 3.4 0.2 - - - -
215B MET* 1.3 76.5 - - - +
217B LYS* 1.3 56.7 + - - +
219B LEU* 3.4 5.6 + - - +
220B GLN* 3.0 40.6 + - - +
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Residues in contact with LYS 217 (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 PRO 3.0 19.7 + - - +
214B ASP* 4.0 6.5 - - - +
216B ARG* 1.3 73.8 - - - +
218B GLY* 1.3 61.1 + - - +
220B GLN* 3.4 12.6 + - - +
221B GLU* 2.9 29.5 + - - +
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Residues in contact with GLY 218 (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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214B ASP 3.0 16.3 + - - -
215B MET* 3.1 10.9 + - - -
217B LYS* 1.3 77.4 - - - +
219B LEU* 1.3 57.3 + - - +
221B GLU* 3.3 8.8 + - - +
222B LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 219 (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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164B TRP* 4.1 17.5 - - + -
197B PRO* 6.2 0.2 - - + -
203B GLN* 3.4 24.2 - - - +
206B ALA* 3.6 43.1 - - + +
207B ARG* 3.6 22.5 + - + +
215B MET* 2.9 40.6 + - + +
216B ARG 3.8 3.8 - - - +
218B GLY* 1.3 74.1 - - - +
220B GLN* 1.3 63.9 + - - +
222B LEU* 3.4 19.0 + - + +
223B LYS* 3.2 17.8 + - - +
228B LEU* 5.2 0.7 - - - +
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Residues in contact with GLN 220 (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 ARG* 3.4 38.7 - - + +
208B GLU* 5.2 2.4 - - - +
216B ARG* 3.0 24.5 + - - +
217B LYS* 3.7 11.5 - - - +
219B LEU* 1.3 74.5 - - - +
221B GLU* 1.3 59.8 + - - +
223B LYS* 3.5 2.9 + - - +
224B ALA* 3.1 30.1 + - - +
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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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217B LYS 2.9 15.2 + - - +
218B GLY* 3.4 12.8 - - - +
220B GLN* 1.3 73.5 - - - +
222B LEU* 1.3 64.3 + - - +
224B ALA* 4.1 4.2 - - - +
225B LYS* 3.0 46.0 + - + +
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Residues in contact with LEU 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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197B PRO* 4.0 20.4 - - + -
218B GLY 3.0 13.5 + - - +
219B LEU* 3.4 30.5 - - + +
221B GLU* 1.3 77.5 - - - +
223B LYS* 1.3 62.6 + - - +
225B LYS* 3.5 1.8 + - - -
226B GLY 3.3 1.6 + - - -
227B LYS* 3.1 59.9 + - + +
228B LEU* 3.7 23.3 + - + -
256B TYR* 5.9 0.7 - - - +
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Residues in contact with LYS 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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199B ASP* 3.6 24.2 + - - -
207B ARG* 4.0 34.5 - - - +
219B LEU 3.2 9.9 + - - +
220B GLN 3.9 6.3 - - - +
221B GLU 3.4 0.2 - - - -
222B LEU* 1.3 78.5 - - - +
224B ALA* 1.3 63.1 + - - +
226B GLY* 3.1 14.9 + - - -
228B LEU* 3.8 25.2 - - + +
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Residues in contact with ALA 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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220B GLN 3.1 18.4 + - - +
221B GLU* 4.1 4.5 - - - +
223B LYS* 1.3 79.6 - - - +
225B LYS* 1.3 61.5 + - + +
226B GLY* 3.1 1.4 + - - -
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Residues in contact with LYS 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 33.4 + - + +
222B LEU* 4.2 2.7 - - - +
224B ALA* 1.3 76.4 - - + +
226B GLY* 1.3 60.5 + - - +
227B LYS* 3.6 19.6 + - + +
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Residues in contact with GLY 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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223B LYS 3.1 12.3 + - - -
224B ALA 3.1 6.6 + - - -
225B LYS* 1.3 78.6 - - - +
227B LYS* 1.3 60.6 + - - +
228B LEU 3.4 9.7 + - - +
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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