Contacts of the helix formed by residues 198 - 218 (chain B) in PDB entry 2P3Z
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 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B HIS* 5.4 0.2 - - - -
56B GLU* 4.5 4.4 - - - +
193B HIS 4.7 0.3 - - - +
194B TRP* 3.3 32.3 - - + -
195B GLY 2.7 36.3 + - - +
197B HIS* 1.3 95.1 + - - +
199B GLY* 1.3 63.8 + - - +
201B ALA* 3.4 11.1 + - + +
202B GLY* 3.2 26.7 + - - +
205B LYS* 5.1 2.4 + - - +
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Residues in contact with GLY 199 (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 GLY 3.7 2.4 + - - -
196B PRO 3.0 14.7 + - - -
197B HIS 3.4 1.0 - - - -
198B ASP* 1.3 77.1 - - - +
200B ASP* 1.3 63.7 + - - -
202B GLY* 3.0 11.1 + - - -
203B ILE* 3.2 20.6 + - - +
235B TYR* 3.6 6.1 - - - -
238B LYS* 5.0 4.3 - - - -
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Residues in contact with ASP 200 (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 ASP 3.6 0.2 + - - -
199B GLY* 1.3 71.9 - - - -
201B ALA* 1.3 56.5 + - - +
203B ILE* 3.2 9.3 + - - +
204B ARG* 2.9 45.2 + - - +
238B LYS* 3.0 32.1 + - - +
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Residues in contact with ALA 201 (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 ASP* 3.4 8.9 + - + +
199B GLY 3.2 0.8 - - - -
200B ASP* 1.3 77.9 - - - +
202B GLY* 1.3 57.3 + - - +
204B ARG* 3.4 23.3 + - - +
205B LYS* 2.8 55.3 + - - +
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Residues in contact with GLY 202 (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 TRP* 3.4 27.5 - - - -
198B ASP* 3.2 11.3 + - - +
199B GLY 3.0 8.0 + - - -
201B ALA* 1.3 80.6 - - - +
203B ILE* 1.3 61.5 + - - +
205B LYS* 3.4 2.8 + - - +
206B ASP* 3.1 29.3 + - - +
235B TYR* 3.4 9.4 - - - -
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Residues in contact with ILE 203 (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 GLY 3.2 22.6 + - - +
200B ASP* 3.7 7.4 - - - +
201B ALA 3.2 0.4 - - - -
202B GLY* 1.3 73.9 - - - +
204B ARG* 1.3 60.6 + - - +
206B ASP* 3.2 1.7 + - - +
207B ALA* 2.8 34.1 + - - +
235B TYR* 3.6 29.8 - - + -
238B LYS* 3.7 40.8 - - + +
239B LEU* 4.2 26.7 - - + +
242B ALA* 3.5 29.8 - - + -
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Residues in contact with ARG 204 (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 ASP* 2.9 32.7 + - - +
201B ALA* 3.5 28.6 - - - +
203B ILE* 1.3 77.6 - - - +
205B LYS* 1.3 59.5 + - + +
207B ALA* 3.9 3.5 - - - +
208B ALA* 2.9 36.5 + - + +
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Residues in contact with LYS 205 (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 TRP* 3.3 66.8 - - + +
198B ASP* 5.1 2.2 - - - +
201B ALA* 2.8 42.1 + - - +
202B GLY 4.6 0.8 - - - +
204B ARG* 1.3 77.5 - - + +
206B ASP* 1.3 59.5 + - - +
208B ALA* 3.5 6.2 - - - +
209B MET* 2.9 28.6 + - - +
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Residues in contact with ASP 206 (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 THR* 3.6 16.7 - - + +
193B HIS* 3.2 25.0 + - - -
194B TRP* 3.2 38.9 + - - +
202B GLY 3.1 15.0 + - - +
203B ILE* 4.2 2.0 - - - +
205B LYS* 1.3 76.6 - - - +
207B ALA* 1.3 62.5 + - - +
209B MET* 3.4 25.2 + - + +
210B VAL* 3.1 26.0 + - - +
225B LEU* 5.0 1.6 - - + -
235B TYR* 4.6 1.6 + - - -
239B LEU* 4.3 16.5 - - + +
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Residues in contact with ALA 207 (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 ILE 2.8 18.9 + - - +
204B ARG* 3.9 4.5 - - - +
206B ASP* 1.3 74.9 - - - +
208B ALA* 1.3 53.6 + - - +
210B VAL* 2.9 5.2 + - - +
211B ALA* 2.7 34.2 + - - +
239B LEU* 4.4 1.9 - - + +
242B ALA* 4.0 29.8 - - + +
243B CYS* 4.0 18.6 - - - -
246B PHE* 4.1 8.1 - - + -
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Residues in contact with ALA 208 (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 ARG* 2.9 23.5 + - + +
205B LYS* 3.5 6.5 - - - +
207B ALA* 1.3 71.1 - - - +
209B MET* 1.3 66.5 + - - +
211B ALA* 3.0 11.3 + - - +
212B ASP* 2.9 25.2 + - - +
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Residues in contact with MET 209 (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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190B MET* 4.0 21.5 - - + +
191B PRO 3.2 22.0 - - - +
193B HIS* 3.5 27.8 - - - -
205B LYS 2.9 18.0 + - - +
206B ASP* 3.4 26.9 - - - +
208B ALA* 1.3 76.7 - - - +
210B VAL* 1.3 59.5 + - + +
212B ASP* 3.6 8.6 - - - +
213B MET* 3.4 23.1 + - + +
225B LEU* 3.7 23.8 - - + -
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Residues in contact with VAL 210 (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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190B MET* 3.7 23.1 - - + -
206B ASP 3.1 16.7 + - - +
207B ALA 2.9 10.0 + - - +
209B MET* 1.3 74.9 - - + +
211B ALA* 1.3 66.0 + - - +
212B ASP 3.2 0.7 - - - -
213B MET 3.2 1.6 + - - -
214B ARG* 3.0 20.3 + - - +
223B LEU* 3.6 18.2 - - + +
225B LEU* 3.8 28.3 - - + -
243B CYS* 4.3 7.4 - - - -
246B PHE* 4.3 18.6 - - + +
248B LEU* 3.9 22.9 - - + -
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Residues in contact with ALA 211 (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 ALA 2.7 15.9 + - - +
208B ALA* 3.4 13.5 - - - +
210B VAL* 1.3 72.2 - - - +
212B ASP* 1.3 59.7 - - - +
214B ARG* 3.4 3.7 + - - +
215B GLU* 3.2 23.4 + - - +
246B PHE* 3.6 38.7 - - + -
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Residues in contact with ASP 212 (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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208B ALA 2.9 15.1 + - - +
209B MET* 3.6 8.9 - - - +
211B ALA* 1.3 73.6 - - - +
213B MET* 1.3 66.4 + - - +
215B GLU* 3.3 18.1 - - - +
216B LYS* 2.9 68.8 + - - +
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Residues in contact with MET 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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175B ALA 3.8 11.0 - - - +
176B ARG* 4.2 7.2 - - - +
177B PRO* 3.5 21.1 - - + -
178B ASP* 3.6 47.3 - - - +
190B MET* 3.7 22.9 - - - -
209B MET* 3.4 8.2 + - + +
210B VAL 3.2 4.7 + - - +
212B ASP* 1.3 80.4 - - - +
214B ARG* 1.3 64.8 + - - +
216B LYS* 4.4 16.4 - - - +
217B CYS* 2.9 32.0 + - - +
223B LEU* 3.6 24.2 - - + -
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Residues in contact with ARG 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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210B VAL 3.0 13.4 + - - +
211B ALA* 3.6 9.0 - - - +
213B MET* 1.3 75.6 - - - +
215B GLU* 1.3 57.7 + - - +
217B CYS* 5.0 1.4 - - - +
218B GLY* 2.8 52.4 + - - -
219B PRO* 3.9 20.3 + - - +
221B PHE* 2.5 30.5 + - - +
222B TRP* 4.7 1.0 - - - +
223B LEU* 3.4 39.1 - - + +
246B PHE* 3.1 35.3 + - + +
247B ASN* 3.2 32.3 + - - +
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Residues in contact with GLU 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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211B ALA 3.2 10.6 + - - +
212B ASP* 3.3 27.4 - - - +
214B ARG* 1.3 80.1 - - - +
216B LYS* 1.3 65.2 + - - +
218B GLY* 3.9 4.5 + - - -
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Residues in contact with LYS 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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176B ARG* 5.6 1.8 - - - +
178B ASP* 3.9 37.2 + - + +
181B LYS* 4.8 6.2 - - - +
212B ASP* 2.9 51.9 + - - +
213B MET* 4.2 13.7 - - - +
215B GLU* 1.3 78.6 - - - +
217B CYS* 1.3 59.5 + - - +
218B GLY 3.7 0.4 - - - -
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Residues in contact with CYS 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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177B PRO* 3.8 5.4 - - - -
178B ASP* 3.4 40.2 - - - -
181B LYS* 3.2 34.9 + - + +
213B MET* 2.9 24.1 + - - +
214B ARG* 4.9 2.0 - - - +
216B LYS* 1.3 79.2 - - - +
218B GLY* 1.3 66.2 + - - +
221B PHE* 3.5 40.2 + - + +
223B LEU* 4.8 1.1 - - + -
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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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181B LYS* 5.6 0.7 - - - -
214B ARG* 2.8 37.3 + - - -
215B GLU 3.9 4.4 + - - -
216B LYS 3.7 1.2 - - - -
217B CYS* 1.3 82.3 - - - +
219B PRO* 1.3 71.3 - - - +
220B ASP 3.3 3.6 + - - -
221B PHE 3.8 1.4 + - - -
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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