Contacts of the helix formed by residues 187 - 201 (chain B) in PDB entry 4HRE
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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B ASP* 5.0 7.7 + - - +
185B VAL* 4.0 6.4 + - + +
186B ILE* 1.3 71.4 - - - +
188B TYR* 1.3 59.9 + - - +
189B GLU* 3.9 11.8 + - - +
190B LEU* 3.3 43.0 + - + +
191B ILE* 3.0 33.1 + - - +
224B HIS* 4.7 7.3 + - + +
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Residues in contact with TYR 188 (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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186B ILE* 3.5 49.9 + - + +
187B ASP* 1.3 72.4 + - - +
189B GLU* 1.3 68.3 + - + +
191B ILE* 3.4 11.1 + - + +
192B ASP* 3.0 23.7 + - - +
227B LYS* 5.2 4.9 - - + -
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Residues in contact with GLU 189 (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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187B ASP* 3.9 9.6 + - - +
188B TYR* 1.3 77.8 - - + +
190B LEU* 1.3 51.4 + - - +
192B ASP* 3.3 7.4 + - - +
193B GLN* 2.6 42.9 + - + +
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Residues in contact with LEU 190 (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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182B ASP* 5.7 3.1 - - - +
187B ASP* 3.3 34.5 + - + +
188B TYR 3.3 0.2 - - - -
189B GLU* 1.3 76.7 - - - +
191B ILE* 1.3 55.7 + - - +
193B GLN* 3.8 11.7 - - + -
194B ASP* 2.6 50.7 + - - +
220B ARG* 3.5 39.3 - - - +
224B HIS* 3.8 12.8 - - + +
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Residues in contact with ILE 191 (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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186B ILE* 3.6 25.6 - - + -
187B ASP 3.0 23.9 + - - +
188B TYR* 3.6 12.3 - - + +
189B GLU 3.3 0.2 - - - -
190B LEU* 1.3 76.0 - - - +
192B ASP* 1.3 63.7 + - - +
195B ALA* 2.9 23.0 + - - +
224B HIS* 3.3 22.7 - - + +
227B LYS* 3.6 53.8 - - + +
228B VAL* 3.7 15.2 - - + +
231B ARG* 4.1 9.6 - - + -
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Residues in contact with ASP 192 (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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188B TYR 3.0 13.6 + - - +
189B GLU* 3.5 8.7 - - - +
191B ILE* 1.3 74.2 - - - +
193B GLN* 1.3 68.3 + - - +
195B ALA* 2.9 3.1 + - - +
196B ARG* 2.9 35.7 + - - +
231B ARG* 3.0 32.4 + - + +
235B TYR* 2.5 30.0 + - - -
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Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 2.6 27.9 + - + +
190B LEU* 3.3 17.5 - - + +
192B ASP* 1.3 75.3 + - - +
194B ASP* 1.3 62.8 + - - +
196B ARG* 3.1 12.5 + - - +
197B GLU* 3.0 38.8 + - - +
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Residues in contact with ASP 194 (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 LEU* 2.6 20.8 + - - +
193B GLN* 1.3 72.7 - - - +
195B ALA* 1.3 60.9 + - - +
197B GLU* 3.6 6.8 - - - +
198B LEU* 3.0 28.8 + - - +
216B ILE* 3.5 26.8 - - + +
220B ARG* 2.9 41.2 + - - -
224B HIS* 2.6 28.8 + - - -
228B VAL* 3.8 21.3 - - + -
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Residues in contact with ALA 195 (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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191B ILE 2.9 18.2 + - - +
192B ASP 2.9 5.9 + - - +
194B ASP* 1.3 76.8 - - - +
196B ARG* 1.3 62.4 + - - +
198B LEU* 4.8 0.2 - - - -
199B TYR* 3.4 18.0 + - - +
228B VAL* 3.7 12.5 - - - +
231B ARG* 3.7 23.6 - - + -
232B TYR* 3.5 32.0 - - - +
235B TYR* 4.2 7.7 - - + -
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Residues in contact with ARG 196 (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 ASP* 2.9 28.3 + - - +
193B GLN* 3.6 13.7 + - - +
195B ALA* 1.3 74.2 - - - +
197B GLU* 1.3 55.7 + - + +
199B TYR* 3.4 11.4 + - - +
200B ASP* 2.7 65.1 + - - +
204B LYS* 5.4 7.1 - - - +
235B TYR* 3.4 46.6 - - + -
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Residues in contact with GLU 197 (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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193B GLN* 3.0 29.6 + - - +
194B ASP* 3.6 19.9 - - - +
196B ARG* 1.3 74.6 - - + +
198B LEU* 1.3 66.7 + - - +
200B ASP* 2.9 9.5 + - + +
201B ALA* 2.7 29.3 + - - +
212B LYS* 1.8 52.0 - - + +
213B TRP* 5.3 0.2 - - - -
216B ILE* 3.7 14.4 - - + +
220B ARG* 5.1 2.8 + - - -
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Residues in contact with LEU 198 (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 ASP 3.0 13.0 + - - +
195B ALA 3.9 0.2 - - - +
197B GLU* 1.3 76.5 - - - +
199B TYR* 1.3 57.0 + - - +
202B GLY* 3.0 17.2 + - - -
213B TRP* 2.9 50.7 + - + +
216B ILE* 4.2 22.9 - - + -
217B MET* 3.8 16.8 - - + -
228B VAL* 3.8 28.0 - - + -
229B PHE* 3.9 14.1 - - + -
232B TYR* 3.7 22.3 - - + -
240B MET* 3.9 19.3 - - - -
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Residues in contact with TYR 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 ALA 3.4 11.0 + - - +
196B ARG* 3.4 13.4 + - - +
197B GLU 3.1 0.4 - - - -
198B LEU* 1.3 80.2 - - - +
200B ASP* 1.3 64.2 + - - +
202B GLY* 2.8 20.6 + - - -
203B VAL* 3.5 32.5 - - + -
204B LYS* 3.1 51.4 + - + +
232B TYR* 3.4 12.9 - - + -
235B TYR* 3.0 44.9 + + + -
236B SER* 3.9 11.2 - - - -
237B PRO* 4.5 3.8 - - + +
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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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196B ARG* 2.7 53.3 + - - +
197B GLU* 2.9 11.9 + - + +
199B TYR* 1.3 76.9 - - - +
201B ALA* 1.3 56.4 + - - +
202B GLY 3.1 0.6 + - - -
204B LYS* 3.1 41.2 + - + +
205B ARG* 3.7 20.1 + - - +
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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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197B GLU 2.7 16.1 + - - +
198B LEU 3.8 0.4 - - - -
200B ASP* 1.3 73.0 - - - +
202B GLY* 1.3 58.2 + - - +
205B ARG* 4.4 4.9 + - - +
207B GLY 4.1 0.2 - - - +
208B THR* 3.4 14.9 - - - +
209B ASP* 3.1 51.7 + - + +
212B LYS* 3.6 22.4 - - + -
213B TRP* 4.2 8.9 + - - +
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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