Contacts of the helix formed by residues 211 - 226 (chain B) in PDB entry 5HVM
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 THR 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B PHE* 3.9 1.4 - - - +
210B HIS* 1.3 87.5 - - + +
212B TYR* 1.3 64.7 + - - +
213B ASP* 3.4 16.0 + - - +
214B TYR* 3.2 41.7 + - + +
215B THR* 3.4 11.6 + - - -
246B ALA* 3.6 7.0 - - - -
388B MET* 5.0 3.4 - - + -
413B GLY* 4.1 23.6 - - - +
416B GLN* 3.6 25.7 + - + +
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Residues in contact with TYR 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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211B THR* 1.3 71.0 - - - +
213B ASP* 1.3 64.0 + - - +
215B THR* 3.0 24.4 + - + -
216B ARG* 2.8 53.8 + - + +
219B LEU* 4.2 5.4 - - + +
232B PRO* 2.8 44.0 + - + +
233B ASN* 4.3 11.0 - - - -
246B ALA* 3.5 16.1 - - + +
416B GLN* 5.0 1.0 + - - -
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Residues in contact with ASP 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 THR* 3.2 6.8 + - - +
212B TYR* 1.3 79.1 + - - +
214B TYR* 1.3 66.1 + - + +
216B ARG* 3.0 39.9 + - - +
217B HIS* 3.0 30.9 + - - +
416B GLN* 3.0 34.5 + - - +
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Residues in contact with TYR 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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180B THR 4.1 5.6 - - - -
181B PRO* 3.4 38.0 - - + +
182B PHE* 3.7 26.7 - - - +
209B PHE* 3.8 14.8 - - + -
210B HIS* 4.1 10.1 - - + -
211B THR* 3.2 37.2 + - + +
212B TYR 3.2 0.4 - - - -
213B ASP* 1.3 81.5 - - + +
215B THR* 1.3 63.3 + - - +
217B HIS* 3.1 11.9 + + - +
218B PHE* 3.1 18.4 + - - +
386B ASP 3.1 24.9 + - - -
387B GLY* 3.1 21.9 + - - -
411B PHE 4.7 2.6 + - - -
412B ALA 4.8 0.2 - - - -
413B GLY* 3.9 6.9 + - - -
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Residues in contact with THR 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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209B PHE* 3.5 21.0 - - + +
211B THR 3.4 10.8 + - - -
212B TYR* 3.0 24.1 + - + -
214B TYR* 1.3 76.2 - - - +
216B ARG* 1.3 66.1 + - - +
218B PHE* 3.1 2.3 + - - +
219B LEU* 2.9 45.5 + - + +
244B CYS* 3.8 29.2 - - + +
245B GLY 3.7 20.0 + - - +
246B ALA 4.0 0.2 + - - -
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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
----------------------------------------------------------
212B TYR* 2.8 33.0 + - + +
213B ASP* 3.0 51.4 + - - +
215B THR* 1.3 76.8 - - - +
217B HIS* 1.3 84.7 + - - +
219B LEU* 3.5 10.5 + - - +
220B SER* 2.9 29.4 + - - -
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Residues in contact with HIS 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TYR* 4.2 11.4 + - - -
182B PHE* 3.5 23.5 - - + +
183B PRO 3.4 20.6 - - - +
184B SER* 3.8 22.2 - - - -
185B SER* 4.3 2.8 + - - -
213B ASP* 3.0 25.8 + - + +
214B TYR* 3.1 9.6 + + - +
216B ARG* 1.3 102.5 + - - +
218B PHE* 1.3 61.2 + - - +
220B SER* 3.3 9.7 - - - -
221B ALA* 2.8 28.4 + - - +
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Residues in contact with PHE 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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155B MET* 5.5 2.2 - - + -
182B PHE* 3.5 32.5 - + + -
198B LEU* 3.2 25.4 - - + -
201B VAL* 3.8 26.9 - - + -
202B LEU* 4.4 5.2 - - + -
207B ILE* 3.8 22.4 - - + -
209B PHE* 3.6 30.7 - + + -
214B TYR 3.1 8.4 + - - +
215B THR 3.1 7.7 + - - +
217B HIS* 1.3 74.3 - - - +
219B LEU* 1.3 67.4 + - - +
221B ALA* 3.0 4.2 + - - +
222B CYS* 3.0 40.1 + - - -
235B ILE* 4.0 13.9 - - + -
244B CYS* 4.1 13.2 - - - -
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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
----------------------------------------------------------
212B TYR* 4.2 4.9 - - - +
215B THR* 2.9 41.9 + - + +
216B ARG* 3.9 8.3 - - - +
218B PHE* 1.3 75.3 - - + +
220B SER* 1.3 61.2 + - - +
222B CYS* 3.1 6.1 + - - +
223B SER* 2.9 26.7 + - - -
230B THR* 3.9 17.4 - - + +
231B THR 3.7 14.4 - - - +
232B PRO* 3.8 18.6 - - + +
234B GLY 4.0 7.2 - - - +
235B ILE* 3.6 35.4 - - + -
244B CYS* 4.0 15.7 - - + -
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Residues in contact with SER 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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185B SER* 2.9 20.7 + - - -
216B ARG 2.9 20.0 + - - -
217B HIS* 3.3 13.0 - - - -
219B LEU* 1.3 77.6 - - - +
221B ALA* 1.3 60.7 + - - +
223B SER* 3.4 5.6 + - - -
224B ARG* 3.0 42.0 + - - +
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Residues in contact with ALA 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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182B PHE* 3.8 20.0 - - + -
185B SER* 3.9 15.0 + - - +
188B TYR* 4.4 11.0 - - + -
198B LEU* 3.7 16.3 - - + +
217B HIS 2.8 14.0 + - - +
218B PHE 3.0 8.9 + - - +
220B SER* 1.3 75.8 - - - +
222B CYS* 1.3 58.3 + - - +
225B LEU* 2.9 37.5 + - + +
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Residues in contact with CYS 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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198B LEU* 4.3 14.8 - - - -
202B LEU* 4.4 20.9 - - - -
218B PHE* 3.0 44.7 + - - -
219B LEU* 3.1 9.1 + - - +
221B ALA* 1.3 79.0 - - - +
223B SER* 1.3 50.8 + - - +
226B LEU* 2.7 41.2 + - - +
228B LEU* 3.8 8.1 + - + +
230B THR* 4.4 4.0 - - + -
235B ILE* 4.3 20.2 - - + -
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Residues in contact with SER 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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219B LEU 2.9 16.8 + - - -
220B SER* 3.4 9.7 + - - -
222B CYS* 1.3 71.4 - - - +
224B ARG* 1.3 60.6 + - - +
226B LEU 2.6 20.9 - - - +
227B GLY* 4.3 2.8 - - - -
228B LEU 3.3 25.1 + - - -
230B THR* 4.2 10.7 + - - +
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Residues in contact with ARG 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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185B SER* 4.6 12.6 - - - +
220B SER* 3.0 31.3 + - - +
221B ALA* 4.2 2.0 - - - +
223B SER* 1.3 81.2 - - - +
225B LEU* 1.3 69.4 + - + +
226B LEU 4.4 0.5 - - - +
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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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185B SER* 5.5 4.9 - - - +
188B TYR* 3.6 36.3 - - + -
189B ARG* 4.4 19.7 - - + +
194B ARG* 4.0 36.3 - - + +
195B ASN* 3.9 20.1 + - - +
198B LEU* 4.2 8.5 - - + -
221B ALA* 2.9 21.6 + - + +
224B ARG* 1.3 86.0 - - + +
226B LEU* 1.3 65.9 + - + +
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Residues in contact with LEU 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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195B ASN* 3.5 42.2 - - + +
198B LEU* 4.2 23.6 - - + -
199B LEU* 4.2 21.1 - - + -
202B LEU* 3.8 18.6 - - + -
222B CYS* 2.7 18.5 + - - +
223B SER 2.6 21.8 - - - +
224B ARG 4.8 0.4 - - - -
225B LEU* 1.3 77.4 - - + +
227B GLY* 1.3 59.8 + - - +
228B LEU* 2.8 33.1 + - + -
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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
------------------------------------------------------------
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