Contacts of the helix formed by residues 199 - 210 (chain B) in PDB entry 5W0P
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 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B TRP* 3.3 13.3 + - + -
195B LYS 2.9 11.6 + - - -
196B PRO* 3.4 15.6 + - - +
197B GLU 3.3 14.3 + - - -
198B VAL* 1.3 80.5 + - - +
200B ASN* 1.3 63.6 + - - +
201B GLU* 3.1 6.8 - - + +
202B SER* 3.2 26.3 + - - +
203B PHE* 3.5 2.6 + - - +
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Residues in contact with ASN 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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176B SER* 2.6 37.6 + - - -
190B ASP* 2.6 40.1 + - - +
191B TYR 5.8 0.4 - - - -
193B THR 2.7 23.4 + - - +
194B LEU* 4.6 5.6 - - + -
195B LYS* 3.5 20.2 + - - +
198B VAL* 3.4 10.2 - - - +
199B ASN* 1.3 73.4 - - - +
201B GLU* 1.3 63.1 - - - +
203B PHE* 3.9 5.2 - - - -
204B VAL* 3.1 31.4 + - + +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.7 10.5 - - + +
199B ASN* 3.1 4.9 - - + +
200B ASN* 1.3 80.0 - - - +
202B SER* 1.3 61.3 + - - +
204B VAL* 3.8 2.6 + - - +
205B ILE* 3.2 32.9 + - + +
276B PHE* 3.8 35.2 - - + -
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Residues in contact with SER 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TRP* 2.8 34.7 + - - -
199B ASN* 3.2 13.9 + - - +
201B GLU* 1.3 77.5 - - - +
203B PHE* 1.3 54.9 + - - +
205B ILE* 3.3 10.6 + - - +
206B TYR* 2.7 35.5 + - - +
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B CYS* 3.6 29.6 - - - -
170B PRO* 4.2 10.8 - - + -
171B PRO* 3.9 8.7 - - + -
175B TRP* 3.6 53.6 - + + +
176B SER* 3.6 27.1 - - - -
189B ILE* 4.2 22.4 - - + -
190B ASP 5.4 2.0 - - - -
199B ASN 3.5 8.0 + - - +
200B ASN* 3.4 4.0 + - - +
201B GLU 3.4 0.4 - - - -
202B SER* 1.3 81.6 + - - +
204B VAL* 1.3 58.3 + - + +
206B TYR* 3.4 11.9 + + - +
207B MET* 2.8 54.9 + - + +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP 4.6 4.0 - - - +
191B TYR* 4.0 33.7 - - + +
194B LEU* 6.4 1.1 - - + -
200B ASN* 3.1 20.2 + - + +
201B GLU* 4.1 3.8 - - - +
203B PHE* 1.3 80.5 - - + +
205B ILE* 1.3 56.6 + - + +
207B MET* 3.3 7.6 + - + +
208B PHE* 2.7 38.0 + - + +
272B ALA* 4.7 24.9 - - + +
273B PHE* 6.1 0.4 - - - -
276B PHE* 5.0 17.3 - - + -
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Residues in contact with ILE 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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201B GLU* 3.2 30.0 + - + +
202B SER* 3.3 10.7 + - - +
204B VAL* 1.3 76.8 - - + +
206B TYR* 1.3 60.0 + - - +
208B PHE* 3.7 5.1 - - - -
209B VAL* 2.9 44.8 + - + +
276B PHE* 4.8 13.0 - - + -
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Residues in contact with TYR 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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163B MET* 5.4 1.2 - - - +
166B ALA* 3.4 33.5 + - - +
167B CYS* 4.9 1.3 - - - -
175B TRP* 3.4 34.5 - + + -
202B SER 2.7 21.3 + - - +
203B PHE* 3.5 16.2 - + - +
205B ILE* 1.3 72.8 - - - +
207B MET* 1.3 60.5 + - + +
209B VAL* 5.2 0.9 - - - -
210B VAL* 3.0 61.1 + - + +
211B HIS* 3.1 33.5 + + - -
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Residues in contact with MET 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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122B GLU* 4.3 8.3 - - - +
167B CYS* 3.5 29.2 - - - -
189B ILE* 3.8 23.1 - - + -
203B PHE* 2.8 42.9 + - + +
204B VAL* 3.4 9.4 - - - +
205B ILE 3.2 0.2 - - - -
206B TYR* 1.3 76.7 - - + +
208B PHE* 1.3 56.8 + - - +
211B HIS* 3.1 28.3 + - + +
212B PHE* 3.0 27.7 + - + +
265B TRP* 5.3 10.8 - - + -
268B TYR* 6.4 2.7 - - + -
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Residues in contact with PHE 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 VAL* 2.7 25.4 + - + +
205B ILE* 3.2 7.2 + - - +
207B MET* 1.3 74.7 - - - +
209B VAL* 1.3 61.3 + - + +
212B PHE* 3.3 21.1 - + + +
213B THR* 2.6 48.9 + - - -
269B ALA* 4.2 35.4 - - + -
272B ALA* 6.6 0.2 - - + -
273B PHE* 4.7 24.7 - + + -
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Residues in contact with VAL 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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205B ILE* 2.9 30.4 + - + +
206B TYR* 5.2 0.9 - - - -
208B PHE* 1.3 87.7 - - + +
210B VAL* 1.3 68.2 + - + +
213B THR* 3.6 9.9 - - + +
214B ILE* 3.2 39.4 + - + +
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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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126B TRP* 3.6 7.6 - - + -
163B MET* 3.9 21.3 - - + -
206B TYR* 3.0 38.0 + - + +
209B VAL* 1.3 83.7 - - + +
211B HIS* 1.3 80.0 + - + +
212B PHE 3.4 0.2 - - - -
214B ILE* 3.7 16.0 - - + +
215B PRO* 3.2 20.3 - - - +
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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