Contacts of the helix formed by residues 186 - 203 (chain B) in PDB entry 1YWT
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 SER 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B ARG* 4.9 1.1 + - - -
180B HIS* 2.8 37.3 + - - +
184B ALA* 4.1 10.0 - - - +
185B ASN* 1.3 73.9 - - - +
187B PRO* 1.3 66.1 - - - +
188B GLU* 3.2 6.6 + - - +
189B GLU* 3.4 24.9 + - - -
190B ALA 3.2 14.9 + - - -
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Residues in contact with PRO 187 (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 TYR* 3.4 38.9 - - + +
185B ASN 3.4 9.6 - - - +
186B SER* 1.3 86.0 - - - +
188B GLU* 1.3 86.9 + - + +
190B ALA* 3.3 1.0 + - - +
191B ILE* 3.0 35.0 + - + +
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Residues in contact with GLU 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 SER* 4.7 3.6 - - - -
187B PRO* 1.3 94.2 - - + +
189B GLU* 1.3 62.7 + - - +
191B ILE* 3.3 8.2 + - - +
192B SER* 3.1 22.3 + - - -
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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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148B ARG* 4.5 10.6 + - - -
180B HIS* 3.3 33.4 + - + +
186B SER* 3.4 24.9 + - - +
188B GLU* 1.3 76.9 - - - +
190B ALA* 1.3 66.5 + - - +
192B SER* 3.1 8.8 + - - +
193B LEU* 3.1 26.4 + - + +
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Residues in contact with ALA 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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177B SER* 3.3 29.2 - - - +
180B HIS* 3.6 10.7 - - + +
181B TYR* 3.5 29.4 - - + +
186B SER 3.2 5.2 + - - +
187B PRO 3.6 7.0 - - - +
188B GLU 3.3 0.2 - - - -
189B GLU* 1.3 78.9 - - - +
191B ILE* 1.3 57.1 + - - +
193B LEU* 4.8 0.2 - - - -
194B ALA* 3.0 31.4 + - - +
230B TRP* 3.6 9.7 - - + -
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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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181B TYR* 5.1 0.4 - - + -
187B PRO* 3.0 28.9 + - + +
188B GLU* 3.7 7.6 - - - +
190B ALA* 1.3 76.9 - - - +
192B SER* 1.3 59.2 + - - +
194B ALA 3.4 0.2 + - - -
195B LYS* 2.9 34.7 + - + +
227B LEU* 3.6 17.6 - - + +
230B TRP* 3.9 44.0 - - + +
231B THR* 4.2 16.8 - - + +
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU 3.1 12.7 + - - -
189B GLU* 3.1 18.9 + - - +
191B ILE* 1.3 78.9 - - - +
193B LEU* 1.3 49.9 + - - +
195B LYS* 3.8 5.9 - - - +
196B THR* 2.7 45.4 + - - -
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Residues in contact with LEU 193 (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* 4.5 17.7 - - - -
159B LYS* 5.4 7.9 - - - +
173B ALA* 4.0 12.3 - - + +
176B PHE* 4.2 13.2 - - + -
177B SER* 4.0 20.2 - - - +
180B HIS* 3.9 28.7 - - + +
189B GLU* 3.1 17.5 + - + +
190B ALA 3.9 2.2 - - - +
192B SER* 1.3 74.3 + - - +
194B ALA* 1.3 59.7 + - - +
196B THR* 3.7 7.8 - - + -
197B THR* 2.6 50.3 + - - +
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Residues in contact with ALA 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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173B ALA 5.8 0.2 - - - -
177B SER* 4.2 6.1 - - - +
190B ALA 3.0 18.6 + - - +
191B ILE 3.7 3.6 - - - +
193B LEU* 1.3 77.5 - - - +
195B LYS* 1.3 58.8 + - - +
197B THR* 3.9 2.0 - - - -
198B PHE* 3.1 29.1 + - - +
223B LEU* 4.1 28.1 - - + +
226B ASN* 5.6 0.4 - - + -
227B LEU* 4.1 16.2 - - + +
230B TRP* 3.8 18.8 - - + -
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Residues in contact with LYS 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 24.1 + - + +
192B SER* 3.8 5.6 - - - +
194B ALA* 1.3 75.8 - - - +
196B THR* 1.3 60.7 + - - +
198B PHE* 3.3 2.1 + - - +
199B ASP* 3.0 57.1 + - - +
224B ARG* 6.1 1.2 - - - +
227B LEU* 4.0 22.4 - - + +
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Residues in contact with THR 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 SER* 2.7 30.9 + - - -
193B LEU* 3.9 8.1 - - + -
195B LYS* 1.3 71.5 - - - +
197B THR* 1.3 65.2 + - - +
199B ASP* 4.2 5.3 - - - +
200B GLU* 3.2 46.3 + - - +
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Residues in contact with THR 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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164B PRO 4.8 1.5 - - - +
169B ARG* 6.4 1.1 - - + -
170B LEU* 3.6 25.7 - - + +
173B ALA* 3.5 32.0 - - + +
193B LEU* 2.6 34.7 + - - +
194B ALA* 3.9 6.3 - - - -
196B THR* 1.3 75.7 - - - +
198B PHE* 1.3 65.5 + - - +
200B GLU* 4.1 2.8 - - - +
201B ALA* 3.1 24.3 + - - +
223B LEU* 3.9 12.1 - - + -
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Residues in contact with PHE 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 ALA 3.1 18.5 + - - +
195B LYS* 3.5 7.0 - - - +
196B THR 3.3 0.2 - - - -
197B THR* 1.3 75.5 - - - +
199B ASP* 1.3 72.3 + - - +
201B ALA* 3.0 7.8 + - - +
202B MET* 2.8 55.2 + - + +
220B MET* 3.1 45.5 - - + +
221B GLN* 5.3 1.8 - - - -
223B LEU* 4.1 15.2 - - + +
224B ARG* 3.1 42.8 - - + -
227B LEU* 4.7 3.4 - - + -
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Residues in contact with ASP 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 LYS* 3.0 44.9 + - - +
196B THR* 4.2 6.0 + - - +
198B PHE* 1.3 88.5 - - - +
200B GLU* 1.3 59.8 + - + +
201B ALA 3.0 0.3 + - - -
202B MET* 3.1 6.8 + - - +
203B ALA* 2.9 32.1 + - - +
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Residues in contact with GLU 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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164B PRO* 3.5 23.2 - - + +
169B ARG* 4.3 16.3 + - - +
196B THR* 3.2 37.6 + - + +
197B THR* 4.1 3.6 - - - +
199B ASP* 1.3 79.6 - - + +
201B ALA* 1.3 60.2 + - - +
203B ALA* 4.1 7.6 + - - +
204B ASP* 3.5 22.0 + - - +
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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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164B PRO 3.9 18.6 - - - +
165B THR* 3.5 10.8 - - + +
170B LEU* 4.0 9.9 - - + -
197B THR 3.1 16.2 + - - +
198B PHE* 3.0 11.2 + - - +
199B ASP 3.0 0.2 - - - -
200B GLU* 1.3 76.8 - - - +
202B MET* 1.3 67.4 + - - +
204B ASP 3.1 3.5 + - - -
205B LEU* 3.0 18.9 + - - +
220B MET* 3.5 25.5 - - + +
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Residues in contact with MET 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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198B PHE* 2.8 44.2 + - + +
199B ASP* 3.6 8.7 - - - +
201B ALA* 1.3 68.0 - - - +
203B ALA* 1.3 53.1 + - - +
204B ASP 2.6 18.1 + - - -
205B LEU* 2.8 38.3 + - + +
206B HIS* 4.5 1.7 + - - -
220B MET* 3.4 18.1 - - + +
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Residues in contact with ALA 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 ASP 2.9 17.1 + - - +
200B GLU* 4.1 9.4 - - - +
201B ALA 3.3 0.2 - - - -
202B MET* 1.3 72.9 - - - +
204B ASP* 1.3 65.4 + - - +
206B HIS* 3.2 17.4 - - - -
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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