Contacts of the helix formed by residues 181 - 198 (chain B) in PDB entry 1Y8Q
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 GLU 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ARG* 3.2 37.5 + - - -
170B PHE* 4.2 0.5 - - - -
180B SER* 1.3 81.5 - - - +
182B PRO* 1.3 76.0 - - + +
183B ILE* 3.2 18.3 - - + +
184B HIS* 2.7 53.1 + - + +
185B CYS* 3.6 4.5 + - - -
368B MET* 3.6 8.2 - - - +
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Residues in contact with PRO 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B SER 4.7 0.2 - - - +
181B GLU* 1.3 88.0 - - + +
183B ILE* 1.3 63.0 + - + +
185B CYS* 2.9 17.3 + - - +
186B ILE* 3.0 18.6 + - + +
363B MET* 3.9 31.1 - - + +
368B MET* 3.9 9.6 - - + -
369B ASN 5.0 5.2 - - - +
371B LYS* 3.9 25.4 - - + -
379B MET* 5.2 3.1 - - - -
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 5.9 1.1 - - - +
170B PHE* 3.7 33.0 - - + -
181B GLU* 3.8 30.3 - - + +
182B PRO* 1.3 79.7 - - + +
184B HIS* 1.3 58.7 + - + +
186B ILE* 3.4 13.4 + - + +
187B VAL* 2.9 40.5 + - + +
379B MET* 4.2 36.0 - - + +
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Residues in contact with HIS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 5.4 0.4 + - - -
170B PHE* 3.4 38.4 - + + -
171B PRO* 6.1 0.2 - - - +
174B THR* 5.0 9.9 + - - -
175B ILE* 4.0 16.7 - - + +
178B THR 5.6 0.4 - - - -
179B PRO* 3.9 20.2 - - + -
180B SER* 3.1 17.1 + - - -
181B GLU* 2.7 64.0 + - + +
182B PRO 3.0 0.6 - - - -
183B ILE* 1.3 76.2 - - - +
185B CYS* 1.3 58.9 + - - +
187B VAL* 3.4 7.0 + - - +
188B TRP* 3.0 26.4 + - - +
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Residues in contact with CYS 185 (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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179B PRO* 4.6 3.6 - - - -
181B GLU 3.9 4.3 - - - -
182B PRO 2.9 6.3 + - - +
184B HIS* 1.3 76.9 - - - +
186B ILE* 1.3 56.6 + - - +
188B TRP* 3.1 6.6 + - - +
189B ALA* 2.8 33.8 + - - +
359B ALA* 3.6 20.9 - - - +
362B ARG* 3.6 32.3 - - + +
363B MET* 3.3 28.0 - - + -
368B MET* 3.5 26.0 - - - -
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Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO 3.0 15.5 + - - +
183B ILE* 3.6 12.6 - - + +
185B CYS* 1.3 76.1 - - - +
187B VAL* 1.3 62.2 + - + +
189B ALA* 3.1 2.9 + - - +
190B LYS* 3.0 26.1 + - + +
355B VAL* 4.4 5.4 - - + -
359B ALA* 4.0 20.0 - - + -
363B MET* 4.1 7.4 - - + -
376B ILE* 4.2 17.3 - - + -
379B MET* 3.7 45.1 - - + -
380B ALA* 3.6 36.1 - - + +
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Residues in contact with VAL 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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170B PHE* 4.0 27.8 - - + -
175B ILE* 3.8 13.2 - - + -
183B ILE* 2.9 34.2 + - + +
184B HIS* 3.6 7.2 - - - +
185B CYS 3.3 0.2 - - - -
186B ILE* 1.3 75.0 - - + +
188B TRP* 1.3 57.6 + - - +
190B LYS* 3.2 9.0 + - + +
191B TYR* 2.9 66.7 + - + +
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Residues in contact with TRP 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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175B ILE* 3.3 33.6 - - + +
176B ARG* 4.9 1.1 - - + -
184B HIS 3.0 13.9 + - - +
185B CYS 3.1 12.3 - - - +
187B VAL* 1.3 77.5 - - - +
189B ALA* 1.3 69.7 + - - +
191B TYR* 3.2 6.8 + + - +
192B LEU* 2.9 47.8 + - + +
205B GLU 5.6 0.2 - - - -
206B VAL* 3.1 46.5 + - + +
258B LEU* 4.3 19.7 - - + -
259B PHE* 3.8 26.2 - + - -
358B ALA* 3.8 22.4 - - + -
362B ARG* 3.0 49.7 - - + +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B CYS 2.8 16.1 + - - +
186B ILE 3.1 8.0 + - - +
188B TRP* 1.3 81.3 - - + +
190B LYS* 1.3 56.4 + - - +
192B LEU* 3.3 7.5 + - - +
193B PHE* 3.0 26.0 + - - +
354B PHE* 3.9 5.0 - - - -
355B VAL* 3.4 36.9 - - + +
358B ALA* 3.9 6.3 - - + -
359B ALA* 3.7 13.5 - - + +
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Residues in contact with LYS 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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186B ILE* 3.0 23.4 + - + +
187B VAL* 3.2 8.0 + - - +
189B ALA* 1.3 72.8 - - - +
191B TYR* 1.3 68.8 + - + +
193B PHE* 3.4 10.8 + - - +
194B ASN* 3.1 22.9 + - - +
344B TRP* 3.8 26.7 - - + +
355B VAL* 4.0 24.2 - - + -
380B ALA* 2.8 41.2 + - + +
382B ASN* 4.4 7.3 + - - -
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Residues in contact with TYR 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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170B PHE* 4.8 4.5 + - - -
172B GLY* 5.6 2.1 - - - -
175B ILE* 3.8 33.7 - - + +
176B ARG* 5.9 0.9 - - + -
187B VAL* 2.9 40.3 + - + +
188B TRP* 3.5 7.6 - + - +
190B LYS* 1.3 78.1 - - + +
192B LEU* 1.3 64.9 + - - +
194B ASN* 3.0 9.3 + - - +
195B GLN* 3.0 27.3 + - - +
203B ASP 3.9 17.3 + - - -
204B GLN* 3.3 58.8 - - + +
205B GLU 4.6 6.7 - - - +
206B VAL* 5.3 2.5 - - + -
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TRP* 2.9 25.3 + - + +
189B ALA 3.3 7.2 - - - +
191B TYR* 1.3 77.0 - - - +
193B PHE* 1.3 62.2 + - - +
195B GLN* 3.5 5.7 + - + +
196B LEU* 3.0 41.6 + - + +
206B VAL* 3.6 30.4 - - + +
240B THR* 5.4 0.4 - - + -
258B LEU* 3.5 36.3 - - + -
322B PHE* 4.5 2.7 - - + -
354B PHE* 3.3 29.6 - - + -
358B ALA* 3.9 19.1 - - + -
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Residues in contact with PHE 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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189B ALA 3.0 12.4 + - - +
190B LYS* 3.5 11.7 - - - +
191B TYR 3.1 0.4 + - - -
192B LEU* 1.3 76.8 - - - +
194B ASN* 1.3 62.9 + - - +
196B LEU* 3.2 1.4 + - - -
197B PHE* 2.8 46.8 + + + -
198B GLY 3.5 2.0 + - - -
329B LEU* 3.5 32.1 - - + -
342B LEU* 4.2 25.1 - - + -
343B ILE 4.2 2.9 - - - -
344B TRP* 3.5 62.1 - + + -
351B ALA* 4.3 9.4 - - + -
354B PHE* 3.8 28.0 - + + -
355B VAL* 4.7 0.7 - - + -
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Residues in contact with ASN 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 LYS* 3.1 19.8 + - - +
191B TYR* 3.0 4.8 + - - +
193B PHE* 1.3 85.4 - - - +
195B GLN* 1.3 65.6 + - + +
198B GLY* 2.8 37.9 + - - +
199B GLU* 3.2 26.0 + - - +
204B GLN* 3.1 34.3 + - - +
342B LEU 5.3 0.9 - - - +
344B TRP* 4.5 10.0 + - - +
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Residues in contact with GLN 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 TYR 3.0 20.7 + - - +
192B LEU* 3.7 7.6 - - - +
194B ASN* 1.3 76.6 - - - +
196B LEU* 1.3 58.3 + - + +
199B GLU 4.8 1.3 - - - -
200B GLU* 4.3 10.5 - - - +
201B ASP 3.2 40.2 + - - +
204B GLN* 3.2 28.0 + - - +
205B GLU* 3.3 21.6 + - - +
206B VAL* 4.3 10.6 + - + +
240B THR* 4.4 22.2 - - + -
241B LYS* 2.9 36.5 + - - +
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Residues in contact with LEU 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 LEU* 3.0 31.3 + - + +
195B GLN* 1.3 76.0 - - - +
197B PHE* 1.3 78.2 + - + +
240B THR* 4.1 19.1 - - + +
241B LYS* 2.8 14.6 + - - +
243B TRP* 5.7 0.2 - - + -
244B ALA* 3.5 30.3 - - + -
249B TYR* 2.8 26.0 + - + -
254B LEU* 4.1 22.9 - - + -
258B LEU* 5.1 2.7 - - + -
322B PHE* 5.8 0.7 - - + -
354B PHE* 3.6 33.0 - - + -
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Residues in contact with PHE 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 PHE* 2.8 35.9 + + + +
196B LEU* 1.3 97.2 - - + +
198B GLY* 1.3 57.9 + - - +
241B LYS* 4.2 4.4 + - - +
249B TYR* 4.2 20.6 - + - -
254B LEU* 5.7 0.2 - - + -
326B ILE* 4.4 20.9 - - + -
329B LEU* 3.6 39.5 - - + -
330B ARG* 3.8 15.9 - - + -
333B LEU* 3.7 25.8 - - + +
341B GLU* 3.6 5.4 - - - -
342B LEU* 2.7 46.0 + - + +
354B PHE* 4.3 9.6 - + - -
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 3.5 4.6 + - - -
194B ASN* 2.8 24.8 + - - +
197B PHE* 1.3 77.0 - - - +
199B GLU* 1.3 62.6 + - - -
200B GLU* 3.7 5.5 + - - +
241B LYS* 4.2 8.5 + - - -
341B GLU* 3.2 17.4 - - - +
342B LEU 3.1 22.9 + - - -
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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