Contacts of the helix formed by residues 184 - 200 (chain B) in PDB entry 1YCH
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B VAL* 1.3 75.6 - - - +
185B ALA* 1.3 64.7 + - - +
186B GLY* 2.8 29.3 + - - -
187B LEU* 2.9 40.1 + - + +
188B ILE* 3.2 21.5 + - - +
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Residues in contact with ALA 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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180B ASP 5.8 0.7 - - - -
183B VAL 3.3 4.9 + - - -
184B ASP* 1.3 73.6 + - - +
186B GLY* 1.3 61.8 + - - +
188B ILE* 3.3 9.4 - - - +
189B MET* 3.2 25.6 + - - +
238B ARG* 3.3 29.1 + - - +
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Residues in contact with GLY 186 (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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184B ASP* 2.8 14.6 + - - -
185B ALA* 1.3 75.0 - - - +
187B LEU* 1.3 63.4 + - - -
189B MET* 3.6 4.6 + - - +
190B ASP* 3.2 23.2 + - - +
238B ARG* 5.7 0.4 - - - -
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Residues in contact with LEU 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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33B ARG* 4.0 32.1 - - - +
183B VAL* 5.3 3.1 - - + -
184B ASP* 2.9 37.9 + - + +
186B GLY* 1.3 78.0 - - - +
188B ILE* 1.3 58.5 + - - +
190B ASP* 3.2 8.3 + - - +
191B GLU* 3.1 32.1 + - + +
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Residues in contact with ILE 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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171B GLN* 3.5 30.5 - - + +
173B ILE* 3.9 24.9 - - + -
175B THR* 6.3 0.2 - - + -
180B ASP* 5.5 4.5 - - + +
183B VAL* 3.6 24.4 - - + +
184B ASP 3.2 12.0 + - - +
185B ALA* 3.3 16.8 - - - +
187B LEU* 1.3 76.8 - - - +
189B MET* 1.3 66.7 + - + +
191B GLU* 3.5 4.7 + - + +
192B ALA* 3.0 26.2 + - - +
230B ILE* 4.1 19.3 - - + -
232B TRP* 4.2 21.4 - - + -
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Residues in contact with MET 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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185B ALA 3.2 16.0 + - - +
186B GLY* 4.0 5.8 - - - +
187B LEU 3.3 0.2 - - - -
188B ILE* 1.3 80.9 - - + +
190B ASP* 1.3 58.7 + - - +
192B ALA* 3.5 4.3 + - - +
193B ALA* 3.1 25.8 + - - +
232B TRP* 4.0 25.6 - - + -
238B ARG* 3.6 42.4 - - + +
239B ILE* 4.2 15.9 - - + +
242B ALA* 4.1 24.2 - - - -
246B TRP* 4.3 9.9 - - + -
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Residues in contact with ASP 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 GLY 3.2 18.6 + - - +
187B LEU* 3.4 9.1 - - - +
188B ILE 3.2 0.2 - - - -
189B MET* 1.3 77.0 - - - +
191B GLU* 1.3 63.2 + - - +
193B ALA* 3.2 5.0 + - - +
194B LYS* 2.9 24.1 + - - +
299B LYS* 3.1 40.6 + - - +
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Residues in contact with GLU 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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29B PHE* 5.6 0.5 - - - -
33B ARG* 3.6 33.2 + - - +
171B GLN* 3.8 16.9 - - + +
172B HIS 4.3 17.9 + - - +
173B ILE* 4.0 21.7 - - + +
187B LEU 3.1 20.0 + - - +
188B ILE* 3.7 10.1 - - + +
190B ASP* 1.3 80.4 - - - +
192B ALA* 1.3 63.5 + - - +
194B LYS* 3.2 20.6 + - - +
195B TYR* 3.0 22.9 + - - +
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Residues in contact with ALA 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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169B PHE 5.6 0.2 - - - +
170B GLY 4.2 7.1 - - - +
171B GLN* 3.8 19.2 - - + +
188B ILE 3.0 18.4 + - - +
189B MET* 3.5 10.3 - - - +
190B ASP 3.2 0.2 - - - -
191B GLU* 1.3 76.5 - - - +
193B ALA* 1.3 56.4 + - - +
195B TYR* 3.4 2.9 - - - +
196B TYR* 3.0 26.5 + - - +
232B TRP* 4.4 3.4 - - + -
239B ILE* 4.2 25.4 - - + -
243B TYR* 5.1 3.1 + - + -
246B TRP* 4.0 5.4 - - + -
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Residues in contact with ALA 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 MET 3.1 13.4 + - - +
190B ASP* 3.2 8.7 + - - +
192B ALA* 1.3 73.9 - - - +
194B LYS* 1.3 60.6 + - - +
195B TYR 3.1 0.2 - - - -
196B TYR* 4.4 0.7 - - - +
197B ALA* 2.9 32.9 + - - +
246B TRP* 3.4 34.3 - - + +
299B LYS* 4.2 11.7 - - + -
302B LEU* 3.8 8.4 - - + +
303B ASP* 6.1 0.7 - - - +
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Residues in contact with LYS 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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29B PHE* 3.6 14.8 - - + -
30B SER* 2.9 37.1 + - - -
32B HIS* 3.6 18.8 - - - +
190B ASP 2.9 8.9 + - - +
191B GLU* 3.2 24.2 + - - +
193B ALA* 1.3 76.3 - - - +
195B TYR* 1.3 62.5 + - - +
198B ASN* 3.0 38.9 + - - +
295B ASN* 3.7 24.5 - - - +
296B ASP* 3.3 24.7 + - - +
299B LYS* 3.6 27.1 - - + +
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Residues in contact with TYR 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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29B PHE* 4.1 9.1 - - + -
167B ASP* 2.9 55.2 + - + +
170B GLY 3.2 28.5 - - - +
171B GLN* 3.8 8.3 - - - -
172B HIS* 3.8 34.5 - + - +
191B GLU 3.0 12.1 + - - +
192B ALA 3.4 10.1 - - - +
194B LYS* 1.3 76.1 - - - +
196B TYR* 1.3 70.4 + - - +
198B ASN* 3.4 1.4 + - - +
199B ILE* 3.0 50.7 + - + +
200B LEU* 4.6 5.4 - - + -
228B HIS* 3.6 12.3 - + - -
243B TYR* 4.3 10.5 - - - -
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Residues in contact with TYR 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 ALA 3.0 14.0 + - - +
193B ALA* 3.9 3.1 - - - +
195B TYR* 1.3 83.5 - - - +
197B ALA* 1.3 64.3 + - - +
200B LEU* 2.9 45.8 + - + +
201B MET* 3.1 20.5 + - - -
204B SER* 3.1 26.8 + - - -
207B ILE* 4.1 8.6 - - + +
243B TYR* 3.5 42.6 - + + -
246B TRP* 3.7 33.4 - + + -
247B ALA* 3.5 17.3 - - - +
302B LEU* 3.4 32.5 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.6 + - - +
194B LYS 4.0 2.7 - - - +
196B TYR* 1.3 82.6 - - - +
198B ASN* 1.3 58.0 + - - +
201B MET* 3.3 27.9 - - + +
298B ILE* 3.4 23.0 - - + +
299B LYS* 3.6 28.3 - - - -
302B LEU* 4.0 14.4 - - + -
332B LEU* 4.2 2.3 - - - +
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Residues in contact with ASN 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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315A ASN* 5.0 2.3 + - - -
701A FMN 6.2 0.2 - - - +
29B PHE* 3.7 20.3 - - + -
194B LYS* 3.0 29.8 + - - +
196B TYR 3.2 0.8 - - - -
197B ALA* 1.3 77.9 - - - +
199B ILE* 1.3 62.8 + - - +
294B ARG* 5.0 0.2 + - - -
295B ASN* 3.2 51.9 + - - +
298B ILE* 3.3 27.9 - - - +
328B ASP* 4.4 3.6 - - - +
332B LEU* 3.5 21.6 - - - +
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Residues in contact with ILE 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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315A ASN* 5.0 3.8 - - - +
701A FMN 5.4 5.4 - - + -
24B PHE* 6.1 0.2 - - + -
25B HIS* 4.4 23.8 - - + -
29B PHE* 4.7 11.7 - - + -
148B HIS* 4.5 25.2 + - + +
167B ASP* 5.8 1.3 - - + -
172B HIS* 4.3 13.0 - - + +
195B TYR* 3.0 51.9 + - + +
198B ASN* 1.3 85.5 - - - +
200B LEU* 1.3 81.6 + - + +
201B MET 3.6 1.1 - - - -
202B PRO* 3.7 10.8 - - - +
203B PHE* 3.9 12.6 - - - -
332B LEU* 5.2 0.2 - - - +
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Residues in contact with LEU 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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147B LEU* 4.6 6.1 - - + -
148B HIS* 4.4 15.3 - - + +
167B ASP* 6.3 1.1 - - + -
168B ALA* 4.5 15.0 - - + +
195B TYR* 4.6 6.7 - - + -
196B TYR* 2.9 34.1 + - + +
199B ILE* 1.3 90.7 - - + +
201B MET* 1.3 65.6 + - - +
202B PRO* 3.3 3.6 - - - -
203B PHE* 2.9 32.6 + - + +
204B SER 3.7 3.6 + - - -
207B ILE* 4.4 15.7 - - + -
243B TYR* 3.4 40.2 - - + +
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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