Contacts of the helix formed by residues 191 - 203 (chain B) in PDB entry 1WVV
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 TRP 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B HIS* 3.2 26.9 - - + -
165B TYR* 3.3 56.1 - + - +
166B CYS 3.9 2.5 - - - -
167B ASP* 3.9 19.7 - - + -
181B TYR* 2.9 17.7 + - - +
190B SER* 1.3 87.4 - - - +
192B ASN* 1.3 66.5 + - - +
193B PHE* 3.6 43.7 - + + -
194B ASN* 3.0 15.3 + - - -
195B TYR* 3.1 13.3 + - - -
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Residues in contact with ASN 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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165B TYR 3.1 6.8 + - - +
167B ASP* 2.9 54.2 + - - +
170B GLN* 3.7 12.7 - - - +
172B TYR* 3.8 2.5 - - - -
173B GLY 3.0 28.5 + - - +
174B CYS* 3.4 15.0 - - - -
181B TYR* 3.6 22.9 - - + +
191B TRP* 1.3 71.2 - - - +
193B PHE* 1.3 62.9 + - - +
195B TYR* 3.5 1.2 + - - +
196B LYS* 2.9 28.6 + - - +
207B LEU* 3.6 11.6 - - + +
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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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167B ASP* 3.7 24.0 - - + -
170B GLN* 4.2 9.6 - - + +
172B TYR* 3.0 25.8 + - - +
191B TRP* 3.6 40.4 - + + -
192B ASN* 1.3 87.7 + - - +
194B ASN* 1.3 96.9 + - - +
196B LYS* 3.6 1.7 + - - +
197B ALA* 3.0 27.7 + - - +
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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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189B LEU* 3.9 18.5 - - + +
190B SER* 2.8 28.3 + - - +
191B TRP* 3.0 6.3 + - - +
193B PHE* 1.3 103.3 + - - +
195B TYR* 1.3 59.7 + - - +
197B ALA* 4.0 4.5 - - - +
198B ALA* 2.9 32.6 + - - +
226B TRP* 4.1 15.8 - - + -
231B GLN* 5.6 1.6 + - - -
402B GOL 5.9 4.2 - - - -
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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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181B TYR* 3.7 35.0 - + + -
182B TYR 2.7 19.1 + - - -
184B ARG* 2.9 24.8 + - - +
189B LEU* 2.8 45.5 + - + +
190B SER* 3.8 2.0 - - - -
191B TRP 3.1 25.5 + - - -
192B ASN 3.8 6.1 - - - +
194B ASN* 1.3 72.1 - - - +
196B LYS* 1.3 64.8 + - - +
198B ALA* 4.6 0.2 - - - -
199B GLY* 3.0 19.1 + - - -
206B LEU* 3.5 33.3 - - + +
207B LEU 4.0 3.5 + - - +
210B PRO* 3.6 36.1 - - + -
213B VAL* 3.8 11.7 - - + -
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Residues in contact with LYS 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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172B TYR* 3.8 39.0 - - + -
192B ASN 2.9 18.9 + - - +
193B PHE 3.6 5.8 - - - +
195B TYR* 1.3 77.7 - - - +
197B ALA* 1.3 57.0 + - - +
199B GLY* 3.8 0.3 - - - -
200B ASP* 2.8 70.0 + - - +
205B ASN* 5.5 1.3 - - - +
207B LEU* 3.8 34.2 - - + +
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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 PHE 3.0 18.3 + - - +
194B ASN* 4.0 4.7 - - - +
196B LYS* 1.3 73.5 - - - +
198B ALA* 1.3 68.4 + - - +
200B ASP* 3.4 8.3 + - - +
201B ALA* 3.1 24.1 + - - +
226B TRP* 3.9 18.5 + - + +
231B GLN* 5.8 0.7 - - - +
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Residues in contact with ALA 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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189B LEU* 4.1 16.8 - - + -
194B ASN 2.9 18.4 + - - +
195B TYR 4.1 1.3 - - - +
197B ALA* 1.3 77.6 - - - +
199B GLY* 1.3 56.8 + - - +
201B ALA* 3.2 3.6 + - - +
202B LEU* 2.9 35.2 + - + +
206B LEU* 4.3 6.1 - - + -
223B THR* 4.7 5.6 - - + -
226B TRP* 3.6 38.0 - - + +
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Residues in contact with GLY 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 TYR 3.0 17.7 + - - -
196B LYS 3.8 0.4 - - - -
198B ALA* 1.3 74.3 - - - +
200B ASP* 1.3 66.4 + - - +
202B LEU* 3.1 2.0 + - - -
203B GLY* 2.8 22.0 + - - -
204B ILE 2.9 31.0 + - - -
205B ASN* 5.5 0.2 - - - -
206B LEU* 3.8 11.8 - - - +
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Residues in contact with ASP 200 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B LYS* 2.8 57.3 + - - +
197B ALA* 3.7 6.7 - - - +
199B GLY* 1.3 77.0 - - - +
201B ALA* 1.3 63.5 + - - +
202B LEU 3.4 0.2 + - - -
203B GLY* 3.4 9.0 + - - +
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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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121B TYR* 4.1 9.4 + - - +
197B ALA 3.1 10.7 + - - +
198B ALA 3.5 8.1 - - - +
200B ASP* 1.3 78.4 - - - +
202B LEU* 1.3 60.8 + - - +
203B GLY 3.7 0.3 + - - -
226B TRP* 3.5 27.4 - - + +
230B SER* 6.1 0.7 - - - -
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Residues in contact with LEU 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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120B ALA* 4.2 10.3 - - + -
121B TYR* 3.9 29.6 - - + +
198B ALA 2.9 22.6 + - - +
199B GLY* 4.0 3.6 - - - +
201B ALA* 1.3 77.0 - - - +
203B GLY* 1.3 62.5 + - - +
204B ILE* 3.5 23.3 + - + +
206B LEU* 4.4 6.1 - - + -
219B VAL* 4.9 0.7 - - + +
222B LYS* 3.8 49.7 + - + +
223B THR* 4.0 18.2 - - + +
226B TRP* 4.5 5.6 - - + -
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Residues in contact with GLY 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 GLY 2.8 6.0 + - - -
200B ASP 3.4 6.2 + - - -
201B ALA 3.4 3.6 - - - -
202B LEU* 1.3 79.1 - - - +
204B ILE* 1.3 60.3 + - - +
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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