Contacts of the helix formed by residues 188 - 195 (chain B) in PDB entry 1WWL
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 LEU 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B LEU* 4.1 31.2 - - + -
182B LEU* 4.4 21.3 - - + -
185B ASN* 2.9 23.4 + - + +
187B GLU* 1.3 82.2 - - - +
189B GLY* 1.3 71.0 + - - +
192B GLY* 3.4 47.1 + - - +
193B LEU* 4.0 16.8 - - + +
196B ALA* 4.8 2.2 - - + -
210B LEU* 4.8 0.9 - - + -
213B ALA* 3.6 8.1 - - + +
215B MET* 3.8 17.5 - - + -
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Residues in contact with GLY 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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187B GLU 3.5 2.1 - - - -
188B LEU* 1.3 83.4 - - - +
190B GLU* 1.3 59.5 + - - -
191B ARG 3.5 0.7 - - - -
193B LEU 3.1 17.2 + - - -
213B ALA 3.0 11.0 + - - -
214B GLY* 3.4 22.1 - - - -
215B MET* 3.3 16.0 - - - +
216B GLU* 6.0 0.9 - - - -
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Residues in contact with GLU 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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189B GLY* 1.3 70.0 - - - -
191B ARG* 1.3 67.3 + - + +
193B LEU* 3.4 15.2 + - - +
194B ILE* 3.6 6.7 + - - +
214B GLY 4.4 0.8 + - - +
215B MET* 3.7 19.0 - - - -
216B GLU* 2.7 39.8 + - + +
217B THR* 2.9 19.2 + - - +
220B GLY* 3.3 40.6 - - - +
221B VAL* 4.2 4.5 - - + +
224B ALA* 3.7 12.3 - - + +
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Residues in contact with ARG 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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189B GLY* 3.5 0.6 - - - -
190B GLU* 1.3 74.3 - - + +
192B GLY* 1.3 68.4 + - - +
194B ILE* 3.0 31.3 + - + +
195B SER* 3.5 7.4 + - - -
1415B NAG 5.2 9.5 - - + +
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Residues in contact with GLY 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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164B LEU 4.9 1.4 - - - +
188B LEU* 3.4 38.5 + - - +
190B GLU 3.4 0.2 - - - -
191B ARG* 1.3 80.6 - - - +
193B LEU* 1.3 61.4 + - - +
195B SER* 3.1 19.2 + - - -
196B ALA* 3.4 7.6 + - - +
1415B NAG 6.0 1.8 - - - -
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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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182B LEU* 4.1 13.2 - - + -
188B LEU* 3.8 9.2 - - + +
189B GLY 3.1 15.3 + - - +
190B GLU* 3.6 9.9 - - - +
191B ARG 3.1 0.6 - - - -
192B GLY* 1.3 76.7 - - - +
194B ILE* 1.3 63.6 + - - +
196B ALA* 3.0 12.0 + - - +
197B LEU* 3.2 39.9 + - + +
208B LEU* 4.6 1.8 - - + -
210B LEU* 3.6 45.3 - - + -
215B MET* 4.0 8.1 - - + -
221B VAL* 4.5 6.5 - - + -
224B ALA* 3.9 19.5 - - + -
225B LEU* 4.4 9.6 - - + -
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Residues in contact with ILE 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 GLU 3.8 10.3 - - - +
191B ARG* 3.0 18.0 + - + +
193B LEU* 1.3 78.8 - - - +
195B SER* 1.3 62.6 + - - +
196B ALA 3.3 0.9 + - - -
197B LEU* 3.6 17.1 + - - +
198B CYS* 4.8 0.3 + - - -
199B PRO* 5.6 2.6 - - - +
223B SER* 5.5 0.7 - - - +
224B ALA* 3.7 38.4 - - + +
227B ALA* 4.1 26.0 - - + +
228B ALA* 5.2 3.4 - - - +
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Residues in contact with SER 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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164B LEU 3.4 9.0 - - - +
165B ASN* 3.6 26.4 + - - -
166B PHE* 3.7 13.9 + - - +
168B CYS* 4.2 12.8 - - - -
191B ARG 3.5 4.8 + - - -
192B GLY* 3.1 14.6 + - - -
194B ILE* 1.3 78.2 - - - +
196B ALA* 1.3 58.9 + - - +
197B LEU 3.6 0.2 - - - -
1415B NAG 3.4 32.0 + - - +
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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