Contacts of the helix formed by residues 183 - 197 (chain B) in PDB entry 2WOE
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 MET 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B LEU* 3.8 3.2 - - - +
182B GLY* 1.3 68.6 - - - -
184B LYS* 1.3 60.1 + - - +
186B CYS* 3.1 4.9 + - - +
187B ARG* 2.8 55.6 + - - +
224B TYR* 3.3 53.2 - - + +
225B PHE* 3.6 23.1 - - + +
227B THR 4.0 5.4 - - - +
228B ASP* 6.0 0.4 - - + -
258B THR* 4.8 7.5 - - + +
259B TYR* 3.5 22.9 - - + +
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Residues in contact with LYS 184 (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 ARG 4.4 6.1 - - - +
182B GLY* 3.1 0.8 - - - -
183B MET* 1.3 78.5 - - - +
185B ALA* 1.3 62.5 + - + +
187B ARG* 3.2 23.6 + - + +
188B GLU* 3.2 32.4 + - + +
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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
----------------------------------------------------------
176B HIS* 3.7 26.3 + - + +
181B ARG* 3.3 37.3 + - + +
182B GLY 3.2 4.7 + - - +
184B LYS* 1.3 79.7 - - - +
186B CYS* 1.3 56.9 + - - +
188B GLU* 3.4 18.0 + - - +
189B GLU* 3.0 26.0 + - - +
192B ARG* 4.7 0.5 + - - -
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Residues in contact with CYS 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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173B MET* 3.6 43.2 - - + +
176B HIS* 4.2 3.8 - - - -
177B LEU* 3.4 43.5 - - - -
182B GLY 3.3 3.1 + - - -
183B MET* 3.1 11.5 + - - +
185B ALA* 1.3 74.9 - - - +
187B ARG* 1.3 58.1 + - - +
189B GLU* 3.6 7.4 - - - +
190B ALA* 2.8 31.5 + - - +
224B TYR* 4.2 1.6 - - + -
225B PHE* 3.5 9.7 - - + -
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Residues in contact with ARG 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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183B MET* 2.8 33.4 + - - +
184B LYS* 3.5 13.9 - - - +
186B CYS* 1.3 71.6 - - - +
188B GLU* 1.3 60.4 + - + +
190B ALA* 3.5 1.9 + - - +
191B ASN* 2.9 30.5 + - - +
202B PHE* 6.1 0.8 - - - -
225B PHE* 3.1 66.6 + - + +
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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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184B LYS* 3.2 34.3 + - + +
185B ALA* 3.6 15.8 - - - +
186B CYS 3.3 0.2 - - - -
187B ARG* 1.3 77.2 - - + +
189B GLU* 1.3 57.0 + - - +
191B ASN* 3.3 7.8 + - - +
192B ARG* 3.0 54.7 + - - +
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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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169B THR* 4.0 21.1 + - + +
172B ARG* 3.3 48.9 + - + +
173B MET* 4.1 9.2 - - + -
176B HIS* 2.9 29.0 + - + +
185B ALA 3.0 15.2 + - - +
186B CYS 3.6 4.9 - - - +
187B ARG 3.3 0.2 - - - -
188B GLU* 1.3 75.3 - - - +
190B ALA* 1.3 65.1 + - - +
192B ARG* 2.9 43.8 + - - +
193B LEU* 3.1 12.6 + - - +
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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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169B THR* 4.4 11.8 - - - +
173B MET* 5.0 1.6 - - - -
186B CYS 2.8 21.6 + - - +
187B ARG 3.9 2.2 - - - +
189B GLU* 1.3 71.4 - - - +
191B ASN* 1.3 58.4 + - - +
193B LEU* 3.2 5.0 + - - +
194B VAL* 3.0 32.2 + - - +
202B PHE* 4.3 7.6 - - + -
221B LEU* 4.1 22.0 - - + -
225B PHE* 3.7 24.0 - - + -
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Residues in contact with ASN 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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187B ARG 2.9 19.8 + - - +
188B GLU* 3.6 7.6 - - - +
189B GLU 3.2 0.2 - - - -
190B ALA* 1.3 75.4 - - - +
192B ARG* 1.3 59.5 + - - +
194B VAL* 3.4 12.6 + - - +
195B HIS* 3.0 65.2 + - - -
202B PHE* 6.1 0.2 - - - -
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Residues in contact with ARG 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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176B HIS* 4.4 6.1 + - - -
185B ALA 4.7 0.6 + - - -
188B GLU* 3.0 34.2 + - - +
189B GLU* 2.9 60.3 + - - +
191B ASN* 1.3 72.9 - - - +
193B LEU* 1.3 59.8 + - - +
195B HIS* 3.3 9.5 + - - +
196B GLN* 2.9 30.8 + - - +
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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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165B ALA* 3.6 32.5 - - + -
166B ALA* 4.5 1.3 - - - -
169B THR* 3.5 39.5 + - + +
189B GLU 3.1 9.5 + - - +
190B ALA 3.2 8.0 + - - +
192B ARG* 1.3 76.4 - - - +
194B VAL* 1.3 57.8 + - + +
196B GLN* 3.1 13.3 + - - +
197B HIS* 2.8 28.7 + - + +
200B PHE* 3.6 41.1 - - + -
217B MET* 4.0 17.7 - - + -
221B LEU* 4.7 8.5 - - + -
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Residues in contact with VAL 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 ALA 3.0 16.8 + - - +
191B ASN* 3.8 13.9 - - - +
192B ARG 3.3 0.2 - - - -
193B LEU* 1.3 76.0 - - + +
195B HIS* 1.3 66.1 + - + +
197B HIS 3.2 7.3 - - - -
198B ARG* 3.2 27.2 - - + +
200B PHE* 3.9 26.0 - - + +
201B HIS* 3.8 29.4 - - + +
202B PHE* 4.1 16.2 - - + -
221B LEU* 5.7 1.3 - - + -
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Residues in contact with HIS 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 ASN* 3.0 47.9 + - - +
192B ARG* 3.6 8.7 - - - +
193B LEU 3.3 0.2 - - - -
194B VAL* 1.3 82.2 - - + +
196B GLN* 1.3 62.3 + - - +
198B ARG* 5.1 0.7 + - - +
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Residues in contact with GLN 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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165B ALA* 4.0 20.9 - - - +
169B THR* 5.6 1.0 + - - -
172B ARG* 6.1 1.0 - - - +
192B ARG 2.9 13.3 + - - +
193B LEU* 3.5 14.7 - - - +
195B HIS* 1.3 80.2 - - - +
197B HIS* 1.3 91.6 + - + +
198B ARG 4.1 0.4 + - - -
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Residues in contact with HIS 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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161B PRO* 4.1 18.3 + - + +
162B LEU* 3.9 24.2 - - + +
165B ALA* 3.6 29.7 - - + +
193B LEU* 2.8 14.2 + - + +
194B VAL* 3.2 6.4 - - - +
196B GLN* 1.3 107.3 + - + +
198B ARG* 1.3 65.2 + - - +
199B ASP* 3.1 5.5 + - + +
200B PHE* 3.1 31.7 + + + +
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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