Contacts of the helix formed by residues 193 - 211 (chain B) in PDB entry 2WO6
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 LYS 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B TYR* 4.5 24.2 - - + -
191B LYS 2.9 8.7 + - - +
192B ASN* 1.3 74.4 - - - +
194B LYS* 1.3 66.5 + - - +
195B ALA* 3.3 4.0 - - + +
196B PHE* 3.2 22.8 + - + +
197B LEU* 3.0 20.9 + - - +
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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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193B LYS* 1.3 72.7 - - - +
195B ALA* 1.3 54.6 + - - +
197B LEU* 3.5 13.7 - - + +
198B ASN* 2.7 66.1 + - - +
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Residues in contact with ALA 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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193B LYS* 3.3 2.4 - - + +
194B LYS* 1.3 79.4 - - - +
196B PHE* 1.3 64.4 + - + +
198B ASN* 3.4 8.0 + - - +
199B GLN* 3.1 22.2 + - - +
12C LEU* 3.4 26.9 - - + +
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Residues in contact with PHE 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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145B TYR* 5.6 4.3 - + - -
169B SER 4.1 7.9 - - - -
170B PHE* 3.2 60.4 - + + -
190B ILE* 4.1 17.7 - - + +
191B LYS* 3.8 36.8 - - + -
193B LYS* 3.2 19.8 + - + +
194B LYS 3.2 0.2 - - - -
195B ALA* 1.3 77.8 - - + +
197B LEU* 1.3 60.6 + - - +
199B GLN* 3.2 2.7 + - - +
200B ALA* 2.9 31.2 + - - +
11C ALA* 5.8 2.2 - - + -
12C LEU* 3.4 29.8 - - + -
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Residues in contact with LEU 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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190B ILE* 4.7 4.5 - - - -
191B LYS 4.4 5.6 + - - +
192B ASN* 6.3 0.2 - - - -
193B LYS 3.0 14.6 + - - +
194B LYS* 3.5 16.6 - - + +
196B PHE* 1.3 77.4 - - - +
198B ASN* 1.3 64.9 + - - +
200B ALA* 3.5 5.4 + - - +
201B GLN* 3.2 45.8 + - - +
229B MET* 4.5 20.0 - - + -
234B LEU* 3.9 31.9 - - + +
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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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194B LYS* 2.7 55.2 + - - +
195B ALA* 3.6 7.7 - - - +
197B LEU* 1.3 77.7 - - - +
199B GLN* 1.3 62.6 + - - +
201B GLN* 3.6 25.9 + - - +
202B ILE* 3.7 18.7 + - - +
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Residues in contact with GLN 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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170B PHE* 4.7 11.2 - - + -
195B ALA 3.1 16.0 + - - +
196B PHE* 3.2 4.0 + - - +
198B ASN* 1.3 74.4 - - - +
200B ALA* 1.3 64.9 + - - +
202B ILE* 3.3 28.1 + - - +
203B GLU* 3.1 19.9 + - - +
308B PHE 5.4 0.4 + - - -
309B GLY* 3.0 30.4 + - - +
310B SER* 4.7 2.0 - - - +
311B SER 3.9 17.8 + - - -
318B ILE* 4.4 5.9 - - - +
319B TYR* 2.4 39.8 + - + +
12C LEU* 4.3 13.5 - - + -
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Residues in contact with ALA 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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170B PHE* 6.3 0.9 - - + -
190B ILE* 4.0 28.0 - - + -
196B PHE 2.9 16.3 + - - +
197B LEU 4.0 1.8 - - - +
198B ASN 3.4 0.2 - - - -
199B GLN* 1.3 76.9 - - - +
201B GLN* 1.3 57.5 + - - +
203B GLU* 3.4 14.8 - - - +
204B VAL* 2.8 33.4 + - - +
234B LEU* 3.6 22.0 - - + -
236B LEU* 4.8 2.6 - - + +
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Residues in contact with GLN 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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197B LEU* 3.2 38.8 + - + +
198B ASN* 3.7 23.1 + - - +
199B GLN 3.2 0.6 - - - -
200B ALA* 1.3 75.8 - - - +
202B ILE* 1.3 60.6 + - + +
204B VAL* 3.8 8.2 + - + +
205B ARG* 3.0 25.7 + - - +
229B MET* 6.2 0.6 - - - -
234B LEU* 4.4 6.9 - - + +
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Residues in contact with ILE 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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198B ASN 3.7 15.5 + - - +
199B GLN* 3.3 29.3 + - - +
201B GLN* 1.3 74.5 - - + +
203B GLU* 1.3 55.1 + - - +
205B ARG* 2.9 27.6 + - - +
206B LEU* 2.7 44.2 + - + +
311B SER 4.1 19.3 - - - +
312B CYS* 5.5 2.5 - - - -
318B ILE* 4.2 18.2 - - + -
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Residues in contact with GLU 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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188B LYS* 2.7 32.5 + - - -
190B ILE* 4.8 3.3 - - - +
199B GLN* 3.1 9.4 + - - +
200B ALA* 3.4 20.1 - - - +
202B ILE* 1.3 78.0 - - - +
204B VAL* 1.3 64.0 + - - +
206B LEU* 2.9 8.3 + - - +
207B LEU* 2.9 35.4 + - + +
236B LEU* 3.9 17.8 - - - +
238B PHE* 4.2 7.4 - - - -
307B ASP* 4.5 0.5 - - - -
308B PHE* 3.5 34.9 + - + +
309B GLY* 3.9 16.7 - - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA 2.8 25.6 + - - +
201B GLN* 3.8 7.6 - - + +
203B GLU* 1.3 72.7 - - - +
205B ARG* 1.3 56.2 + - - +
207B LEU* 3.4 2.0 + - - +
208B GLU* 2.9 44.7 + - + +
224B LEU* 4.2 10.3 - - + -
227B HIS* 3.6 37.0 - - + +
234B LEU* 4.4 7.0 - - + -
236B LEU* 3.6 35.0 - - + -
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Residues in contact with ARG 205 (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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201B GLN 3.0 15.7 + - - +
202B ILE* 2.9 32.0 + - - +
204B VAL* 1.3 78.4 - - - +
206B LEU* 1.3 70.5 + - - +
208B GLU* 3.5 7.6 + - - +
209B LEU* 3.0 40.0 + - + +
312B CYS* 6.1 0.2 - - - +
313B GLN* 2.9 33.9 + - - +
316B GLN* 3.2 20.6 + - - +
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Residues in contact with LEU 206 (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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202B ILE* 2.7 25.7 + - + +
203B GLU* 2.9 6.0 + - - +
205B ARG* 1.3 93.1 - - - +
207B LEU* 1.3 58.7 + - - +
209B LEU* 3.2 7.3 + - + +
210B MET* 2.9 40.3 + - + +
283B ILE* 4.2 20.0 - - + +
308B PHE* 4.6 8.1 - - + +
311B SER* 3.6 45.8 - - - +
312B CYS* 4.0 7.0 - - - +
313B GLN* 3.9 30.1 - - + +
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Residues in contact with LEU 207 (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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203B GLU* 2.9 39.4 + - + +
204B VAL 3.9 2.7 - - - +
206B LEU* 1.3 71.6 - - - +
208B GLU* 1.3 65.0 + - - +
210B MET* 3.3 24.5 + - + +
211B ASN* 3.0 23.4 + - - +
221B ILE* 4.5 0.9 - - + -
222B VAL* 4.0 28.3 - - + +
224B LEU* 4.1 28.6 - - + +
236B LEU* 4.5 2.5 - - + -
238B PHE* 3.9 27.1 - - + -
308B PHE* 4.2 17.7 - - + +
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Residues in contact with GLU 208 (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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204B VAL* 2.9 37.0 + - + +
205B ARG* 4.0 6.7 - - - +
207B LEU* 1.3 76.8 - - - +
209B LEU* 1.3 60.9 + - - +
211B ASN* 3.3 9.9 + - - +
212B LYS* 2.7 38.8 + - - +
224B LEU* 4.5 9.3 - - + +
227B HIS* 3.2 23.8 + - - -
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Residues in contact with LEU 209 (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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358A GLU* 3.8 27.4 - - - +
205B ARG* 3.0 29.2 + - + +
206B LEU* 3.4 10.3 - - + +
208B GLU* 1.3 75.2 - - - +
210B MET* 1.3 65.7 + - - +
212B LYS* 3.2 19.0 + - + +
213B HIS* 3.4 14.9 + - - +
280B GLU 4.1 7.2 - - - +
281B LEU* 3.8 19.7 - - + -
283B ILE* 4.9 1.3 - - + -
313B GLN* 3.4 36.1 - - - +
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Residues in contact with MET 210 (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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206B LEU* 2.9 25.7 + - + +
207B LEU* 3.7 35.4 - - + +
209B LEU* 1.3 76.1 - - - +
211B ASN* 1.3 57.5 + - - +
212B LYS 3.1 5.5 + - - -
213B HIS* 3.2 16.8 + - - +
218B LYS* 3.5 13.8 - - + +
221B ILE* 3.7 24.5 - - + -
275B PHE* 3.7 21.2 - - + -
276B LEU* 3.8 24.0 - - - -
281B LEU* 4.0 10.1 - - + -
283B ILE* 3.7 17.3 - - + -
308B PHE* 4.0 18.8 - - + -
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Residues in contact with ASN 211 (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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255A ARG* 4.4 11.5 + - - +
207B LEU 3.0 16.4 + - - +
208B GLU* 3.7 9.4 - - - +
209B LEU 3.2 1.0 - - - -
210B MET* 1.3 75.0 - - - +
212B LYS* 1.3 66.3 + - - +
213B HIS 3.3 1.2 + - - -
218B LYS* 3.3 30.9 + - + +
223B HIS* 3.3 33.8 + - + +
224B LEU 5.4 1.6 - - - +
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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