Contacts of the helix formed by residues 206 - 216 (chain E) in PDB entry 2WJZ
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 206 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E LYS 5.7 1.1 - - - -
205E GLY* 1.3 83.6 - - - +
207E MET* 1.3 68.3 - - + +
208E GLU* 2.9 27.9 + - - +
209E HIS* 3.0 40.9 + - + +
210E PHE* 3.3 8.1 - - - -
232E ILE* 3.3 19.6 - - + +
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Residues in contact with MET 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E LYS* 1.3 76.3 - - + +
208E GLU* 1.3 71.4 + - - +
210E PHE* 3.0 21.1 + - - +
211E LEU 3.5 3.3 + - - -
232E ILE* 3.7 16.4 - - + +
233E ASP 5.3 0.4 - - - +
236E GLU* 4.1 13.9 - - - +
237E LEU* 3.8 48.0 - - + +
240E TYR* 3.8 41.9 - - + -
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Residues in contact with GLU 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E LYS* 2.9 38.4 + - - +
207E MET* 1.3 83.8 - - - +
209E HIS* 1.3 67.2 + - + +
211E LEU* 3.0 5.8 + - + +
212E GLU* 2.9 38.8 + - + +
240E TYR* 3.3 29.5 - - + +
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Residues in contact with HIS 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E LYS 3.5 17.3 - - - -
180E SER* 3.5 11.7 + - - -
181E GLY* 3.3 37.2 - - - -
182E TYR* 3.4 24.0 - - + +
204E ALA* 4.6 0.4 - - - -
205E GLY 3.1 20.7 + - - +
206E LYS* 3.0 41.1 + - + +
208E GLU* 1.3 78.6 - - + +
210E PHE* 1.3 57.7 + - + +
212E GLU* 3.5 24.9 + - - +
213E ALA 3.1 21.8 + - - -
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Residues in contact with PHE 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 4.2 9.9 - - + -
182E TYR* 3.6 24.5 - + - -
204E ALA* 4.2 11.4 - - + -
206E LYS 3.3 14.4 - - - -
207E MET 3.0 10.0 + - - +
208E GLU 3.0 0.2 - - - -
209E HIS* 1.3 76.4 - - + +
211E LEU* 1.3 63.2 + - - +
213E ALA* 3.3 4.0 + - - +
214E PHE* 2.9 34.4 + - + -
221E ALA* 3.4 33.0 - - + -
223E ALA* 4.0 9.9 - - + -
227E PHE* 4.0 24.7 - + - -
232E ILE* 3.7 23.6 - - + -
237E LEU* 4.0 31.0 - - + -
241E LEU* 4.2 6.3 - - + -
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Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E MET 3.5 2.0 + - - -
208E GLU* 3.0 8.9 + - + +
210E PHE* 1.3 78.4 - - - +
212E GLU* 1.3 60.6 + - + +
214E PHE* 3.1 5.6 + - - +
215E LEU* 2.9 53.8 + - + +
240E TYR* 3.9 24.0 - - + +
241E LEU* 3.8 13.8 - - + +
244E HIS* 4.0 33.7 - - + +
246E VAL* 3.4 29.8 - - + -
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Residues in contact with GLU 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E GLY* 4.7 4.3 - - - -
182E TYR 5.0 1.7 + - - +
184E THR* 3.6 19.2 - - + +
188E ARG* 4.3 3.1 + - - +
208E GLU* 2.9 28.1 + - + +
209E HIS* 3.6 32.0 - - - +
211E LEU* 1.3 79.3 - - + +
213E ALA* 1.3 56.7 + - - +
215E LEU* 3.4 14.4 + - + +
216E ALA* 3.0 27.7 + - - +
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Residues in contact with ALA 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E TYR* 3.7 25.1 - - + -
184E THR* 4.2 2.6 - - - +
187E ILE* 4.1 16.8 - - + +
200E ALA* 4.1 9.6 - - + -
209E HIS 3.1 17.3 + - - +
210E PHE* 3.6 6.1 - - - +
211E LEU 3.2 0.4 - - - -
212E GLU* 1.3 76.7 - - - +
214E PHE* 1.3 60.2 + - - +
216E ALA* 3.3 4.4 + - - +
217E GLY 3.3 5.5 + - - -
218E ALA* 3.0 29.0 + - + +
221E ALA* 4.8 5.4 - - + -
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Residues in contact with PHE 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LYS* 3.6 34.1 - - + -
5E ARG 3.8 18.2 - - - -
6E ILE* 4.1 7.6 - - + -
210E PHE* 2.9 26.4 + - + -
211E LEU* 3.1 9.2 + - - +
213E ALA* 1.3 76.7 - - - +
215E LEU* 1.3 65.8 + - - +
217E GLY* 3.3 12.8 + - - -
218E ALA* 3.3 19.4 + - + +
220E ALA* 3.9 25.1 - - - -
221E ALA* 3.9 13.9 - - + -
241E LEU* 3.9 23.8 - - + -
246E VAL* 4.1 27.6 - - + -
248E VAL* 5.4 0.2 - - + -
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Residues in contact with LEU 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E ARG* 3.5 21.7 + - - +
211E LEU* 2.9 43.5 + - + +
212E GLU* 3.7 13.0 - - + +
214E PHE* 1.3 76.8 - - + +
216E ALA* 1.3 62.5 + - - +
217E GLY* 3.1 2.2 + - - -
244E HIS 6.0 0.7 - - - +
246E VAL* 5.8 2.5 - - + -
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Residues in contact with ALA 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E THR* 3.6 34.1 - - + +
187E ILE* 3.7 15.1 - - + +
188E ARG* 3.4 38.7 + - + +
191E ARG* 4.1 5.0 - - - +
212E GLU 3.0 17.5 + - - +
213E ALA 3.5 7.9 - - - +
214E PHE 3.2 0.4 - - - -
215E LEU* 1.3 75.7 - - - +
217E GLY* 1.3 57.3 + - - +
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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