Contacts of the helix formed by residues 206 - 221 (chain B) in PDB entry 2AXV
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 ASN 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TYR* 5.0 8.2 - - + -
201B SER* 2.9 19.0 + - - +
204B ASN* 3.0 13.0 - - + +
205B ARG* 1.3 74.9 - - - +
207B LEU* 1.3 58.2 + - - +
208B LYS* 3.5 9.7 + - - +
209B GLU* 3.3 36.0 + - + +
210B ALA* 3.0 27.4 + - - +
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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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201B SER 5.3 0.2 - - - +
202B ILE* 5.3 4.0 - - + -
205B ARG* 3.0 45.4 + - + +
206B ASN* 1.3 72.2 + - - +
208B LYS* 1.3 66.9 + - - +
210B ALA* 3.9 5.8 - - + -
211B GLN* 3.1 20.4 + - - +
243B TYR* 3.4 24.6 + - + +
246B LEU* 4.2 25.6 - - + +
247B THR* 3.7 40.2 - - + +
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Residues in contact with LYS 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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206B ASN* 3.3 8.8 + - - +
207B LEU* 1.3 80.1 - - - +
209B GLU* 1.3 71.0 + - + +
211B GLN* 3.3 21.9 + - - +
212B TYR* 3.2 19.2 + - - +
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TYR* 2.8 36.3 + - + +
169B SER* 4.4 0.5 - - - -
173B LYS* 2.8 31.7 + - - -
201B SER* 3.6 15.3 - - - +
206B ASN* 3.3 30.6 + - - +
208B LYS* 1.3 84.2 - - + +
210B ALA* 1.3 67.4 + - - +
212B TYR* 2.9 17.4 + - - +
213B TYR* 3.0 20.7 + - - -
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Residues in contact with ALA 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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198B LEU* 3.2 29.1 - - + +
201B SER* 3.4 11.3 - - - -
202B ILE* 4.1 20.0 - - + +
206B ASN 3.0 19.7 + - - +
207B LEU* 3.8 9.6 - - + +
208B LYS 3.3 0.2 - - - -
209B GLU* 1.3 77.0 - - - +
211B GLN* 1.3 63.5 + - - +
213B TYR* 3.2 0.9 + - - -
214B ILE* 3.0 21.9 + - - +
243B TYR* 4.2 6.1 - - + -
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Residues in contact with GLN 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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207B LEU 3.1 18.5 + - - +
208B LYS* 3.5 22.3 + - - +
209B GLU 3.2 0.2 - - - -
210B ALA* 1.3 75.2 - - - +
212B TYR* 1.3 61.9 + - - +
214B ILE* 3.3 13.5 + - + +
215B ASN* 2.9 47.7 + - - +
243B TYR* 3.7 24.4 + - + +
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Residues in contact with TYR 212 (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 ILE* 4.7 1.7 - - + +
173B LYS* 3.2 59.0 + - + +
176B TYR* 3.7 17.4 + + + +
208B LYS 3.2 11.6 + - - +
209B GLU* 2.9 15.6 + - - +
211B GLN* 1.3 74.4 - - - +
213B TYR* 1.3 96.2 + + - +
215B ASN* 3.0 10.2 + - - +
216B GLN* 2.8 52.0 + - + +
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Residues in contact with TYR 213 (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* 2.8 29.0 + + - -
172B ILE* 3.4 36.7 - - + +
173B LYS* 4.6 2.4 + - - -
193B VAL* 5.3 0.2 - - + -
194B LEU* 4.0 26.7 - - + +
197B ALA* 3.2 31.6 - - + -
198B LEU* 3.8 22.0 - - + -
201B SER* 3.6 18.2 - - - -
209B GLU* 3.0 21.5 + - + -
210B ALA 3.6 4.7 - - - +
212B TYR* 1.3 99.9 - + - +
214B ILE* 1.3 64.5 + - - +
216B GLN* 3.2 3.2 + - - +
217B PHE* 2.9 25.5 + - - +
236B ILE* 6.4 0.4 - - - -
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 3.8 24.9 - - + -
210B ALA 3.0 27.0 + - - +
211B GLN* 3.5 12.1 - - + +
213B TYR* 1.3 75.9 - - - +
215B ASN* 1.3 66.1 + - - +
217B PHE* 3.3 6.2 + - - +
218B GLU* 2.9 44.8 + - + +
236B ILE* 5.1 5.2 - - + -
240B LYS* 3.9 31.6 - - + -
243B TYR* 4.2 28.7 - - + -
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Residues in contact with ASN 215 (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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211B GLN* 2.9 45.9 + - - +
212B TYR* 3.3 9.7 - - - +
214B ILE* 1.3 83.3 - - - +
216B GLN* 1.3 63.4 + - - +
218B GLU* 3.2 7.1 + - - +
219B HIS* 2.8 30.9 + - - +
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Residues in contact with GLN 216 (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 TYR* 3.4 18.8 - - + +
177B PRO* 3.0 45.4 - - - +
178B ILE 4.3 1.0 - - - +
194B LEU* 3.9 19.6 - - + +
212B TYR* 2.8 51.3 + - + +
213B TYR* 3.2 5.4 + - - +
215B ASN* 1.3 80.2 - - - +
217B PHE* 1.3 58.4 + - - +
219B HIS* 3.5 9.4 + - - +
220B LEU* 3.3 24.5 + - - +
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Residues in contact with PHE 217 (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 GLN* 3.8 26.5 - - + -
194B LEU* 3.8 16.3 - - + +
213B TYR 2.9 16.9 + - - +
214B ILE* 3.6 5.8 - - - +
216B GLN* 1.3 72.0 - - - +
218B GLU* 1.3 73.0 + - - +
219B HIS 3.0 2.0 - - - -
220B LEU* 3.0 31.1 + - + +
221B LYS* 3.4 30.5 + - - +
228B ILE* 3.8 17.0 - - + -
232B TYR* 4.6 5.6 - - + -
233B ASP* 3.5 31.2 - - - -
236B ILE* 3.7 43.5 - - + -
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Residues in contact with GLU 218 (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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214B ILE* 2.9 36.5 + - + +
215B ASN* 3.9 7.9 - - - +
217B PHE* 1.3 85.0 - - - +
219B HIS* 1.3 60.9 + - - +
221B LYS* 2.9 58.5 + - + +
222B THR* 3.8 8.3 - - - +
233B ASP* 4.7 0.2 - - - +
236B ILE* 5.2 2.3 - - - +
237B ASN* 5.5 3.2 + - - -
240B LYS* 4.0 17.5 + - - +
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Residues in contact with HIS 219 (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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177B PRO* 3.8 21.0 - - + +
178B ILE 3.5 26.5 + - - -
179B VAL* 5.3 1.6 - - - +
215B ASN 2.8 16.5 + - - +
216B GLN* 3.5 11.7 - - - +
217B PHE 3.0 0.2 - - - -
218B GLU* 1.3 75.5 - - - +
220B LEU* 1.3 70.0 + - + +
221B LYS 2.9 2.0 - - - -
222B THR* 2.8 50.4 + - + +
223B ILE* 3.8 8.1 + - + +
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Residues in contact with LEU 220 (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 TYR* 5.2 0.7 - - + -
178B ILE* 3.7 38.1 - - + +
190B ILE* 3.8 15.9 - - + -
191B GLN* 3.6 28.5 - - + -
194B LEU* 3.5 26.7 - - + -
216B GLN* 3.3 12.3 + - - +
217B PHE* 3.0 17.3 + - + +
219B HIS* 1.3 79.5 - - + +
221B LYS* 1.3 57.4 + - - +
223B ILE* 2.9 35.6 + - + +
226B ILE* 3.4 13.3 - - + +
228B ILE* 4.1 11.2 - - + -
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Residues in contact with LYS 221 (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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231A TYR* 5.3 0.2 - - - -
267A ILE 3.9 12.5 + - - -
217B PHE* 3.4 29.2 - - - +
218B GLU* 2.9 48.9 + - + +
219B HIS 2.9 0.2 - - - -
220B LEU* 1.3 77.5 - - - +
222B THR* 1.3 60.4 + - + +
223B ILE 3.4 2.1 + - - +
226B ILE* 3.9 10.5 - - - +
228B ILE* 3.9 22.9 - - + -
233B ASP* 2.9 32.7 + - - -
237B ASN* 5.5 1.8 - - - +
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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