Contacts of the helix formed by residues 206 - 221 (chain D) in PDB entry 2AXZ
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D TYR* 4.9 13.7 - - - +
200D ILE* 4.2 1.2 + - - +
201D SER* 2.7 25.9 + - - +
204D ASN* 3.2 36.9 - - - +
205D ARG* 1.3 71.5 - - - +
207D LEU* 1.3 55.1 + - - +
208D LYS* 3.1 3.4 - - - -
209D GLU* 2.8 43.6 + - + -
210D ALA* 3.0 10.0 + - - +
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Residues in contact with LEU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ILE* 4.0 15.5 - - + -
205D ARG* 3.3 18.2 + - - +
206D ASN* 1.3 73.8 - - - +
208D LYS* 1.3 61.2 + - + +
210D ALA* 3.8 4.5 - - - -
211D GLN* 3.2 19.1 + - - +
243D TYR* 3.5 36.3 + - + +
246D LEU* 4.0 28.0 - - + +
247D THR* 3.7 21.3 - - + -
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Residues in contact with LYS 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ASN 2.9 1.8 + - - -
207D LEU* 1.3 75.7 - - + +
209D GLU* 1.3 68.8 + - + +
211D GLN* 3.6 6.7 + - - +
212D TYR* 3.3 19.2 + - - +
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Residues in contact with GLU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D TYR* 2.7 37.6 + - + +
169D SER* 4.9 2.3 - - - -
173D LYS* 3.4 20.1 + - - -
201D SER* 3.3 18.4 - - - +
206D ASN* 2.8 22.1 + - + +
208D LYS* 1.3 79.7 - - + +
210D ALA* 1.3 65.7 + - - +
212D TYR* 3.1 21.2 + - - +
213D TYR* 3.1 17.7 + - + -
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 3.5 22.0 - - + +
201D SER* 3.6 13.6 - - - -
202D ILE* 3.9 25.1 - - + +
206D ASN 3.0 11.3 + - - +
207D LEU* 3.8 11.7 - - - +
209D GLU* 1.3 77.7 - - - +
211D GLN* 1.3 62.3 + - - +
213D TYR* 3.3 2.8 + - - -
214D ILE* 3.0 27.2 + - - +
243D TYR* 4.1 5.6 - - + -
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Residues in contact with GLN 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LEU 3.2 15.5 + - - +
208D LYS* 3.7 7.6 - - - +
209D GLU 3.2 0.2 - - - -
210D ALA* 1.3 77.3 - - - +
212D TYR* 1.3 64.3 + - - +
214D ILE* 3.1 12.4 + - - +
215D ASN* 2.9 54.2 + - - +
240D LYS* 5.3 1.9 + - - -
243D TYR* 3.0 38.4 + - - +
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Residues in contact with TYR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ILE* 5.4 2.0 - - + -
173D LYS* 3.1 65.1 + - + +
176D TYR* 4.1 8.8 + + + +
208D LYS 3.3 10.3 + - - +
209D GLU* 3.1 11.9 - - - +
211D GLN* 1.3 79.6 - - - +
213D TYR* 1.3 83.3 + + - +
215D ASN* 3.2 11.9 + - + +
216D GLN* 2.9 57.7 + - + +
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Residues in contact with TYR 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D TYR* 2.6 36.9 + + - -
172D ILE* 3.8 24.2 - - + +
173D LYS* 3.8 4.5 + - - -
193D VAL* 5.7 0.2 - - + -
194D LEU* 3.6 29.0 - - + +
197D ALA* 3.3 29.8 - - + -
198D LEU* 3.8 22.7 - - + -
201D SER* 3.4 23.1 - - - -
209D GLU* 3.1 22.4 + - + -
210D ALA 3.8 4.5 - - - +
212D TYR* 1.3 96.0 - + - +
214D ILE* 1.3 65.4 + - - +
215D ASN 3.1 1.6 - - - -
216D GLN* 3.2 4.5 + - - +
217D PHE* 3.0 24.9 + - - +
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Residues in contact with ILE 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 3.6 25.1 - - + -
210D ALA 3.0 19.4 + - - +
211D GLN* 3.1 11.4 + - - +
213D TYR* 1.3 77.5 - - - +
215D ASN* 1.3 65.4 + - - +
217D PHE* 3.7 4.8 + - + +
218D GLU* 2.9 34.3 + - + +
236D ILE* 5.5 3.6 - - + -
240D LYS* 3.1 63.7 - - + +
243D TYR* 3.8 33.4 - - + -
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Residues in contact with ASN 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D GLN* 2.9 49.6 + - - +
212D TYR* 3.3 11.0 - - + +
214D ILE* 1.3 82.5 - - - +
216D GLN* 1.3 61.8 + - + +
218D GLU* 3.3 8.4 + - - +
219D HIS* 2.9 28.1 + - - +
240D LYS* 5.7 0.4 - - - +
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Residues in contact with GLN 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D TYR* 3.8 17.9 - - + +
177D PRO* 3.5 33.3 - - - +
178D ILE 4.9 0.4 - - - +
194D LEU* 3.6 30.9 - - + +
212D TYR* 2.9 56.1 + - + +
213D TYR* 3.2 3.5 + - - +
215D ASN* 1.3 78.8 - - - +
217D PHE* 1.3 61.7 + - - +
219D HIS* 3.3 11.4 + - - +
220D LEU* 3.2 25.5 + - - +
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Residues in contact with PHE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D GLN* 4.1 14.1 - - + -
194D LEU* 3.4 13.6 - - + +
213D TYR 3.0 17.2 + - - +
214D ILE 3.9 3.1 - - - +
216D GLN* 1.3 73.7 - - - +
218D GLU* 1.3 80.5 + - + +
220D LEU* 3.1 31.0 + - + +
221D LYS* 3.4 26.8 + - - +
228D ILE* 3.6 26.2 - - + -
232D TYR* 5.0 0.2 - - + -
233D ASP* 3.3 36.3 - - - -
236D ILE* 3.4 48.7 - - + -
237D ASN* 5.3 2.0 - - - -
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Residues in contact with GLU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ILE* 2.9 30.5 + - + +
215D ASN* 3.3 8.9 + - - +
217D PHE* 1.3 89.7 - - - +
219D HIS* 1.3 63.1 + - - +
221D LYS* 3.2 47.5 + - - +
222D THR* 3.9 8.3 + - - +
236D ILE* 5.6 0.9 - - - +
237D ASN* 4.5 5.5 - - - +
240D LYS* 4.1 25.9 - - - +
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Residues in contact with HIS 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D PRO* 3.8 24.0 - - + +
178D ILE 3.2 29.4 + - - -
179D VAL* 5.2 2.4 - - - +
215D ASN 2.9 14.1 + - - +
216D GLN* 3.4 16.8 - - - +
217D PHE 3.1 0.2 - - - -
218D GLU* 1.3 75.1 - - - +
220D LEU* 1.3 62.2 + - + +
222D THR* 2.4 47.2 + - - +
223D ILE* 3.7 11.5 + - + +
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Residues in contact with LEU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D TYR* 5.5 0.7 - - + -
178D ILE* 3.6 41.3 - - + +
190D ILE* 4.6 13.9 - - + +
191D GLN* 3.9 30.3 - - + -
194D LEU* 3.9 22.4 - - + -
216D GLN 3.3 13.7 - - - +
217D PHE* 3.1 15.0 + - + +
219D HIS* 1.3 79.4 - - + +
221D LYS* 1.3 62.1 + - - +
222D THR 3.1 0.4 - - - -
223D ILE* 3.1 20.4 + - + +
226D ILE* 3.5 28.5 - - + +
228D ILE* 4.7 5.9 - - + +
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Residues in contact with LYS 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C TYR* 4.5 1.2 + - - -
267C ILE 4.8 7.8 + - - -
268C GLY* 6.4 0.2 - - - -
269C LYS* 5.6 3.2 - - - +
217D PHE* 3.4 26.9 - - - +
218D GLU* 3.2 39.9 - - - +
219D HIS 3.1 0.4 - - - -
220D LEU* 1.3 75.9 - - - +
222D THR* 1.3 60.5 + - + +
223D ILE 3.4 1.9 - - - -
224D LYS* 5.2 0.7 + - - -
228D ILE* 3.2 31.7 - - + +
233D ASP* 2.8 34.1 + - - -
237D ASN* 5.6 0.7 - - - -
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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