Contacts of the helix formed by residues 203 - 215 (chain D) in PDB entry 1AX4
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 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D TRP* 5.4 0.2 - - - -
201D VAL 3.9 0.2 + - - -
202D SER* 1.3 74.1 - - - +
204D SER* 1.3 58.5 + - - +
206D LEU* 3.5 5.7 + - - +
207D LYS* 3.0 29.2 + - + +
234D ILE* 4.0 15.0 - - + +
238D ASP* 4.2 9.8 + - - +
240D LYS* 5.2 2.9 - - - +
241D TYR* 3.6 39.0 - - + +
249D VAL* 3.6 23.8 - - + +
252D ASP* 3.6 23.3 - - + -
253D MET* 3.8 33.9 - - + -
256D TYR* 3.9 20.6 - - + +
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Residues in contact with SER 204 (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 SER* 3.4 10.6 + - - -
203D MET* 1.3 79.8 - - - +
205D ASN* 1.3 56.8 + - - +
207D LYS* 3.4 9.8 + - - +
208D GLU* 2.9 31.3 + - - +
238D ASP* 5.2 3.2 + - - -
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Residues in contact with ASN 205 (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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166D ASP* 3.3 28.0 + - - +
167D PHE* 2.7 58.3 + - - +
169D ILE* 3.8 18.8 - - - +
201D VAL* 3.6 3.9 - - + +
202D SER* 3.1 21.1 + - - +
204D SER* 1.3 73.3 + - - +
206D LEU* 1.3 66.6 + - - +
208D GLU* 3.2 5.4 + - - +
209D VAL* 2.9 27.9 + - - +
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Residues in contact with LEU 206 (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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167D PHE* 5.2 1.8 - - + -
189D SER* 4.0 28.3 - - - +
191D VAL* 4.1 19.5 - - + -
201D VAL* 3.7 24.5 - - + +
202D SER 3.0 18.6 + - - +
203D MET* 3.7 11.9 - - - +
205D ASN* 1.3 78.0 + - - +
207D LYS* 1.3 62.8 + - - +
209D VAL* 3.8 5.8 - - - +
210D TYR* 3.0 24.3 + - - +
222D MET* 4.1 10.3 - - + -
230D ASN* 4.8 0.4 - - - +
234D ILE* 4.8 0.2 - - + -
253D MET* 4.0 34.5 - - + -
256D TYR* 3.6 17.9 - - + +
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Residues in contact with LYS 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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203D MET* 3.0 19.8 + - + +
204D SER* 3.6 9.2 - - - +
206D LEU* 1.3 76.5 - - - +
208D GLU* 1.3 57.0 + - - +
210D TYR* 3.2 2.9 + - - +
211D GLU* 2.9 61.0 + - - +
256D TYR* 3.5 45.6 - - + +
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Residues in contact with GLU 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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169D ILE* 3.9 36.7 - - + +
173D LYS* 4.7 6.6 + - - -
204D SER 2.9 18.2 + - - +
205D ASN* 3.2 5.6 + - - +
207D LYS* 1.3 74.3 - - - +
209D VAL* 1.3 64.1 + - - +
211D GLU* 3.3 14.2 + - + +
212D ILE* 3.1 35.0 + - + +
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Residues in contact with VAL 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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167D PHE* 3.5 42.2 - - + -
169D ILE* 3.7 17.3 - - + -
172D LEU* 4.2 18.4 - - + +
187D ILE* 3.8 30.9 - - + +
189D SER* 4.4 5.2 - - - +
205D ASN 2.9 20.3 + - - +
206D LEU* 3.8 5.2 - - - +
208D GLU* 1.3 77.2 - - - +
210D TYR* 1.3 57.9 + - - +
212D ILE* 3.4 2.6 + - - +
213D ALA* 2.9 26.7 + - - +
220D VAL* 5.2 3.8 - - + -
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Residues in contact with TYR 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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206D LEU 3.0 17.1 + - - +
207D LYS 3.6 3.6 - - - +
209D VAL* 1.3 78.9 - - - +
211D GLU* 1.3 61.3 + - + +
213D ALA* 3.1 5.5 + - - +
214D LYS* 3.0 60.3 + - + +
220D VAL* 3.9 12.8 - - + +
255D LYS 3.6 15.5 - - - -
256D TYR* 3.3 33.6 + + + +
257D ALA* 3.6 14.6 - - - -
258D ASP* 2.8 30.7 + - - -
279D ARG* 3.4 17.7 + - - -
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Residues in contact with GLU 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 LYS* 2.9 58.2 + - + +
208D GLU* 3.7 14.6 - - + +
210D TYR* 1.3 76.4 - - + +
212D ILE* 1.3 64.1 + - + +
214D LYS* 3.4 7.1 + - - +
215D GLN* 3.1 29.0 + - - +
256D TYR* 6.1 1.3 - - + -
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Residues in contact with ILE 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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169D ILE* 3.9 28.5 - - + -
172D LEU* 4.0 19.3 - - + -
173D LYS* 4.1 26.0 - - + +
176D ILE* 3.7 27.8 - - + -
208D GLU* 3.1 26.4 + - + +
209D VAL 3.7 3.1 - - - +
211D GLU* 1.3 76.7 - - + +
213D ALA* 1.3 65.0 + - - +
215D GLN* 3.3 15.7 + - - +
216D HIS* 2.9 35.5 + - + +
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Residues in contact with ALA 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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187D ILE* 3.8 16.8 - - + +
209D VAL 2.9 13.6 + - - +
210D TYR 3.1 6.3 + - - +
212D ILE* 1.3 77.9 - - - +
214D LYS* 1.3 55.1 + - - +
216D HIS* 3.2 3.5 + - - -
217D GLY 3.0 8.0 + - - -
218D ILE* 2.7 42.6 + - + +
220D VAL* 3.4 33.9 - - + -
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Residues in contact with LYS 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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210D TYR* 3.0 52.9 + - + +
211D GLU* 3.8 6.3 - - - +
212D ILE 3.3 0.2 - - - -
213D ALA* 1.3 74.7 - - - +
215D GLN* 1.3 64.9 + - - +
217D GLY* 3.1 15.8 + - - +
218D ILE 2.8 28.4 + - - +
219D PHE* 4.1 2.6 - - - +
258D ASP* 2.6 34.4 + - - +
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Residues in contact with GLN 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 GLU* 3.1 19.9 + - - +
212D ILE* 3.4 18.2 - - - +
214D LYS* 1.3 75.5 - - - +
216D HIS* 1.3 81.7 + - + +
217D GLY 3.7 0.2 + - - -
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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