Contacts of the helix formed by residues 203 - 216 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A SER* 1.3 73.3 - - - +
204A SER* 1.3 58.0 - - - +
206A LEU* 3.3 7.0 + - - +
207A LYS* 2.9 29.8 + - + +
234A ILE* 3.8 15.8 - - + +
238A ASP* 4.2 10.0 + - - +
240A LYS* 5.2 2.7 - - + +
241A TYR* 3.6 38.4 - - + +
249A VAL* 3.4 35.2 - - + +
252A ASP* 3.5 13.5 - - + -
253A MET* 3.7 34.1 - - + +
256A TYR* 3.8 21.3 - - + +
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A SER* 3.3 11.5 + - - -
203A MET* 1.3 78.8 - - - +
205A ASN* 1.3 59.0 + - - +
207A LYS* 3.4 10.2 + - - +
208A GLU* 3.0 30.4 + - - +
238A ASP* 5.1 4.1 + - - -
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Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 3.3 23.1 + - - +
167A PHE* 2.7 61.1 + - - +
169A ILE* 3.7 18.8 - - - +
201A VAL* 3.6 4.1 - - + +
202A SER* 3.1 22.9 + - - +
204A SER* 1.3 74.0 + - - +
206A LEU* 1.3 63.9 + - - +
208A GLU* 3.2 5.4 + - - +
209A VAL* 2.9 27.0 + - - +
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PHE* 5.1 1.6 - - + -
189A SER* 4.0 28.5 - - - +
191A VAL* 4.1 20.0 - - + -
201A VAL* 3.7 25.1 - - + +
202A SER 3.1 18.5 + - - +
203A MET* 3.3 12.1 + - - +
205A ASN* 1.3 73.6 - - - +
207A LYS* 1.3 63.3 + - - +
209A VAL* 3.8 6.0 - - - +
210A TYR* 3.0 24.9 + - - +
222A MET* 4.2 10.1 - - + -
230A ASN* 4.7 0.7 - - - +
234A ILE* 4.8 0.2 - - + -
253A MET* 4.0 34.5 - - + -
256A TYR* 3.6 17.7 - - + +
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET* 2.9 19.7 + - + +
204A SER* 3.6 10.5 - - - +
206A LEU* 1.3 77.4 - - - +
208A GLU* 1.3 57.9 + - - +
210A TYR* 3.3 3.1 + - - +
211A GLU* 2.9 61.6 + - - +
256A TYR* 3.4 45.0 - - + +
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 3.9 38.0 - - + +
173A LYS* 4.7 6.4 + - - -
204A SER 3.0 17.7 + - - +
205A ASN* 3.2 5.1 + - - +
207A LYS* 1.3 74.8 - - - +
209A VAL* 1.3 62.4 + - - +
211A GLU* 3.3 14.3 + - - +
212A ILE* 3.1 35.3 + - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PHE* 3.5 42.4 - - + -
169A ILE* 3.8 16.8 - - + -
172A LEU* 4.2 18.8 - - + +
187A ILE* 3.8 30.3 - - + -
189A SER* 4.4 5.6 - - - +
205A ASN* 2.9 21.4 + - - +
206A LEU* 3.8 4.7 - - - +
208A GLU* 1.3 76.0 - - - +
210A TYR* 1.3 62.1 + - - +
212A ILE* 3.5 2.6 + - - +
213A ALA* 3.0 21.5 + - - +
220A VAL* 5.3 3.6 - - + -
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Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU 3.0 19.1 + - - +
207A LYS 3.6 3.6 - - - +
209A VAL* 1.3 78.6 - - - +
211A GLU* 1.3 61.5 + - + +
213A ALA* 3.3 4.7 + - - +
214A LYS* 2.9 70.3 + - + +
220A VAL* 3.9 13.7 - - + -
255A LYS 3.6 15.7 - - - -
256A TYR* 3.4 34.8 - + + +
257A ALA* 3.7 11.9 - - - -
258A ASP* 2.9 27.2 + - - -
279A ARG* 3.4 18.6 + - - -
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LYS* 2.9 56.6 + - + +
208A GLU* 3.6 13.8 - - - +
210A TYR* 1.3 77.8 - - + +
212A ILE* 1.3 67.5 + - + +
214A LYS* 3.4 5.7 + - - +
215A GLN* 3.1 28.3 + - - +
256A TYR* 6.1 1.1 - - + -
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 3.9 28.7 - - + -
172A LEU* 4.0 18.6 - - + -
173A LYS* 4.1 26.0 - - + +
176A ILE* 3.7 27.8 - - + -
208A GLU* 3.1 29.9 + - + +
209A VAL 3.7 3.1 - - - +
211A GLU* 1.3 76.4 - - + +
213A ALA* 1.3 62.4 + - - +
215A GLN* 3.3 14.9 + - - +
216A HIS* 3.3 22.8 + - + +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE* 3.8 16.4 - - + +
209A VAL 3.0 13.5 + - - +
210A TYR 3.5 5.6 - - - +
212A ILE* 1.3 77.7 - - - +
214A LYS* 1.3 56.9 + - - +
216A HIS 3.1 2.3 + - - -
217A GLY 2.9 8.5 + - - -
218A ILE* 2.7 44.1 + - + +
220A VAL* 3.4 33.9 - - + -
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Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 2.9 69.8 + - + +
211A GLU* 3.9 5.4 - - - +
212A ILE 3.3 0.2 - - - -
213A ALA* 1.3 74.3 - - - +
215A GLN* 1.3 62.0 + - - +
217A GLY* 3.2 14.3 + - - +
218A ILE 2.8 29.9 + - - +
219A PHE* 4.0 2.2 - - - +
220A VAL* 4.4 0.2 - - - -
258A ASP* 2.6 27.6 + - - +
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Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU 3.1 17.1 + - - +
212A ILE* 3.5 11.7 - - - +
214A LYS* 1.3 76.3 - - - +
216A HIS* 1.3 67.6 + - + +
217A GLY 3.7 0.2 + - - -
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LYS* 5.3 1.6 + - - -
173A LYS* 6.4 2.0 - - + -
176A ILE* 3.5 40.7 - - + +
181A ALA* 3.8 25.1 - - + +
212A ILE* 3.3 21.9 + - + +
213A ALA 3.1 4.6 + - - +
215A GLN* 1.3 84.3 - - + +
217A GLY* 1.3 60.3 + - - +
218A ILE* 3.7 21.8 - - + +
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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