Contacts of the helix formed by residues 203 - 215 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B TRP* 5.4 0.2 - - - -
202B SER* 1.3 74.0 - - - +
204B SER* 1.3 57.2 + - - +
206B LEU* 3.4 6.3 + - - +
207B LYS* 2.9 30.0 + - + +
234B ILE* 3.8 14.9 - - + +
238B ASP* 4.2 9.9 + - - +
240B LYS* 5.2 2.7 - - + +
241B TYR* 3.6 37.7 - - + +
249B VAL* 3.5 35.0 - - + +
252B ASP* 3.5 15.3 - - + -
253B MET* 3.7 32.8 - - + +
256B TYR* 3.9 20.4 - - + +
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Residues in contact with SER 204 (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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202B SER* 3.3 11.0 + - - -
203B MET* 1.3 76.5 - - - +
205B ASN* 1.3 62.6 + - - +
207B LYS* 3.4 9.0 + - - +
208B GLU* 2.9 30.4 + - - +
238B ASP* 5.2 3.7 + - - -
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Residues in contact with ASN 205 (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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166B ASP* 3.4 23.9 + - - +
167B PHE* 2.7 60.7 + - - +
169B ILE* 3.7 20.0 - - - +
201B VAL* 3.5 4.3 - - + +
202B SER* 3.1 17.1 + - - +
204B SER* 1.3 78.3 + - - +
206B LEU* 1.3 67.1 + - - +
208B GLU* 3.2 4.3 + - - +
209B VAL* 2.9 28.8 + - - +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 5.1 2.0 - - + -
189B SER* 4.0 28.3 - - - +
191B VAL* 4.0 17.5 - - + -
201B VAL* 3.6 28.0 - - + +
202B SER 3.0 19.4 + - - +
203B MET* 3.6 13.0 - - - +
205B ASN* 1.3 75.3 - - - +
207B LYS* 1.3 57.3 + - - +
209B VAL* 3.5 6.0 + - - +
210B TYR* 3.0 29.3 + - - +
222B MET* 4.1 9.6 - - + -
230B ASN* 4.6 0.9 - - - +
253B MET* 4.0 32.5 - - + -
256B TYR* 3.7 18.9 - - + +
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Residues in contact with LYS 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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203B MET* 2.9 20.2 + - + +
204B SER* 3.6 9.2 - - - +
206B LEU* 1.3 74.7 - - - +
208B GLU* 1.3 65.3 + - - +
210B TYR* 3.2 2.3 + - - +
211B GLU* 2.9 55.8 + - - +
256B TYR* 3.3 46.4 - - + +
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Residues in contact with GLU 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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169B ILE* 3.8 37.8 - - + +
173B LYS* 4.7 7.1 + - - -
204B SER 2.9 19.5 + - - +
205B ASN* 3.2 4.8 + - - +
207B LYS* 1.3 77.3 - - - +
209B VAL* 1.3 62.6 + - - +
211B GLU* 3.7 12.2 - - + +
212B ILE* 3.1 34.1 + - + +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PHE* 3.5 42.8 - - + -
169B ILE* 3.7 17.7 - - + -
172B LEU* 4.2 18.5 - - + +
187B ILE* 3.8 30.5 - - + +
189B SER* 4.4 5.6 - - - +
205B ASN* 2.9 20.0 + - - +
206B LEU* 3.8 4.7 - - - +
208B GLU* 1.3 76.2 - - - +
210B TYR* 1.3 58.8 + - - +
212B ILE* 3.5 2.3 + - - +
213B ALA* 2.9 26.0 + - - +
220B VAL* 5.3 3.6 - - + -
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Residues in contact with TYR 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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206B LEU 3.0 18.2 + - - +
207B LYS 3.2 4.0 + - - +
209B VAL* 1.3 80.0 - - - +
211B GLU* 1.3 60.8 + - + +
213B ALA* 3.2 4.1 + - - +
214B LYS* 2.9 64.2 + - + +
220B VAL* 3.9 12.3 - - + -
255B LYS 3.7 14.8 - - - -
256B TYR* 3.4 36.1 - + + +
257B ALA 3.7 12.3 - - - -
258B ASP* 3.0 28.9 + - - -
279B ARG* 3.4 18.6 + - - -
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Residues in contact with GLU 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 LYS* 2.9 57.3 + - + +
208B GLU* 3.7 12.8 - - + +
210B TYR* 1.3 76.1 - - + +
212B ILE* 1.3 67.0 + - + +
214B LYS* 3.3 5.7 + - - +
215B GLN* 3.1 31.6 + - - +
256B TYR* 5.7 1.1 - - + -
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Residues in contact with ILE 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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169B ILE* 3.9 28.5 - - + -
172B LEU* 4.1 20.2 - - + -
173B LYS* 4.1 25.6 - - + +
176B ILE* 3.7 26.7 - - + -
208B GLU* 3.1 26.4 + - + +
209B VAL 3.7 3.6 - - - +
211B GLU* 1.3 77.1 - - + +
213B ALA* 1.3 64.7 + - - +
215B GLN* 3.0 24.0 + - - +
216B HIS* 3.3 22.8 + - + +
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Residues in contact with ALA 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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187B ILE* 3.8 17.3 - - + -
209B VAL 2.9 12.9 + - - +
210B TYR 3.2 5.6 + - - +
212B ILE* 1.3 77.9 - - - +
214B LYS* 1.3 57.4 + - - +
216B HIS 3.3 2.8 + - - -
217B GLY 2.9 7.8 + - - -
218B ILE* 2.7 43.6 + - + +
220B VAL* 3.4 33.0 - - + -
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Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B TYR* 2.9 63.5 + - + +
211B GLU* 4.0 5.8 - - - +
213B ALA* 1.3 74.6 - - - +
215B GLN* 1.3 64.3 + - - +
217B GLY* 3.5 12.3 + - - +
218B ILE 2.8 27.6 + - - +
219B PHE* 4.1 1.4 - - - +
258B ASP* 2.6 31.8 + - - +
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Residues in contact with GLN 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 GLU* 3.1 18.7 + - - +
212B ILE* 3.0 20.8 + - - +
214B LYS* 1.3 81.5 - - - +
216B HIS* 1.3 73.1 + - + +
217B GLY 3.4 0.4 + - - -
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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