Contacts of the helix formed by residues 260 - 272 (chain B) in PDB entry 1AOX
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 GLY 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B PHE* 3.7 10.1 - - - -
257B SER* 3.1 22.3 + - - -
258B HIS 3.6 2.6 - - - -
259B ASP* 1.3 71.9 - - - +
261B SER* 1.3 61.7 + - - +
262B MET 2.9 5.8 - - - -
263B LEU* 2.9 22.3 + - - +
299B GLU* 4.2 4.7 - - - -
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Residues in contact with SER 261 (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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259B ASP* 3.0 4.6 + - - -
260B GLY* 1.3 75.8 - - - +
262B MET* 1.3 67.0 + - - +
263B LEU* 3.3 1.6 + - - +
264B LYS* 4.5 4.7 + - - +
265B ALA 5.4 0.2 + - - -
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Residues in contact with MET 262 (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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224B PHE* 3.9 23.8 - - + +
225B GLY* 4.4 5.8 - - - +
228B GLN* 4.5 12.1 - - + +
259B ASP* 3.1 28.5 + - - +
260B GLY 2.9 0.4 - - - -
261B SER* 1.3 86.5 + - - +
263B LEU* 1.3 65.0 + - - +
264B LYS 3.4 0.9 - - - -
265B ALA* 3.2 12.1 + - + +
266B VAL* 3.0 43.0 + - + +
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Residues in contact with LEU 263 (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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224B PHE* 3.6 36.1 - - + -
260B GLY 2.9 17.6 + - - +
261B SER 3.2 1.6 - - - +
262B MET* 1.3 75.8 - - - +
264B LYS* 1.3 67.1 + - + +
266B VAL* 4.0 0.3 - - - -
267B ILE* 3.1 33.1 + - + +
299B GLU* 4.4 15.5 - - + +
302B ALA* 3.9 34.8 - - + +
303B ILE* 4.9 1.3 - - + -
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Residues in contact with LYS 264 (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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261B SER 4.5 4.1 + - - +
262B MET 3.4 0.8 - - - -
263B LEU* 1.3 81.8 - - + +
265B ALA* 1.3 66.1 + - - +
267B ILE* 4.4 2.8 - - - +
268B ASP* 3.0 35.6 + - - +
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Residues in contact with ALA 265 (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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228B GLN* 5.6 0.9 - - - +
261B SER 5.4 0.4 + - - -
262B MET* 3.2 13.9 + - + +
264B LYS* 1.3 80.6 - - - +
266B VAL* 1.3 63.0 + - + +
268B ASP* 3.5 5.3 - - - +
269B GLN* 3.2 36.4 + - - +
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Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PHE* 4.0 21.8 - - + +
227B ILE* 3.3 36.3 - - + -
228B GLN* 3.6 31.2 - - + +
231B ARG* 4.6 1.0 - - - -
262B MET* 3.0 42.2 + - + +
265B ALA* 1.3 75.6 - - + +
267B ILE* 1.3 66.5 + - + +
269B GLN* 3.4 4.0 + - - +
270B CYS* 3.1 23.5 + - - -
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Residues in contact with ILE 267 (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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224B PHE* 4.1 21.5 - - + -
227B ILE* 5.1 2.9 - - + -
263B LEU* 3.1 26.4 + - + +
264B LYS* 4.4 3.4 - - - +
266B VAL* 1.3 83.0 - - + +
268B ASP* 1.3 62.5 + - - +
270B CYS* 3.4 6.1 + - - +
271B ASN* 3.0 45.0 + - - +
277B ARG* 4.1 24.0 + - - +
302B ALA 3.9 20.2 - - - +
303B ILE* 4.2 20.2 - - + +
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Residues in contact with ASP 268 (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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264B LYS* 3.0 28.3 + - - +
265B ALA* 3.5 8.0 - - - +
266B VAL 3.2 0.4 - - - -
267B ILE* 1.3 84.2 - - - +
269B GLN* 1.3 58.5 + - + +
271B ASN* 3.5 7.6 + - - +
272B HIS* 3.1 47.2 + - + -
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Residues in contact with GLN 269 (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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228B GLN* 2.5 32.3 + - - +
231B ARG* 3.7 35.5 - - - +
265B ALA* 3.2 20.1 + - - +
266B VAL 3.9 3.6 - - - +
267B ILE 3.3 0.2 - - - -
268B ASP* 1.3 76.6 - - + +
270B CYS* 1.3 55.0 + - - +
272B HIS* 3.1 10.0 + - - +
273B ASP* 2.8 39.3 + - - +
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Residues in contact with CYS 270 (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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227B ILE* 3.9 25.8 - - - -
231B ARG* 4.1 14.4 - - - +
249B MET* 4.7 3.6 - - - -
266B VAL* 3.1 22.0 + - - +
267B ILE* 3.4 5.4 + - - +
269B GLN* 1.3 76.9 - - - +
271B ASN* 1.3 58.1 + - - +
273B ASP* 3.3 1.8 + - - -
274B ASN 3.0 7.6 + - - -
275B ILE* 2.9 48.1 + - + +
277B ARG* 3.6 31.9 - - - +
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Residues in contact with ASN 271 (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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267B ILE* 3.0 35.1 + - - +
268B ASP* 3.6 10.9 + - - +
270B CYS* 1.3 73.7 - - - +
272B HIS* 1.3 71.7 + - + +
274B ASN* 3.0 20.0 + - - +
275B ILE 4.9 0.8 - - - +
277B ARG* 2.9 27.9 + - - +
305B SER* 5.3 0.2 + - - -
306B ILE* 6.2 1.6 - - - +
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Residues in contact with HIS 272 (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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268B ASP* 3.1 34.7 + - + +
269B GLN* 3.1 10.5 + - - +
271B ASN* 1.3 80.3 - - + +
273B ASP* 1.3 62.8 + - - +
274B ASN* 3.2 18.4 + - - -
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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