Contacts of the helix formed by residues 227 - 237 (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 PHE 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B LEU* 4.7 6.1 - - + -
89B PHE* 3.5 34.3 - + - -
191B VAL* 3.5 14.3 + - + -
224B SER* 3.2 22.0 + - - +
226B ARG* 1.3 77.1 - - - +
228B CYS* 1.3 84.8 + - - +
230B ASN* 3.7 3.5 - - - +
231B ALA* 3.0 26.0 + - - +
250B ILE* 3.9 20.9 - - + -
253B MET* 4.0 4.1 - - + +
254B TYR* 3.1 30.5 - + + +
262B MET* 3.6 20.2 - - + -
267B ASP* 4.4 4.9 - - + -
268B PRO* 4.4 12.6 - - + -
316B LEU* 4.1 13.0 - - + -
320B THR* 5.1 1.6 - - + -
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Residues in contact with CYS 228 (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 PHE* 1.3 105.1 - - - +
229B GLU* 1.3 62.9 + - - +
231B ALA* 3.3 7.3 + - - +
232B TYR* 2.9 24.1 + - - +
250B ILE* 4.3 3.6 - - + -
267B ASP* 2.7 25.0 + - - +
316B LEU 5.1 0.7 - - - -
319B GLY* 3.3 37.7 - - - +
320B THR* 3.9 12.3 - - - -
325B LEU* 3.9 14.1 - - + +
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Residues in contact with GLU 229 (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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192B THR* 3.9 11.0 + - + -
226B ARG* 3.3 18.4 + - - +
228B CYS* 1.3 74.1 - - - +
230B ASN* 1.3 62.6 + - - +
232B TYR* 3.2 11.8 + - - +
233B PHE* 3.2 18.9 + - - -
267B ASP* 2.8 30.6 + - - +
324B TYR* 5.1 0.3 + - - -
325B LEU* 4.4 7.9 - - + -
328B ARG* 2.7 33.6 + - - +
329B ILE* 4.0 21.7 - - + +
352B GLY* 3.3 29.9 - - - -
353B HIS* 3.4 8.8 + - - +
419B ARG* 3.3 4.2 + - - -
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Residues in contact with ASN 230 (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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191B VAL* 3.8 24.3 - - + +
192B THR* 3.4 17.5 - - + +
200B PRO* 3.2 8.4 - - - +
201B VAL 2.9 45.7 + - - -
206B LEU* 4.6 1.0 - - - +
226B ARG 3.1 13.7 + - - +
227B PHE 3.7 8.1 - - - +
229B GLU* 1.3 74.4 - - - +
231B ALA* 1.3 63.3 + - - +
233B PHE* 3.1 8.7 + - - +
234B ILE* 3.0 32.3 + - - +
253B MET* 3.9 11.0 - - + +
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Residues in contact with ALA 231 (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 PHE 3.0 18.2 + - - +
228B CYS 3.3 4.9 + - - +
230B ASN* 1.3 74.4 - - - +
232B TYR* 1.3 62.1 + - - +
234B ILE* 3.2 4.1 + - - +
235B LYS* 3.0 22.5 + - - +
246B ILE* 4.2 11.0 - - + -
249B VAL* 3.5 30.7 - - + +
250B ILE* 3.8 22.7 - - + -
253B MET* 4.0 5.1 - - - -
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Residues in contact with TYR 232 (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 CYS 2.9 15.4 + - - +
229B GLU 3.2 8.2 + - - +
231B ALA* 1.3 74.0 - - - +
233B PHE* 1.3 67.4 + + - +
235B LYS* 3.2 6.0 + - + +
236B ALA* 2.9 41.9 + - + +
246B ILE* 3.9 18.8 - - + +
322B GLU* 4.6 14.6 - - + -
325B LEU* 3.8 20.4 - - + -
326B HIS* 2.7 52.4 + - + -
329B ILE* 3.4 38.8 - - + -
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Residues in contact with PHE 233 (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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163B TRP* 4.2 2.5 - - + -
192B THR* 4.4 4.0 - - + -
198B GLY 4.3 6.1 - - - -
200B PRO* 3.5 33.7 - - + -
229B GLU 3.2 20.3 + - - -
230B ASN 3.1 7.9 + - - +
232B TYR* 1.3 84.7 - + - +
234B ILE* 1.3 60.1 + - - +
236B ALA* 4.3 3.6 - - + -
237B ARG* 2.8 69.5 + - - +
329B ILE* 3.7 30.5 - - + -
350B THR 3.9 7.4 - - - -
351B GLY* 3.8 14.8 - - - -
352B GLY* 3.6 24.5 - - - -
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Residues in contact with ILE 234 (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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163B TRP* 3.8 15.0 - - + -
201B VAL 3.8 16.2 - - - +
202B SER 4.3 0.2 - - - -
203B MET* 3.8 24.5 - - + +
206B LEU* 4.7 0.4 - - + -
230B ASN* 3.0 32.0 + - - +
231B ALA 3.7 6.7 - - - +
232B TYR 3.2 0.4 - - - -
233B PHE* 1.3 75.9 - - - +
235B LYS* 1.3 58.1 + - - +
238B ASP* 2.8 40.3 + - + +
241B TYR* 3.7 30.9 - - + +
249B VAL* 3.9 12.1 - - + -
253B MET* 4.0 25.1 - - + -
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Residues in contact with LYS 235 (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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231B ALA 3.0 12.9 + - - +
232B TYR* 3.2 10.1 + - + +
234B ILE* 1.3 78.7 - - - +
236B ALA* 1.3 59.5 + - - +
238B ASP 4.2 2.9 - - - +
241B TYR* 3.7 19.1 - - - +
242B LYS* 3.6 36.2 + - - +
243B ASN* 4.3 2.4 - - - +
244B ALA 2.5 37.0 + - - +
245B THR* 4.3 1.6 - - - +
246B ILE* 4.1 14.8 - - + +
249B VAL* 4.2 8.7 - - + +
322B GLU* 3.2 41.3 + - - +
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Residues in contact with ALA 236 (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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232B TYR* 2.9 36.6 + - + +
233B PHE* 3.7 9.0 - - + +
235B LYS* 1.3 79.8 - - - +
237B ARG* 1.3 65.9 + - + +
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Residues in contact with ARG 237 (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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160B TYR* 3.7 13.0 + - - +
162B ASP* 2.9 57.6 + - - +
163B TRP* 3.7 19.0 - - + -
199B GLN* 4.7 0.8 + - - -
200B PRO* 3.4 20.6 - - - +
233B PHE* 2.8 47.5 + - - +
236B ALA* 1.3 84.8 - - + +
238B ASP* 1.3 61.2 + - - +
239B PRO* 3.3 11.2 - - - +
349B PRO* 3.6 31.8 - - - +
350B THR 4.4 2.2 + - - -
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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