Contacts of the helix formed by residues 229 - 241 (chain B) in PDB entry 2AX1
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 THR 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ARG* 3.9 26.9 - - + +
58B GLN* 2.6 36.2 + - + +
227B THR 3.5 13.0 - - - +
228B VAL* 1.3 75.4 - - - +
230B GLU* 1.3 72.5 + - - +
231B ASN* 3.4 3.0 + - - -
232B ASP* 2.9 20.6 + - - +
233B ILE* 3.1 25.6 + - - +
278B ARG 4.7 1.3 - - - -
347B SER* 3.8 11.7 - - - +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER* 2.6 36.3 + - - -
56B ARG* 3.9 9.0 + - - -
229B THR* 1.3 77.0 - - - +
231B ASN* 1.3 63.7 + - - +
233B ILE* 3.2 5.3 + - - +
234B ARG* 3.0 36.0 + - - +
262B ILE* 3.8 35.5 - - + +
278B ARG* 3.8 17.7 + - + +
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Residues in contact with ASN 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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58B GLN* 3.4 18.6 + - - +
60B LEU* 3.8 22.7 - - - +
64B TYR* 3.4 18.2 + - - -
229B THR* 3.2 2.1 + - - +
230B GLU* 1.3 80.2 + - - +
232B ASP* 1.3 66.5 + - - +
234B ARG* 2.9 10.4 + - - +
235B VAL* 2.7 43.3 + - - +
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 2.8 21.4 + - - -
64B TYR* 4.1 4.8 + - - -
227B THR 3.6 0.7 - - - +
228B VAL* 3.4 16.7 - - + -
229B THR* 2.9 31.7 + - - +
231B ASN* 1.3 83.1 + - - +
233B ILE* 1.3 58.8 + - - +
235B VAL* 3.3 6.4 + - - +
236B GLU* 3.0 33.7 + - - +
294B THR* 4.3 11.2 + - + +
298B LYS* 2.8 33.7 + - - -
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Residues in contact with ILE 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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228B VAL* 3.7 20.2 - - + -
229B THR 3.1 16.5 + - - +
230B GLU 3.7 6.5 - - - +
231B ASN 3.2 0.2 - - - -
232B ASP* 1.3 75.7 - - - +
234B ARG* 1.3 59.2 + - - +
236B GLU* 3.4 12.0 + - - +
237B GLU* 3.1 23.9 + - - +
257B THR* 3.9 16.2 + - + +
261B TYR* 3.0 36.8 - - + +
262B ILE* 3.6 36.6 - - + +
278B ARG 5.2 0.2 - - - +
279B CYS* 4.2 14.8 - - - -
280B ARG* 4.2 12.1 - - - +
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Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU* 3.0 23.2 + - - +
231B ASN* 2.9 12.2 + - - +
233B ILE* 1.3 73.9 - - - +
235B VAL* 1.3 61.1 + - + +
237B GLU* 3.2 12.3 + - - +
238B SER* 2.9 27.7 + - - -
257B THR* 4.8 3.1 - - + -
258B GLU* 3.2 37.6 + - - +
262B ILE* 3.5 21.0 - - + +
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Residues in contact with VAL 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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64B TYR* 3.5 19.3 - - + +
68B LEU* 3.5 39.5 - - + -
231B ASN* 2.7 31.6 + - - +
232B ASP* 3.6 7.2 - - - +
234B ARG* 1.3 74.5 - - + +
236B GLU* 1.3 65.7 + - + +
238B SER* 2.7 23.2 + - - +
239B ILE* 3.1 13.4 + - + +
297B LEU* 3.8 18.8 - - + -
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Residues in contact with GLU 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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228B VAL* 4.3 2.3 - - - +
232B ASP 3.0 20.7 + - - +
233B ILE* 3.6 12.3 - - - +
234B ARG 3.3 0.2 - - - -
235B VAL* 1.3 78.1 - - + +
237B GLU* 1.3 63.0 + - - +
239B ILE* 3.1 14.1 + - + +
240B TYR* 3.0 43.7 + - + -
261B TYR* 6.1 0.3 - - - +
280B ARG* 2.5 43.0 + - - -
286B THR* 5.4 0.9 - - - -
290B GLY* 3.2 17.9 - - - +
293B LEU* 5.1 7.9 - - + -
294B THR* 2.6 27.4 + - - +
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Residues in contact with GLU 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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233B ILE 3.1 9.3 + - - +
234B ARG* 3.5 13.0 - - - +
235B VAL 3.2 0.4 - - - -
236B GLU* 1.3 79.1 - - - +
238B SER* 1.3 57.7 + - - +
240B TYR* 3.1 12.0 + - - +
241B GLN* 2.8 51.9 + - + +
253B ILE* 4.1 9.4 - - + -
254B LYS* 3.1 31.8 - - - +
257B THR* 3.3 37.6 - - + +
258B GLU* 4.6 6.1 - - - +
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Residues in contact with SER 238 (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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68B LEU* 5.1 0.3 - - - +
72B LYS* 3.2 30.6 + - - -
234B ARG 2.9 13.9 + - - -
235B VAL* 2.7 26.3 + - - +
237B GLU* 1.3 76.9 - - - +
239B ILE* 1.3 60.2 + - - +
241B GLN* 3.4 10.0 + - - +
242B CYS* 3.2 26.6 + - - -
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Residues in contact with ILE 239 (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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68B LEU* 3.9 26.7 - - + -
71B MET* 4.1 28.9 - - + +
72B LYS* 4.2 7.6 - - + -
75B ALA* 3.6 23.5 - - + +
182B LEU* 4.0 15.9 - - + +
186B VAL* 4.6 8.1 - - + -
235B VAL* 3.1 20.1 + - + +
236B GLU* 3.1 13.0 + - + +
238B SER* 1.3 74.9 - - - +
240B TYR* 1.3 66.5 + - + +
242B CYS* 3.1 22.9 + - - +
243B CYS 4.0 0.9 + - - -
293B LEU* 4.6 16.2 - - + -
297B LEU* 5.4 1.6 - - + -
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Residues in contact with TYR 240 (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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175B LEU* 3.9 15.9 - - + -
178B VAL* 3.9 14.3 - - + +
179B VAL* 5.2 0.9 - - + -
182B LEU* 3.7 19.5 - - + -
236B GLU* 3.0 33.6 + - + -
237B GLU* 3.5 13.9 - - - +
239B ILE* 1.3 76.5 - - - +
241B GLN* 1.3 62.9 + - - +
243B CYS* 3.1 25.2 + - - +
245B LEU* 3.5 8.6 - - - +
253B ILE* 4.2 20.9 - - + -
257B THR* 5.3 2.0 - - - -
261B TYR* 5.4 5.8 - + - -
286B THR* 3.6 37.0 - - + +
289B CYS* 4.0 11.9 - - - -
290B GLY* 3.8 21.8 + - - -
293B LEU* 3.9 20.9 - - + -
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Residues in contact with GLN 241 (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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237B GLU* 2.8 47.3 + - + +
238B SER* 3.7 9.9 - - - +
239B ILE 3.2 0.2 - - - -
240B TYR* 1.3 72.9 - - - +
242B CYS* 1.3 62.6 + - - +
243B CYS 3.1 2.0 + - - +
245B LEU* 3.9 4.4 - - - +
250B ARG* 2.9 77.5 + - - +
253B ILE* 3.9 9.9 - - - +
254B LYS* 3.8 8.3 - - - +
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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