Contacts of the helix formed by residues 232 - 242 (chain M) in PDB entry 2O5J
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 GLU 232 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199M VAL 5.5 4.2 + - - -
231M PRO* 1.3 77.3 - - + +
233M GLU* 1.3 56.5 + - - +
234M ALA 3.3 0.2 - - - -
235M LEU* 3.0 42.2 - - + +
236M ILE* 3.8 13.0 - - + +
252M LYS* 5.8 3.8 - - - -
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Residues in contact with GLU 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M PHE* 4.6 6.6 - - - +
230M ARG* 3.6 50.0 + - + +
231M PRO 2.7 5.5 + - - -
232M GLU* 1.3 71.3 - - - +
234M ALA* 1.3 58.9 + - - +
235M LEU 3.0 5.2 - - - -
236M ILE* 3.1 19.6 + - + +
237M ARG* 2.9 42.8 + - - +
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Residues in contact with ALA 234 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M LEU* 4.0 20.9 - - + +
198M ARG* 4.8 5.2 - - + -
199M VAL* 3.2 18.9 - - + +
227M PHE* 4.6 4.9 - - + +
230M ARG 3.5 10.3 + - - +
231M PRO 2.6 19.8 + - - +
233M GLU* 1.3 75.5 + - - +
235M LEU* 1.3 55.6 + - - +
236M ILE 3.4 0.2 - - - -
237M ARG* 3.7 11.3 - - - +
238M LEU* 3.1 35.0 + - - +
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Residues in contact with LEU 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199M VAL* 3.4 33.1 - - + +
232M GLU* 3.0 34.9 - - + +
234M ALA* 1.3 79.2 - - - +
236M ILE* 1.3 55.4 + - + +
238M LEU* 3.8 4.4 + - - +
239M PHE* 2.9 59.8 + - + -
251M ASP 4.5 16.2 - - - +
252M LYS* 5.6 2.5 - - + -
255M ALA* 4.5 14.8 - - + -
296M GLY 5.3 8.5 - - - +
298M PHE* 5.7 5.2 - - + -
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Residues in contact with ILE 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M GLU* 3.8 21.1 - - + +
233M GLU* 3.1 17.4 + - + +
235M LEU* 1.3 78.1 - - + +
237M ARG* 1.3 53.5 + - - +
238M LEU 3.3 0.7 - - - -
239M PHE* 3.3 13.8 - - + +
240M THR* 2.8 37.4 + - - +
248M PRO* 3.5 40.2 - - + +
249M LYS* 6.1 0.2 - - - -
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Residues in contact with ARG 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M LEU* 4.7 14.1 - - + -
227M PHE* 3.1 46.9 - - + -
233M GLU* 2.9 32.4 + - - +
234M ALA* 3.8 12.1 - - - +
235M LEU 3.4 0.2 - - - -
236M ILE* 1.3 74.9 - - - +
238M LEU* 1.3 63.3 + - - +
240M THR* 3.3 13.3 - - - -
241M LEU* 3.1 21.2 + - + +
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Residues in contact with LEU 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191M PHE* 3.8 23.8 - - + -
195M LEU* 3.3 40.2 - - + +
196M LEU* 3.8 22.4 - - + -
199M VAL* 3.6 28.5 - - + -
234M ALA 3.1 19.3 + - - +
235M LEU* 3.9 5.4 - - - +
236M ILE 3.3 0.2 - - - -
237M ARG* 1.3 73.2 - - - +
239M PHE* 1.3 59.5 + - - +
240M THR 3.0 0.2 - - - -
241M LEU* 2.8 30.5 + - + +
242M LEU* 3.2 14.1 + - + +
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Residues in contact with PHE 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M LEU* 2.9 47.2 + - + -
236M ILE* 3.3 15.9 + - + +
238M LEU* 1.3 77.7 - - + +
240M THR* 1.3 61.1 + - - +
242M LEU* 3.4 34.9 + - + +
244M PRO* 5.4 2.3 - - - +
246M ASP* 5.7 4.7 - - - +
247M PRO 5.5 5.2 - - - +
248M PRO* 4.5 14.6 - - + +
250M ARG* 3.7 32.1 - - + -
251M ASP 4.8 0.7 - - - -
253M ALA 5.1 0.9 - - - -
254M VAL* 3.3 44.4 - - + -
255M ALA* 4.3 7.4 - - + -
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Residues in contact with THR 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236M ILE* 2.8 24.5 + - - +
237M ARG* 3.3 15.8 - - - -
238M LEU 3.0 0.2 - - - -
239M PHE* 1.3 75.6 - - - +
241M LEU* 1.3 55.3 + - - +
242M LEU 2.8 18.2 - - - +
248M PRO* 5.6 4.9 - - - +
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Residues in contact with LEU 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M ARG* 5.6 4.7 - - + +
190M LYS 5.0 3.8 - - - +
191M PHE* 3.6 42.4 - - + -
192M PRO* 4.5 0.9 - - + -
195M LEU* 3.7 26.2 - - + -
237M ARG* 3.1 11.7 + - + +
238M LEU* 2.8 17.1 + - + +
240M THR* 1.3 72.2 - - - +
242M LEU* 1.3 65.7 + - + +
243M ARG* 3.7 12.0 - - - +
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Residues in contact with LEU 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186M VAL* 5.7 9.2 - - + -
238M LEU* 3.2 13.2 + - + +
239M PHE* 3.5 35.6 - - + +
240M THR 2.8 18.6 - - - +
241M LEU* 1.3 77.7 - - + +
243M ARG* 1.3 63.3 + - - +
244M PRO* 3.7 10.6 - - + +
246M ASP* 5.7 4.3 - - - +
254M VAL* 4.5 19.3 - - + -
258M TYR* 6.0 3.1 - - + -
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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