Contacts of the helix formed by residues 237 - 249 (chain B) in PDB entry 4U2M
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 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B CYS* 3.4 26.2 - - + +
177B SER* 4.2 0.7 - - - -
209B LEU* 4.4 15.0 - - + +
212B PHE* 3.7 37.0 - - + -
213B MET* 3.8 31.4 - - + -
232B ALA* 2.8 14.4 + - + +
235B LEU* 3.9 26.5 - - + +
236B GLN* 1.3 73.6 - - - +
238B GLU* 1.3 64.5 + - - +
239B HIS 3.3 2.5 - - - -
240B VAL* 3.1 17.4 + - + +
241B VAL* 3.0 23.1 + - - +
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Residues in contact with GLU 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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233B MET* 5.5 1.7 - - - +
236B GLN* 3.6 5.5 + - - +
237B MET* 1.3 74.9 - - - +
239B HIS* 1.3 69.0 + - + +
241B VAL* 3.1 19.7 + - - +
242B ASP* 2.9 52.7 + - - +
245B ARG* 3.4 10.9 + - - -
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Residues in contact with HIS 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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3B PHE* 4.8 12.8 - - + -
9B HIS* 5.0 18.7 - + - -
237B MET 3.3 0.8 - - - -
238B GLU* 1.3 81.7 - - + +
240B VAL* 1.3 59.6 + - + +
242B ASP* 3.5 14.2 + - - +
243B THR* 2.9 30.2 + - - -
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Residues in contact with VAL 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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3B PHE* 4.5 7.4 - - + -
209B LEU* 3.7 23.6 - - + -
212B PHE* 3.7 36.1 - - + -
218B LEU* 3.9 19.5 - - + -
228B VAL* 4.6 0.2 - - + -
232B ALA* 3.8 11.2 - - + -
237B MET* 3.1 23.8 + - + +
239B HIS* 1.3 76.0 - - + +
241B VAL* 1.3 67.8 + - - +
243B THR* 3.2 6.9 + - - -
244B CYS* 2.9 29.1 + - - -
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Residues in contact with VAL 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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229B MET* 4.0 10.0 - - + +
232B ALA* 3.6 8.3 - - + +
233B MET* 3.5 49.6 - - + +
236B GLN* 6.1 0.2 - - - -
237B MET 3.0 14.4 + - - +
238B GLU* 3.1 26.2 + - - +
240B VAL* 1.3 77.6 - - - +
242B ASP* 1.3 56.5 + - - +
244B CYS* 3.1 9.0 + - - +
245B ARG* 2.9 51.6 + - - +
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Residues in contact with ASP 242 (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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238B GLU* 2.9 33.4 + - - +
239B HIS* 3.7 14.9 + - - +
241B VAL* 1.3 75.3 - - - +
243B THR* 1.3 62.5 + - - +
245B ARG* 2.6 40.6 + - - +
246B LYS* 3.0 24.1 + - - +
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Residues in contact with THR 243 (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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2B ASP* 5.5 3.6 - - - +
3B PHE* 3.4 31.8 - - + -
218B LEU* 4.3 12.8 - - + -
220B LEU* 4.6 7.6 - - + -
239B HIS 2.9 16.9 + - - -
240B VAL* 3.2 8.5 + - - -
242B ASP* 1.3 76.1 - - - +
244B CYS* 1.3 64.1 + - - +
246B LYS* 3.4 7.8 + - + +
247B PHE* 3.0 22.7 + - + +
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Residues in contact with CYS 244 (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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218B LEU* 4.8 0.4 - - - -
220B LEU* 4.1 18.4 - - + -
225B ILE* 4.5 6.8 - - + +
228B VAL* 3.9 21.1 - - - -
229B MET* 3.7 38.6 - - + -
240B VAL* 2.9 24.1 + - - +
241B VAL 3.4 7.6 - - - +
243B THR* 1.3 77.6 - - - +
245B ARG* 1.3 62.5 + - - +
247B PHE* 3.2 9.3 + - - +
248B ILE* 3.2 28.5 + - + +
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Residues in contact with ARG 245 (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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229B MET* 3.7 24.9 - - + +
233B MET* 6.0 0.8 - - - +
238B GLU* 3.4 9.1 + - - -
241B VAL* 2.9 28.5 + - - +
242B ASP* 2.6 38.0 + - - +
244B CYS* 1.3 76.9 - - - +
246B LYS* 1.3 62.7 + - - +
248B ILE* 3.1 25.3 + - + +
249B LYS 3.7 3.1 + - - -
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Residues in contact with LYS 246 (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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242B ASP 3.0 17.1 + - - +
243B THR* 3.8 7.6 - - + +
245B ARG* 1.3 76.5 - - - +
247B PHE* 1.3 56.1 + - - +
249B LYS* 2.9 31.1 - - - +
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Residues in contact with PHE 247 (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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220B LEU* 4.1 42.6 - - + -
221B ARG* 4.7 1.1 - - - -
222B GLU* 4.6 20.4 - - + -
225B ILE* 4.5 24.5 - - + -
243B THR* 3.0 17.9 + - + +
244B CYS 3.2 5.8 + - - +
246B LYS* 1.3 70.2 - - - +
248B ILE* 1.3 68.8 + - + +
249B LYS 3.0 3.5 + - - -
250B ALA* 3.3 13.3 + - - +
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Residues in contact with ILE 248 (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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225B ILE* 5.0 16.4 - - + +
226B MET* 4.6 17.5 - - - -
229B MET* 4.3 22.7 - - + -
244B CYS* 3.2 16.0 + - + +
245B ARG* 3.1 14.8 + - + +
247B PHE* 1.3 79.9 - - + +
249B LYS* 1.3 51.6 + - - +
250B ALA* 2.7 23.1 + - - +
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Residues in contact with LYS 249 (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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245B ARG 3.7 3.8 + - - -
246B LYS* 2.9 19.9 + - - +
247B PHE 4.5 0.4 - - - +
248B ILE* 1.3 73.9 - - - +
250B ALA* 1.3 64.3 + - - +
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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