Contacts of the helix formed by residues 237 - 245 (chain B) in PDB entry 4OBQ
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 HIS 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ARG* 4.3 22.4 + - - -
174A VAL* 5.5 11.9 - - + -
186A ASN 5.1 2.4 + - - -
189A ILE* 6.1 0.2 - - - +
210A TYR* 5.4 7.4 - + - -
236B MET* 1.3 72.6 - - - +
238B PRO* 1.4 83.2 - - + +
239B MET* 3.1 41.4 + - + +
240B ARG* 2.8 24.9 + - + +
241B ALA* 3.0 10.6 + - - +
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Residues in contact with PRO 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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186A ASN 3.2 26.9 - - - +
187A THR 3.4 24.9 - - - +
188A PHE 4.3 5.2 - - - +
189A ILE* 3.4 24.0 - - + +
192B PRO* 3.3 17.4 - - + +
193B TYR* 3.4 17.4 - - + +
236B MET 3.9 0.4 - - - +
237B HIS* 1.4 97.8 - - + +
239B MET* 1.3 54.6 + - - +
241B ALA* 3.5 0.8 + - + -
242B LEU* 3.0 26.9 + - - +
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Residues in contact with MET 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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189A ILE* 4.0 24.6 - - + +
195A MET* 3.5 31.9 - - + -
199A VAL* 3.8 27.8 - - + +
200A ILE* 3.9 11.4 - - + -
201A ALA* 4.8 7.5 - - + +
208A ALA* 5.4 3.4 - - + -
210A TYR* 6.4 1.3 - - + -
242A LEU* 3.5 20.4 - - + -
237B HIS* 3.0 26.9 + - + +
238B PRO* 1.3 75.1 - - - +
240B ARG* 1.4 61.8 + - - +
242B LEU* 3.4 18.5 - - - +
243B PHE* 3.3 19.4 + - - +
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Residues in contact with ARG 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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201A ALA* 5.6 2.7 - - - -
206A PRO* 3.0 29.1 + - - +
207A ASP* 3.8 19.9 + - - +
208A ALA 6.2 0.4 - - - +
236B MET* 3.7 32.8 - - + +
237B HIS* 2.8 24.0 + - + +
239B MET* 1.4 75.5 - - - +
241B ALA* 1.3 57.9 + - - +
243B PHE* 3.0 33.5 + - - +
244B LEU* 2.9 48.3 + - + +
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Residues in contact with ALA 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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192B PRO* 4.3 3.1 - - + -
193B TYR* 3.5 36.6 - - + -
233B LEU* 4.1 23.1 - - + +
236B MET* 4.6 3.1 - - + +
237B HIS 3.0 8.3 + - - +
238B PRO 3.7 7.6 - - - +
240B ARG* 1.3 74.9 - - - +
242B LEU* 1.3 55.3 + - - +
244B LEU* 3.1 2.5 + - - +
245B ILE* 2.8 43.1 + - + +
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Residues in contact with LEU 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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189A ILE* 3.7 18.8 - - + -
239A MET* 4.1 13.9 - - + -
242A LEU* 3.4 33.0 - - + -
189B ILE* 4.5 4.7 - - + -
192B PRO* 3.8 23.0 - - + +
195B MET* 4.2 2.2 - - - -
200B ILE* 3.4 49.0 - - + +
238B PRO 3.0 16.1 + - - +
239B MET* 3.4 15.9 - - - +
241B ALA* 1.3 74.0 - - - +
243B PHE* 1.3 59.6 + - - +
246B PRO* 3.3 17.0 - - - +
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Residues in contact with PHE 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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201A ALA* 3.6 37.0 - - + +
202A CYS* 3.3 28.7 - - - -
203A ASP* 4.2 1.1 - - - -
206A PRO* 3.6 26.2 - - + -
239B MET 3.3 4.8 + - - +
240B ARG* 3.0 39.3 + - - +
242B LEU* 1.3 78.2 - - - +
244B LEU* 1.3 72.6 + - + +
246B PRO* 3.5 8.5 - - - +
247B ARG* 3.2 58.3 - - - +
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Residues in contact with LEU 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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233B LEU* 4.1 9.2 - - + -
236B MET* 3.6 30.7 - - + -
240B ARG* 2.9 43.2 + - + +
241B ALA 3.1 3.7 + - - +
243B PHE* 1.3 99.4 - - + +
245B ILE* 1.3 58.3 + - - +
247B ARG* 3.1 6.8 + - + +
248B ASN* 2.7 65.5 + - - +
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Residues in contact with ILE 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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192B PRO* 3.3 30.7 - - + +
193B TYR* 4.4 11.2 - - + +
195B MET 3.5 20.2 - - - +
197B PRO* 4.0 16.6 - - + -
200B ILE* 3.7 19.3 - - + -
217B TRP* 4.4 12.7 - - + -
233B LEU* 3.8 17.7 - - + -
241B ALA* 2.8 31.2 + - + +
242B LEU 4.6 0.7 - - - +
244B LEU* 1.3 72.6 - - - +
246B PRO* 1.3 66.9 - - + +
248B ASN* 3.8 5.4 - - - +
272B LYS* 3.2 17.5 - - - +
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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