Contacts of the helix formed by residues 237 - 246 (chain B) in PDB entry 4I6J
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 SER 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B PRO* 5.2 13.7 + - - +
217B LEU* 4.8 5.2 - - - +
235B LEU 3.6 5.4 + - - -
236B LEU* 1.3 76.2 - - - +
238B ASP* 1.3 65.0 + - - +
239B GLU* 3.6 17.4 + - - +
240B LEU* 2.9 28.4 + - - +
241B LEU* 2.8 28.7 + - - +
270B HIS* 4.9 3.1 - - - -
272B ILE* 4.7 3.1 - - - -
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Residues in contact with ASP 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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237B SER* 1.3 73.3 - - - +
239B GLU* 1.3 69.8 + - - +
241B LEU* 3.3 0.3 + - - +
242B LEU* 2.8 42.2 + - + +
271B THR 4.0 5.5 - - - +
272B ILE* 2.9 16.5 - - - +
273B GLN* 2.7 44.4 + - - +
276B SER* 2.6 29.5 + - - +
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Residues in contact with GLU 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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217B LEU* 3.8 30.2 - - + +
237B SER* 3.6 17.1 - - - +
238B ASP* 1.3 90.7 + - - +
240B LEU* 1.3 52.0 + - - +
242B LEU* 3.8 8.1 - - + +
243B ALA* 2.7 35.5 + - - +
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Residues in contact with LEU 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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213B PRO 6.0 0.4 - - - +
216B ILE* 4.4 12.8 - - + -
217B LEU* 4.4 11.4 - - + +
220B ALA* 3.5 28.7 - - + -
229B LEU* 4.6 9.0 - - + -
231B LEU* 4.3 20.4 - - + -
235B LEU 3.6 20.9 - - - +
236B LEU* 4.2 18.6 - - + -
237B SER* 2.9 24.3 + - - +
239B GLU* 1.3 74.9 - - - +
241B LEU* 1.3 66.5 + - - +
243B ALA* 3.2 4.0 + - - +
244B LEU* 2.9 34.0 + - + +
255B LEU* 6.0 0.4 - - + -
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 3.8 34.5 - - + -
237B SER 2.8 13.0 + - - +
238B ASP 3.7 6.5 - - - +
240B LEU* 1.3 76.5 - - - +
242B LEU* 1.3 52.0 + - - +
244B LEU* 2.9 11.2 + - + +
245B SER* 2.7 38.2 + - - -
255B LEU* 4.2 6.1 - - + -
272B ILE* 4.0 24.7 - - + -
276B SER* 3.9 20.6 - - - +
277B TRP* 4.1 33.0 - - + -
280B PHE* 3.9 26.1 - - + -
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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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238B ASP* 2.8 31.2 + - + +
239B GLU* 3.8 7.2 - - + +
241B LEU* 1.3 72.5 - - - +
243B ALA* 1.3 65.5 + - - +
244B LEU 2.9 1.8 - - - -
245B SER* 3.7 4.3 - - - +
246B SER* 2.9 25.5 + - - -
275B SER 4.7 2.2 - - - +
276B SER* 3.9 20.2 - - - +
279B ALA* 3.9 26.9 - - + -
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Residues in contact with ALA 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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217B LEU* 4.0 15.5 - - + -
220B ALA* 4.0 21.5 - - + +
221B ASP* 4.6 10.9 - - + +
239B GLU 2.7 22.3 + - - +
240B LEU 3.4 6.1 - - - +
242B LEU* 1.3 72.1 - - - +
244B LEU* 1.3 60.8 + - - +
246B SER* 3.6 13.9 + - - -
249B HIS* 3.6 16.7 - - - -
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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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220B ALA* 4.3 11.0 - - + -
226B LEU* 4.8 10.3 - - + -
229B LEU* 4.1 18.6 - - + -
240B LEU* 2.9 36.3 + - + +
241B LEU* 3.4 16.8 - - + +
242B LEU 2.9 0.6 - - - -
243B ALA* 1.3 78.9 - - - +
245B SER* 1.3 61.4 + - - +
246B SER 3.2 2.1 + - - -
249B HIS* 3.3 43.8 + - + +
252B LEU* 3.6 30.0 - - + +
255B LEU* 5.0 3.4 - - + -
280B PHE* 4.6 11.5 - - + -
283B HIS* 3.5 14.6 - - - -
284B SER* 5.2 0.3 + - - -
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Residues in contact with SER 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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241B LEU 2.7 21.0 + - - -
242B LEU* 3.1 7.8 + - - -
244B LEU* 1.3 71.4 - - - +
246B SER* 1.3 68.4 + - - +
276B SER 4.2 0.2 + - - -
279B ALA* 3.2 27.2 - - - +
280B PHE* 2.9 33.1 + - - +
283B HIS* 3.2 23.2 + - - +
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Residues in contact with SER 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 LEU 2.9 11.2 + - - -
243B ALA* 3.6 18.1 + - - -
244B LEU 3.2 2.4 - - - -
245B SER* 1.3 87.8 - - - +
247B GLU* 1.3 63.8 + - - +
248B LYS* 3.2 17.7 + - - +
249B HIS* 3.7 11.5 + - - +
283B HIS* 3.2 20.0 + - - -
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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