Contacts of the helix formed by residues 232 - 239 (chain B) in PDB entry 4BL8
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 ALA 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B ILE* 5.0 1.1 - - + -
211B TYR* 3.8 7.2 - - - +
215B GLU* 4.5 9.1 - - + +
228B ASN* 3.2 44.6 - - + +
229B GLY 3.0 7.6 + - - +
231B TRP* 1.3 79.7 - - - +
233B TRP* 1.3 64.6 + - - +
234B SER 3.1 4.3 + - - -
235B ASN* 3.3 15.7 + - - +
236B ILE* 3.6 18.9 + - + +
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Residues in contact with TRP 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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115B SER* 5.5 0.8 - - - -
117B ILE* 3.9 22.8 - - + +
228B ASN 5.0 1.4 + - - -
229B GLY 3.9 11.0 + - - -
230B PRO* 3.3 35.8 + - + +
232B ALA* 1.3 77.0 - - - +
234B SER* 1.3 62.6 + - - +
236B ILE* 3.1 10.7 + - - +
237B ASP* 3.1 25.4 + - - +
243B TYR* 4.0 7.4 + + - +
245B VAL* 3.5 27.5 - - + +
299B PRO* 3.7 13.2 - - + -
317B ARG* 3.2 76.7 - - + +
318B ILE* 3.8 23.1 - - + -
321B THR* 3.5 21.3 - - - -
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Residues in contact with SER 234 (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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231B TRP 3.9 1.0 + - - -
232B ALA 3.1 1.0 + - - -
233B TRP* 1.3 79.6 - - - +
235B ASN* 1.3 62.6 - - - +
237B ASP* 3.3 24.5 + - - +
238B THR* 3.4 11.4 + - - -
296B LYS 4.1 6.1 + - - -
297B ASP 2.9 18.7 + - - -
298B LYS* 3.4 29.1 - - - -
299B PRO* 3.8 15.0 - - - +
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Residues in contact with ASN 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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215B GLU* 3.4 27.6 + - - +
219B ASN* 3.2 23.8 + - - +
231B TRP 5.7 0.7 - - - -
232B ALA* 3.3 9.4 + - - +
233B TRP 3.3 0.4 - - - -
234B SER* 1.3 77.8 - - - +
236B ILE* 1.3 59.6 + - - +
237B ASP 3.2 0.2 - - - -
238B THR* 3.5 10.1 + - - -
239B SER* 3.2 19.4 + - - -
298B LYS* 3.6 29.3 - - - +
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Residues in contact with ILE 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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117B ILE* 3.9 31.6 - - + -
215B GLU* 6.1 1.3 - - + +
218B PHE* 3.7 26.5 - - + -
219B ASN* 3.5 15.7 - - - +
226B THR* 5.5 1.6 - - + -
232B ALA* 3.6 19.3 - - + +
233B TRP* 3.1 13.1 + - - +
235B ASN* 1.3 74.7 - - - +
237B ASP* 1.3 65.5 + - - +
239B SER* 3.0 20.5 + - - +
240B LYS* 3.4 6.6 + - - -
241B VAL* 3.7 11.1 + - + +
243B TYR* 3.2 34.7 - - + -
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Residues in contact with ASP 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 TRP 3.1 12.9 + - - +
234B SER* 3.4 14.9 - - - +
236B ILE* 1.3 77.9 - - - +
238B THR* 1.3 61.8 + - - +
240B LYS* 3.3 26.3 + - - +
243B TYR* 3.0 26.9 + - - -
299B PRO* 5.6 1.6 - - - +
317B ARG* 3.8 13.8 + - - -
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Residues in contact with THR 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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234B SER 3.4 12.1 + - - -
235B ASN* 3.5 11.6 + - - -
236B ILE 3.3 0.2 - - - -
237B ASP* 1.3 78.5 - - - +
239B SER* 1.3 61.2 + - - +
240B LYS* 3.5 16.8 + - - +
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Residues in contact with SER 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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219B ASN* 3.3 34.2 - - - +
235B ASN 3.2 11.2 + - - -
236B ILE* 3.0 22.5 + - - -
238B THR* 1.3 76.2 - - - +
240B LYS* 1.3 69.5 + - - +
241B VAL* 3.1 19.5 + - - +
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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