Contacts of the helix formed by residues 233 - 241 (chain B) in PDB entry 1B8I
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 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B TYR* 4.3 19.1 - - + +
229B PRO* 4.4 2.5 - - + -
230B SER* 2.9 28.6 + - - +
232B GLU* 1.3 83.9 - - + +
234B LYS* 1.3 57.3 + - - +
235B GLU 3.5 0.2 - - - -
236B GLU* 3.6 12.9 - - + +
237B LEU* 3.0 31.0 + - - +
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Residues in contact with LYS 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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229B PRO* 3.3 43.8 + - + +
230B SER 3.2 2.3 + - - +
231B GLU* 3.3 30.0 + - - +
232B GLU 2.8 0.2 - - - -
233B ALA* 1.3 77.4 - - - +
235B GLU* 1.3 60.6 + - - +
236B GLU 3.2 1.3 - - - -
237B LEU* 3.6 0.9 + - - -
238B ALA* 2.9 29.2 + - - +
245B VAL* 3.8 31.9 - - + +
248B VAL* 3.7 19.9 - - + +
249B SER* 3.0 29.9 + - - +
252B PHE* 6.3 0.6 - - - +
256B ARG* 5.5 4.0 - - - +
8C T 3.2 25.9 + - - -
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Residues in contact with GLU 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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231B GLU 3.9 7.4 - - - +
232B GLU* 2.8 41.1 + - - +
234B LYS* 1.3 75.2 - - + +
236B GLU* 1.3 56.2 + - - +
238B ALA* 3.6 8.1 - - - +
239B ARG* 2.7 35.7 + - - +
245B VAL* 4.7 14.6 - - + -
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Residues in contact with GLU 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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232B GLU* 3.3 11.1 + - - +
233B ALA* 3.6 21.1 - - + +
235B GLU* 1.3 80.4 - - - +
237B LEU* 1.3 54.3 + - + +
239B ARG* 3.2 5.2 + - - +
240B LYS* 2.7 34.5 + - - +
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Residues in contact with LEU 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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215B ILE* 3.1 34.3 - - + +
216B LEU* 4.6 6.3 - - + +
218B GLU* 5.8 0.7 - - + -
219B TYR* 3.4 50.3 - - + -
229B PRO* 4.7 2.7 - - + -
233B ALA 3.0 25.1 + - - +
234B LYS 4.1 2.7 - - - +
236B GLU* 1.3 76.2 - - + +
238B ALA* 1.3 58.8 + - - +
239B ARG 3.1 2.0 - - - -
240B LYS* 4.0 6.5 - - + -
241B CYS* 2.7 42.1 + - - +
248B VAL* 4.2 23.3 - - + -
252B PHE* 4.6 5.6 - - + -
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Residues in contact with ALA 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 LYS 2.9 20.8 + - - +
235B GLU* 3.7 8.7 - - - +
237B LEU* 1.3 76.2 - - - +
239B ARG* 1.3 56.6 + - - +
242B GLY* 3.0 17.5 + - - -
243B ILE* 2.8 24.7 + - - +
244B THR* 3.6 5.4 - - - -
245B VAL* 3.4 30.7 - - + +
248B VAL* 3.8 7.6 - - + +
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Residues in contact with ARG 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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235B GLU 2.7 18.2 + - - +
236B GLU* 3.4 6.3 - - - +
238B ALA* 1.3 76.2 - - - +
240B LYS* 1.3 70.5 + - - +
242B GLY* 3.1 11.0 + - - -
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Residues in contact with LYS 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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211B GLN* 4.6 8.1 + - - -
215B ILE* 3.7 26.6 - - + +
236B GLU 2.7 20.0 + - - +
237B LEU* 3.7 9.0 - - - +
239B ARG* 1.3 78.1 - - - +
241B CYS* 1.3 59.4 + - - +
242B GLY 3.4 0.2 + - - -
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Residues in contact with CYS 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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209B SER* 4.4 3.8 + - - -
211B GLN* 4.5 8.0 + - - -
212B ALA* 3.1 50.7 - - + +
215B ILE* 3.2 36.3 - - - -
216B LEU* 3.8 15.0 - - - -
237B LEU 2.7 22.9 + - - +
240B LYS* 1.3 73.8 - - - +
242B GLY* 1.3 54.4 + - - +
243B ILE* 3.2 20.1 + - + +
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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