Contacts of the helix formed by residues 229 - 237 (chain B) in PDB entry 5LCM
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 LYS 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B THR* 1.3 72.6 - - - +
230B THR* 1.3 58.4 + - - +
232B CYS* 3.3 6.4 + - - +
233B LYS* 3.0 40.5 + - - +
240B ASP* 3.4 22.4 + - - +
243B LEU* 4.0 25.4 - - + -
244B ASN* 2.6 32.1 + - - +
266B GLN* 2.9 45.5 + - + +
268B PHE* 3.9 17.3 - - + -
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Residues in contact with THR 230 (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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228B THR* 3.2 7.6 - - - -
229B LYS* 1.3 78.4 - - - +
231B GLU* 1.3 56.6 + - - +
233B LYS* 3.3 18.5 + - + +
234B GLU* 3.0 49.9 + - + +
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Residues in contact with GLU 231 (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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226B LEU 4.1 3.1 - - - +
227B LEU* 3.3 21.9 - - + +
228B THR* 2.9 51.2 + - - +
230B THR* 1.3 77.3 - - - +
232B CYS* 1.3 52.9 + - - +
234B GLU* 4.4 11.7 - - - +
235B ASP* 2.7 53.4 + - - +
236B TYR* 5.4 0.2 - - - -
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Residues in contact with CYS 232 (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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227B LEU* 3.8 11.2 - - - +
228B THR 3.1 18.7 + - - -
229B LYS 3.4 8.5 - - - +
231B GLU* 1.3 73.7 - - - +
233B LYS* 1.3 62.6 + - - +
236B TYR* 3.1 33.1 + - - +
237B PHE 3.6 1.2 + - - -
238B LEU* 3.7 5.9 + - + +
243B LEU* 3.9 19.3 - - + -
268B PHE* 3.8 21.3 - - - -
273B VAL* 3.5 36.8 - - + -
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Residues in contact with LYS 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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229B LYS* 3.0 25.4 + - - +
230B THR* 3.3 20.4 + - + +
232B CYS* 1.3 75.1 - - - +
234B GLU* 1.3 59.4 + - + +
237B PHE* 3.0 30.3 + - - -
238B LEU 3.3 23.1 - - - +
239B THR* 5.0 0.7 - - - -
240B ASP* 3.1 38.2 + - - +
243B LEU* 3.7 10.3 - - + -
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Residues in contact with GLU 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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230B THR* 3.0 38.3 + - + +
231B GLU* 3.8 10.4 - - - +
233B LYS* 1.3 76.8 - - + +
235B ASP* 1.3 72.2 + - - +
237B PHE* 3.5 21.6 - - - -
291B TRP* 5.9 0.5 - - - -
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Residues in contact with ASP 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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227B LEU* 4.5 5.2 - - - +
231B GLU* 2.7 38.0 + - - +
234B GLU* 1.3 86.2 - - - +
236B TYR* 1.3 78.2 + - + +
237B PHE* 3.7 3.1 - - - -
270B ARG* 4.4 14.9 + - - -
287B LEU* 3.6 16.8 - - - +
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Residues in contact with TYR 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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227B LEU* 3.7 25.6 - - + -
232B CYS* 3.1 15.3 + - - +
235B ASP* 1.3 92.8 - - + +
237B PHE* 1.3 71.1 + - - +
238B LEU* 3.1 18.6 + - + +
270B ARG* 3.1 27.1 + - + +
273B VAL* 3.3 22.0 - - + -
274B GLU* 3.2 39.1 + - + -
277B ALA* 3.8 20.5 - - + +
278B PHE* 5.1 0.4 - + - -
281B TRP* 3.0 23.0 + - - -
287B LEU* 3.8 21.1 - - + -
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Residues in contact with PHE 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 LYS 3.0 20.3 + - - -
234B GLU* 3.5 18.8 - - - -
235B ASP 4.9 1.6 - - - -
236B TYR* 1.3 75.3 - - - +
238B LEU* 1.3 61.4 + - - +
239B THR* 4.5 3.4 - - - +
280B LYS* 3.0 20.6 + - - -
281B TRP* 3.6 18.0 - - + +
287B LEU* 3.4 33.2 - - + -
290B GLU* 3.8 15.9 - - + -
291B TRP* 3.6 50.9 - + + -
294B ARG* 3.7 39.5 + - + +
8C 6TW 5.4 0.2 + - - -
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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