Contacts of the helix formed by residues 231 - 241 (chain X) in PDB entry 5LIK
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 ASP 231 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190X TYR* 2.2 42.2 + - - +
227X SER 3.2 3.8 + - - +
228X LEU 3.1 15.9 + - - +
229X LEU 3.4 0.6 - - - -
230X GLU* 1.3 75.8 - - - +
232X PRO* 1.4 65.4 - - - +
233X MLZ 3.3 24.6 + - - +
234X ILE* 2.8 21.8 + - + +
235X LYS* 2.7 34.2 + - - +
292X PHE* 5.1 2.4 - - - -
294X ARG* 4.3 5.2 + - - -
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Residues in contact with PRO 232 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230X GLU 3.3 9.8 - - - +
231X ASP* 1.4 91.9 - - - +
233X MLZ 1.3 56.5 + - + +
235X LYS* 3.7 14.5 - - + +
236X GLU* 2.8 40.5 + - + +
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Residues in contact with MLZ 233 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231X ASP* 3.1 16.5 - - - +
232X PRO* 1.3 79.4 - - + +
234X ILE* 1.3 61.8 + - - +
236X GLU* 4.1 14.4 - - - +
237X ILE* 3.7 26.0 + - - +
288X THR* 5.6 0.2 - - - +
292X PHE* 3.4 41.1 - - + -
294X ARG* 5.6 6.1 - - - +
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Residues in contact with ILE 234 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X PRO* 4.0 23.1 - - + -
228X LEU* 4.0 17.3 - - + +
231X ASP* 2.8 28.4 + - + +
233X MLZ 1.3 75.1 + - - +
235X LYS* 1.3 65.9 + - - +
236X GLU 3.2 0.6 + - - -
237X ILE* 3.4 8.0 + - - +
238X ALA* 3.1 18.2 + - - +
245X ALA* 4.1 21.3 - - + -
248X VAL* 4.1 20.7 - - + +
249X LEU* 4.1 13.0 - - + -
289X ILE* 4.7 9.0 - - + -
292X PHE* 3.7 28.5 - - + -
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Residues in contact with LYS 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X LEU 3.8 16.6 - - - +
230X GLU* 3.6 40.7 + - - +
231X ASP 2.7 17.7 + - - +
232X PRO* 3.3 11.3 + - + +
234X ILE* 1.3 72.2 - - - +
236X GLU* 1.3 58.3 + - - +
238X ALA* 3.2 8.8 + - - +
239X ALA* 2.8 30.9 + - - +
245X ALA* 4.5 9.0 - - + -
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Residues in contact with GLU 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X PRO* 2.8 24.5 + - + +
233X MLZ 4.1 16.6 - - - +
235X LYS* 1.3 72.6 - - - +
237X ILE* 1.3 60.6 + - + +
239X ALA* 3.1 8.6 + - - +
240X LYS* 2.9 27.9 + - - +
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Residues in contact with ILE 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233X MLZ 3.7 17.0 + - - +
234X ILE* 3.4 9.1 + - - +
236X GLU* 1.3 80.3 - - + +
238X ALA* 1.3 62.7 + - - +
240X LYS* 3.2 15.2 + - - +
241X HIS* 3.2 16.5 - - - -
248X VAL* 4.1 9.4 - - + -
281X LEU* 3.8 29.4 - - + -
285X GLU* 4.0 30.7 - - + +
288X THR* 4.5 15.3 - - + -
289X ILE* 3.6 29.6 - - + -
292X PHE* 4.7 1.8 - - + -
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Residues in contact with ALA 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234X ILE 3.1 12.2 + - - +
235X LYS* 3.2 9.4 + - - +
237X ILE* 1.3 75.0 - - - +
239X ALA* 1.3 62.9 + - - +
241X HIS* 3.0 4.2 + - - +
242X MLY 3.0 3.1 + - - -
243X MLZ 2.9 44.4 + - - +
244X THR 3.5 23.1 - - - +
245X ALA* 3.7 5.4 - - - +
248X VAL* 3.5 16.1 - - + +
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Residues in contact with ALA 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235X LYS 2.8 13.6 + - - +
236X GLU* 3.4 11.4 - - - +
238X ALA* 1.3 75.5 - - - +
240X LYS* 1.3 58.8 + - - +
242X MLY 2.9 26.9 + - - +
243X MLZ 4.6 2.2 - - - -
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Residues in contact with LYS 240 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236X GLU 2.9 12.7 + - - +
237X ILE* 3.3 13.7 - - - +
238X ALA 3.2 0.2 - - - -
239X ALA* 1.3 76.7 - - - +
241X HIS* 1.3 62.9 + - + +
242X MLY 5.1 1.9 - - - +
285X GLU* 3.5 21.3 - - - +
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Residues in contact with HIS 241 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237X ILE 3.2 22.2 + - - -
238X ALA* 3.0 7.2 + - - +
239X ALA 3.0 0.6 - - - -
240X LYS* 1.3 84.5 + - + +
242X MLY 1.3 73.0 + - - +
243X MLZ 3.1 25.2 + - + +
248X VAL* 5.4 0.4 - - + -
279X PHE* 4.0 18.6 - + + +
280X LYS 3.1 28.1 + - - -
281X LEU* 4.1 13.6 - - + +
282X SER* 4.9 0.7 - - - -
285X GLU* 2.9 34.0 + - - -
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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