Contacts of the strand formed by residues 230 - 236 (chain C) in PDB entry 4LCC
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 GLN 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C ILE* 4.8 15.5 - - + +
59C TRP* 4.5 0.9 - - - -
226C ALA* 3.1 6.3 - - - -
227C TYR 3.0 32.1 + - - +
228C ASP 3.3 0.6 - - - -
229C GLY* 1.3 80.7 - - - +
231C ASP* 1.3 79.1 + - + +
232C PHE* 4.1 0.3 - - - -
245C MET* 5.7 7.4 - - - +
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Residues in contact with ASP 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TRP* 2.3 41.6 + - - +
224C GLN* 4.0 7.5 - - + +
225C TYR 3.9 4.0 - - - -
230C GLN* 1.3 85.6 - - + +
232C PHE* 1.3 61.2 + - - +
234C ILE* 4.7 14.6 - - + +
245C MET* 3.6 36.1 - - + +
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Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LEU* 3.8 33.9 - - + -
197C TYR* 3.2 37.2 - + - -
205C TYR* 4.9 5.2 - + - -
225C TYR* 2.6 29.6 + - + +
226C ALA* 3.8 7.9 - - - -
227C TYR* 4.0 19.1 - - + +
230C GLN 3.2 0.4 + - - -
231C ASP* 1.3 75.3 - - - +
233C LEU* 1.3 84.4 + - + +
245C MET* 3.6 31.0 + - - +
246C ASP* 5.6 0.9 - - + -
248C VAL* 4.6 1.1 - - + -
249C ALA* 3.5 35.6 - - + +
252C ILE* 4.5 7.6 - - + -
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Residues in contact with LEU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C TYR* 6.1 0.2 - - - +
224C GLN* 3.2 5.9 - - - +
225C TYR* 2.9 32.7 + - + +
232C PHE* 1.3 99.0 - - + +
234C ILE* 1.3 66.3 + - - +
242C TRP* 3.7 18.4 - - + -
243C MET 3.4 19.3 - - - +
244C ALA* 3.7 11.2 - - + -
249C ALA* 3.5 20.0 - - + +
252C ILE* 3.6 32.5 - - + -
253C ARG* 4.8 7.2 - - + +
256C TRP* 3.6 22.7 - - + -
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Residues in contact with ILE 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C LEU 3.8 2.5 - - - +
224C GLN* 3.8 35.2 - - + +
231C ASP* 4.7 13.2 - - + +
233C LEU* 1.3 81.7 - - - +
235C PHE* 1.3 69.2 + - - +
236C ASN* 3.8 2.3 + - - +
242C TRP* 3.8 3.1 - - - -
243C MET* 3.0 55.8 + - + +
245C MET* 4.3 24.5 - - - -
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Residues in contact with PHE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C GLY 5.2 4.9 - - - +
222C PHE* 5.2 1.2 - - - -
223C LEU* 3.0 31.1 + - + +
234C ILE* 1.3 77.1 - - - +
236C ASN* 1.3 71.3 + - - +
237C LYS* 3.7 28.0 + - + +
240C LEU* 4.5 6.5 - - + -
241C SER 3.6 13.0 - - - -
242C TRP* 3.5 49.7 - + + -
263C LEU* 4.2 27.1 - - + -
266C GLN* 4.1 21.3 - - + -
267C LYS 4.6 2.5 - - - -
270C LEU* 4.0 24.5 - - + -
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Residues in contact with ASN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ILE 3.8 3.4 + - - +
235C PHE* 1.3 75.0 - - - +
237C LYS* 1.3 60.5 + - - +
238C ASP* 3.2 12.9 + - - +
239C THR* 2.5 53.0 + - - +
240C LEU* 3.1 20.4 + - - -
241C SER* 3.2 18.8 + - - +
243C MET* 6.2 2.0 - - + +
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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