Contacts of the strand formed by residues 219 - 227 (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 ILE 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212C GLU 3.4 8.3 - - - +
213C LEU* 3.8 19.3 - - + -
214C LEU* 4.9 0.7 - - - -
217C GLY 3.7 9.9 - - - +
218C SER* 1.3 88.1 + - - +
220C THR* 1.3 76.9 + - - +
270C LEU 4.5 0.9 - - - +
271C GLU* 3.4 39.9 - - + +
275C ILE* 3.6 28.9 - - + -
279C LYS* 6.2 0.2 - - - -
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Residues in contact with THR 220 (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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211C CYS* 3.3 8.3 - - - +
212C GLU* 3.1 54.9 + - - +
214C LEU* 4.5 10.5 - - + +
218C SER* 5.2 2.9 - - - +
219C ILE* 1.3 86.3 - - - +
221C GLY* 1.3 61.2 + - - +
222C PHE* 5.4 1.4 - - - -
237C LYS* 5.1 5.4 - - - +
270C LEU 5.5 0.7 - - - -
275C ILE* 4.7 0.5 - - - +
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Residues in contact with GLY 221 (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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210C GLY 3.4 10.1 - - - -
211C CYS* 4.1 3.4 - - - -
220C THR* 1.3 80.2 - - - +
222C PHE* 1.3 65.0 + - - +
235C PHE 5.2 2.9 - - - +
237C LYS* 4.3 23.1 - - - +
270C LEU* 4.4 20.3 - - - +
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Residues in contact with PHE 222 (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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117C SER* 5.6 0.4 - - - -
118C LEU 3.8 1.8 - - - -
119C ARG* 3.5 56.1 - - + -
208C MET* 3.9 29.6 - - + -
209C ILE* 3.3 5.2 - - - +
210C GLY 2.9 62.2 + - - +
211C CYS* 3.7 12.6 - - - -
212C GLU* 4.4 13.2 - - + -
220C THR* 5.0 2.0 - - - -
221C GLY* 1.3 80.9 - - - +
223C LEU* 1.3 61.0 + - - +
224C GLN* 4.6 13.0 - - - +
235C PHE 5.2 2.9 - - - -
270C LEU* 4.2 5.2 - - - +
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Residues in contact with LEU 223 (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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207C ARG* 3.5 34.1 - - + +
208C MET 3.2 10.5 - - - +
209C ILE* 3.7 16.8 - - + -
222C PHE* 1.3 75.2 - - - +
224C GLN* 1.3 70.3 + - - +
225C TYR* 4.2 10.8 - - + +
234C ILE* 4.3 0.5 - - - +
235C PHE* 3.0 49.5 + - + +
242C TRP* 3.6 28.3 - - + -
266C GLN* 4.0 26.7 - - + +
270C LEU* 4.6 4.0 - - + +
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Residues in contact with GLN 224 (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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57C LYS 5.1 1.7 - - - +
59C TRP* 3.3 23.5 + - + -
207C ARG* 3.4 3.5 - - - +
208C MET* 2.7 65.9 + - + +
222C PHE* 4.6 11.9 - - - +
223C LEU* 1.3 84.8 - - - +
225C TYR* 1.3 66.4 + - - +
231C ASP* 4.0 9.6 - - - +
233C LEU 3.2 6.7 - - - +
234C ILE* 3.8 33.8 - - + +
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Residues in contact with TYR 225 (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* 3.9 3.8 - - - -
122C ARG* 4.7 3.3 + - - -
185C MET* 5.7 4.0 - - - +
186C PHE* 4.2 5.8 - + - -
189C GLU* 4.2 7.3 + - - -
205C TYR* 3.1 37.7 - + + +
206C GLN 3.2 4.7 - - - -
207C ARG* 2.8 52.2 + - + -
223C LEU* 4.2 6.8 - - + +
224C GLN* 1.3 78.4 - - - +
226C ALA* 1.3 55.4 + - - +
231C ASP* 3.7 2.3 - - - -
232C PHE* 2.6 38.1 + - + +
233C LEU* 2.9 20.0 + - + +
234C ILE* 5.8 0.2 - - - +
242C TRP* 3.8 22.7 - + - -
256C TRP* 3.7 32.0 - + - -
266C GLN* 6.0 0.2 + - - -
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Residues in contact with ALA 226 (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* 3.3 42.6 - - + -
204C THR 4.0 0.2 - - - +
205C TYR* 3.3 11.1 - - - -
206C GLN* 2.6 43.3 + - + +
225C TYR* 1.3 74.6 - - - +
227C TYR* 1.3 58.1 + - - +
228C ASP 4.2 0.4 - - - -
229C GLY 4.8 0.4 - - - -
230C GLN 3.1 18.8 - - - +
232C PHE* 3.8 2.9 - - - -
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Residues in contact with TYR 227 (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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190C LEU* 3.9 17.5 - - + -
193C LEU* 3.5 37.0 - - + -
194C GLN* 3.2 26.4 - - + +
197C TYR* 3.5 32.1 - + + -
199C HIS* 3.3 20.2 - + - -
203C HIS* 3.5 10.8 - - + -
204C THR 3.5 11.0 - - - -
205C TYR* 4.3 4.0 - + - -
226C ALA* 1.3 73.7 - - - +
228C ASP* 1.3 93.3 + - + +
229C GLY 3.1 0.4 - - - -
230C GLN* 3.0 23.6 + - - +
232C PHE* 4.0 23.1 - - + +
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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