Contacts of the helix formed by residues 233 - 239 (chain C) in PDB entry 5Y9F
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 233 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ARG* 2.6 33.6 + - - -
110A GLY* 6.0 0.2 - - - -
370A GLU* 4.1 4.2 - - - +
165C ILE* 2.9 21.3 + - + +
167C GLU* 4.1 17.5 - - + +
192C ASN* 2.7 33.2 + - - +
231C TYR 3.3 2.5 + - - -
232C PRO* 1.3 67.8 - - - +
234C TYR* 1.3 60.0 + - - +
235C LEU* 3.6 7.4 + - - +
236C GLN* 3.2 18.1 + - - +
237C MET* 2.9 32.1 + - - +
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Residues in contact with TYR 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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109A ARG 5.9 1.1 - - - -
110A GLY 5.7 0.4 - - - -
308A ASN* 5.2 5.8 - - - +
156C LEU* 4.2 10.7 - - - +
158C ILE* 3.9 8.1 - - + -
231C TYR* 3.3 37.6 + + - -
232C PRO* 3.0 47.9 + - + +
233C ASP* 1.3 72.2 - - - +
235C LEU* 1.3 65.0 + - + +
237C MET* 4.2 12.8 - - + -
238C SER* 2.9 34.5 + - - -
246C MET* 4.4 5.0 - - + +
249C CYS* 3.6 25.1 - - - -
251C ARG* 3.6 50.3 - - - +
253C GLU* 5.0 0.5 + - - -
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Residues in contact with LEU 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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41A ARG* 4.8 6.7 - - + +
108A GLY* 4.2 5.8 - - - -
109A ARG 3.4 26.2 - - - +
110A GLY* 3.9 13.2 - - - +
308A ASN* 4.1 17.5 - - - +
370A GLU* 3.6 27.4 - - + +
371A PHE 4.3 1.8 - - - +
372A ASP* 3.6 40.7 - - + +
374A GLN* 6.0 0.2 - - - +
233C ASP* 3.2 9.1 + - - +
234C TYR* 1.3 81.9 - - + +
236C GLN* 1.3 59.9 + - - +
238C SER* 3.4 6.5 + - - -
239C ALA* 3.3 23.2 + - - +
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Residues in contact with GLN 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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41A ARG* 4.2 6.5 - - - +
165C ILE* 3.4 33.5 - - - +
192C ASN* 4.4 11.5 + - - +
233C ASP* 3.2 28.3 + - - +
235C LEU* 1.3 78.5 - - - +
237C MET* 1.3 73.0 + - - +
239C ALA* 3.2 7.2 + - + +
240C ASP* 3.1 23.3 + - - +
245C SER* 5.6 0.2 + - - -
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Residues in contact with MET 237 (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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158C ILE* 3.7 26.7 - - + -
164C ALA* 4.1 10.5 - - + -
165C ILE* 3.4 40.6 - - + +
232C PRO* 4.4 1.1 - - + -
233C ASP 2.9 27.1 + - - +
234C TYR* 4.1 6.1 - - + +
236C GLN* 1.3 88.5 + - - +
238C SER* 1.3 60.2 + - - +
240C ASP* 3.3 20.7 - - - +
243C GLY* 4.9 1.0 - - - -
245C SER* 4.1 12.1 - - - -
246C MET* 3.6 38.9 + - + +
317C GLN* 3.7 12.1 + - - -
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Residues in contact with SER 238 (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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106A GLU* 5.7 0.3 + - - -
372A ASP* 5.4 0.3 + - - -
374A GLN* 5.1 6.1 + - - -
464A PRO* 3.7 19.5 - - - +
467A ARG* 3.6 22.7 + - - -
468A LYS* 6.3 1.1 - - - -
234C TYR* 2.9 20.4 + - - -
235C LEU* 3.4 7.8 + - - -
237C MET* 1.3 78.0 - - - +
239C ALA* 1.3 62.4 + - - +
240C ASP 3.2 3.0 + - - +
246C MET* 3.7 7.1 - - - +
317C GLN* 3.7 19.6 + - - +
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Residues in contact with ALA 239 (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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372A ASP* 5.2 5.4 - - - +
464A PRO* 4.6 13.0 - - + -
235C LEU 3.3 15.6 + - - +
236C GLN* 3.2 9.9 + - + +
238C SER* 1.3 77.4 + - - +
240C ASP* 1.3 66.4 + - - +
241C ALA* 3.6 1.6 + - - -
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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