Contacts of the strand formed by residues 234 - 238 (chain L) in PDB entry 6O81
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 TYR 234 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193L ASP* 3.4 5.8 - - - +
194L ILE* 2.8 45.2 + - + +
196L VAL* 3.3 34.1 - - + -
207L VAL* 5.5 11.0 - - + -
226L ILE* 5.8 5.6 - - + -
227L ASN 3.4 9.0 - - - +
228L LEU* 3.7 33.0 - - + -
229L ILE* 4.3 3.4 - - - +
230L ALA 4.5 1.3 - - - -
231L PRO 4.1 20.2 - - - -
232L PRO 4.5 1.8 - - - -
233L ARG* 1.3 78.9 - - - +
235L VAL* 1.3 60.4 + - - +
236L MET 4.1 0.2 - - - -
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Residues in contact with VAL 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192L ALA 3.5 8.1 - - - +
193L ASP* 4.4 4.7 - - + +
225L LYS 3.5 2.6 - - - +
226L ILE* 3.5 2.1 - - - -
227L ASN* 2.9 43.0 + - + +
229L ILE* 4.3 15.6 - - + +
234L TYR* 1.3 74.0 - - - +
236L MET* 1.3 60.3 + - - +
237L THR* 3.8 4.1 + - - +
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Residues in contact with MET 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L ILE 4.0 2.6 - - - +
192L ALA* 2.7 39.4 + - + +
193L ASP* 4.7 0.2 - - - +
194L ILE* 5.6 9.4 - - + -
224L ILE* 5.7 7.6 - - + -
225L LYS 3.5 7.4 - - - +
226L ILE* 4.4 7.9 - - + +
234L TYR* 4.1 1.6 + - + -
235L VAL* 1.3 69.1 - - - +
237L THR* 1.3 62.7 + - - +
238L THR* 5.4 0.2 - - - -
250L LEU* 5.5 4.6 - - + +
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Residues in contact with THR 237 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L LYS* 6.5 1.1 - - - -
190L ILE 3.8 4.0 - - - -
191L ARG* 4.2 13.9 - - - +
223L PRO 4.7 0.2 - - - -
224L ILE* 3.4 3.8 - - - +
225L LYS* 2.9 41.7 + - - +
235L VAL* 3.8 4.8 - - - -
236L MET* 1.3 76.0 - - - +
238L THR* 1.3 64.2 + - - +
239L THR 4.3 0.4 - - - -
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Residues in contact with THR 238 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L LYS* 3.4 2.5 - - - -
190L ILE* 2.8 48.4 + - - +
222L MET* 5.4 7.2 - - - -
223L PRO 4.0 12.1 - - - -
224L ILE* 4.6 8.1 - - - -
236L MET 5.4 0.2 - - - -
237L THR* 1.3 79.9 - - - +
239L THR* 1.3 59.4 + - - +
240L THR* 3.6 6.1 + - - +
246L GLY* 5.3 5.6 - - - -
250L LEU* 5.2 10.1 - - - -
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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