Contacts of the strand formed by residues 237 - 242 (chain B) in PDB entry 3K74
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 THR 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B SER* 4.4 4.9 - - - -
181B CYS 3.2 18.6 - - - +
182B ALA* 4.4 6.7 - - + +
188B PHE* 3.7 4.8 - - - -
231B ARG* 3.3 5.0 - - - +
232B ASP 2.8 29.6 + - - -
235B LYS* 3.2 23.2 + - - +
236B ASN* 1.3 78.8 + - - +
238B LEU* 1.3 67.3 + - - +
239B TYR* 3.4 41.4 + - + +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B SER* 3.4 3.8 - - - -
181B CYS* 2.8 41.5 + - + +
188B PHE* 4.2 8.9 - - + -
193B MET* 3.7 26.9 - - + -
194B TYR 3.8 18.2 - - - +
195B TRP* 3.4 27.9 - - + +
210B ILE* 3.6 28.7 - - + -
229B ILE* 4.1 4.0 - - + -
230B SER 3.3 16.2 - - - +
231B ARG* 4.0 7.6 - - + -
237B THR* 1.3 78.4 - - - +
239B TYR* 1.3 63.1 + - - +
255B CYS* 3.9 11.4 - - + -
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Residues in contact with TYR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ARG* 3.2 42.8 - - + +
179B LEU 3.4 3.1 - - - -
180B SER* 3.5 25.8 - - - -
195B TRP* 3.1 13.4 + - - -
228B THR 4.5 0.2 - - - -
229B ILE* 3.5 2.9 - - - +
230B SER* 2.8 52.4 + - - +
231B ARG* 4.3 1.8 - - - -
232B ASP* 4.0 14.7 + - + +
235B LYS* 4.1 21.5 + - - +
237B THR* 3.4 39.2 + - + +
238B LEU* 1.3 76.7 - - - +
240B LEU* 1.3 61.5 + - - +
241B GLN 4.1 0.9 - - - +
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B LEU 3.8 0.7 - - - +
178B ARG* 3.3 4.8 - - - -
179B LEU* 2.8 40.9 + - + -
195B TRP* 3.4 41.2 - - + +
207B VAL* 4.3 1.6 - - + -
208B SER* 3.5 25.4 - - - +
227B PHE* 3.9 28.3 - - + -
228B THR 3.5 13.2 - - - +
229B ILE 4.4 0.9 - - - +
239B TYR* 1.3 74.0 - - - +
241B GLN* 1.3 59.4 + - - +
242B MET* 3.6 19.7 + - + +
253B TYR* 4.0 23.1 - - + -
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B SER* 4.0 9.7 - - - -
177B LEU 3.8 11.5 + - - -
178B ARG* 3.6 31.1 + - + +
226B ARG 3.9 0.5 - - - +
227B PHE* 3.0 8.1 - - - +
228B THR* 2.9 51.0 + - + +
239B TYR* 4.1 1.0 - - - +
240B LEU* 1.3 71.2 - - - +
242B MET* 1.3 68.1 + - - +
243B ASN* 3.2 34.2 + - - +
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Residues in contact with MET 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B SER* 3.1 4.7 - - - -
177B LEU* 2.8 44.0 + - - +
179B LEU* 4.0 30.5 - - - -
227B PHE* 2.8 51.4 - - + -
240B LEU* 3.8 15.5 - - + +
241B GLN* 1.3 75.9 - - - +
243B ASN* 1.3 63.3 + - - +
245B LEU* 3.9 20.4 - - + +
253B TYR* 3.4 27.6 - - + +
272B VAL* 4.6 8.3 - - + -
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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