Contacts of the strand formed by residues 229 - 235 (chain O) in PDB entry 3V3K
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 CYS 229 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155O LEU* 3.9 7.9 - - + -
162O CYS* 3.3 25.4 + - - +
163O GLY* 3.6 18.5 - - - -
164O HIS 4.2 1.0 + - - -
198O PHE* 3.9 19.7 - - + -
224O HIS* 4.6 1.0 + - - -
227O LEU* 3.7 4.9 - - - +
228O ASP* 1.3 78.3 - - - +
230O CYS* 1.3 81.4 + - - +
231O VAL* 4.4 0.2 - - - -
273O LEU* 4.1 8.9 - - - +
276O LYS* 4.9 0.9 - - - -
277O PRO* 3.5 27.4 - - + -
279O LEU* 4.3 15.5 - - - -
398O LEU* 4.8 4.5 - - - -
400O PHE* 5.4 0.7 - - - -
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Residues in contact with CYS 230 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164O HIS 3.9 9.4 - - - +
218O LEU* 4.1 27.8 - - - -
224O HIS* 4.3 11.7 - - + -
229O CYS* 1.3 83.2 - - - +
231O VAL* 1.3 68.6 + - - +
232O VAL* 4.6 3.1 - - - -
265O PHE* 4.4 8.3 - - - -
273O LEU* 3.8 33.9 - - + -
277O PRO 3.3 6.6 + - - +
278O LYS* 3.5 6.7 - - + -
279O LEU 2.9 25.5 + - - +
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Residues in contact with VAL 231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164O HIS 3.3 7.2 + - - +
165O CYS* 3.4 19.0 - - - -
166O LEU 3.3 19.4 + - - -
193O PHE* 3.6 34.8 - - + -
198O PHE* 3.5 37.9 - - + -
218O LEU* 4.2 2.9 - - - +
229O CYS* 4.4 0.4 - - - -
230O CYS* 1.3 78.3 - - - +
232O VAL* 1.3 72.7 + - - +
233O VAL* 4.2 3.4 - - + -
279O LEU* 3.6 15.9 - - + -
281O PHE* 3.8 17.0 - - + -
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Residues in contact with VAL 232 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166O LEU* 3.6 10.1 - - + +
168O ILE* 5.8 0.2 - - + -
215O LEU* 3.4 24.9 - - + -
218O LEU* 3.7 22.7 - - + -
230O CYS* 4.6 4.0 - - - -
231O VAL* 1.3 80.3 - - - +
233O VAL* 1.3 68.6 + - - +
234O ILE* 4.4 13.3 - - + +
261O ILE* 4.8 0.4 - - + -
265O PHE* 3.9 20.6 - - + -
279O LEU 3.0 10.2 + - - +
280O PHE* 3.4 26.6 - - + +
281O PHE 3.1 21.6 + - - +
282O ILE* 5.8 0.2 - - - +
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Residues in contact with VAL 233 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166O LEU 3.0 10.0 + - - +
167O ILE* 3.5 20.8 - - + -
168O ILE* 3.2 21.9 + - - +
189O LEU* 3.8 16.6 - - + -
193O PHE* 3.6 31.6 - - + -
231O VAL* 4.2 3.8 - - + -
232O VAL* 1.3 78.1 - - - +
234O ILE* 1.3 69.0 + - - +
235O LEU* 3.6 28.7 - - + -
281O PHE* 3.4 27.4 - - + +
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Residues in contact with ILE 234 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O ILE* 3.5 21.3 - - + +
211O MET* 4.3 15.7 - - + -
215O LEU* 4.9 1.1 - - + -
232O VAL* 4.4 12.1 - - + +
233O VAL* 1.3 79.7 - - - +
235O LEU* 1.3 65.7 + - - +
236O SER* 4.4 10.5 - - - +
243O VAL* 4.1 29.4 - - + -
261O ILE* 3.4 41.1 - - + -
280O PHE* 6.3 0.4 - - + -
281O PHE 2.9 11.8 + - - +
282O ILE* 3.9 12.7 - - + -
283O GLN 3.0 30.0 + - - +
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Residues in contact with LEU 235 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167O ILE* 4.8 4.7 - - + -
168O ILE 2.8 13.6 + - - +
169O ASN* 3.7 22.0 - - + +
170O ASN 2.8 31.0 + - - +
179O ARG* 3.5 8.7 - - - +
182O SER* 3.8 8.7 - - - +
185O ASP* 3.7 15.9 - - + +
186O CYS* 3.7 33.9 - - + +
189O LEU* 4.4 2.2 - - + -
233O VAL* 3.6 22.4 - - + -
234O ILE* 1.3 79.3 - - - +
236O SER* 1.3 60.6 + - - +
283O GLN* 3.6 21.5 - - + -
350O VAL* 4.3 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