Contacts of the strand formed by residues 232 - 236 (chain K) in PDB entry 1I43
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 LEU 232 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K LEU* 4.6 22.0 - - + +
202K ASN 3.1 17.6 + - - +
203K LEU* 3.2 15.5 - - + +
204K PHE* 2.5 36.9 + - - +
227K HIS* 5.1 0.9 - - + +
230K GLY 5.2 2.7 - - - +
231K ALA* 1.3 79.1 - - - +
233K VAL* 1.3 58.4 - - - +
253K ASP* 3.3 32.3 - - + +
254K LEU* 5.1 1.6 - - + -
280K LEU* 4.0 32.1 - - + -
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Residues in contact with VAL 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K LEU* 4.9 1.1 - - - -
204K PHE* 3.5 13.0 - - + +
219K ILE* 5.6 0.4 - - + +
222K VAL* 4.5 4.5 - - + +
223K SER* 3.9 33.4 - - - +
226K CYS* 3.6 31.2 - - + -
227K HIS* 4.4 2.9 - - - +
232K LEU* 1.3 77.8 - - - +
234K CYS* 1.3 63.4 + - - +
235K ILE* 4.2 21.8 - - + -
252K ALA* 4.2 7.2 - - - -
253K ASP* 2.6 49.2 + - - +
254K LEU* 3.0 7.4 + - - +
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Residues in contact with CYS 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K MET* 4.0 10.8 - - - -
203K LEU* 4.1 18.4 - - + -
204K PHE 3.0 8.3 + - - +
205K PHE* 3.5 26.4 - - + -
206K THR 3.1 25.5 + - - +
232K LEU 4.2 0.2 - - - -
233K VAL* 1.3 75.5 - - - +
235K ILE* 1.3 68.4 + - - +
254K LEU* 3.2 25.6 - - + +
256K LEU* 3.8 23.8 - - - -
274K ILE* 6.4 0.4 - - - -
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Residues in contact with ILE 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204K PHE* 5.1 1.8 - - + -
206K THR* 3.0 32.8 - - + +
208K SER* 4.2 20.6 - - - +
217K VAL* 5.3 3.4 - - + -
219K ILE* 4.1 24.9 - - + -
222K VAL* 5.7 0.9 - - + -
233K VAL* 4.2 13.5 - - + -
234K CYS* 1.3 79.5 - - - +
236K ASP* 1.3 68.2 + - - +
237K GLY 3.4 5.3 + - - +
245K GLN* 4.5 6.7 - - - +
247K ALA* 4.0 20.0 - - + -
252K ALA* 3.9 19.7 - - + -
254K LEU 2.9 7.6 + - - +
255K VAL* 3.2 5.5 - - - -
256K LEU 3.0 23.9 + - - -
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Residues in contact with ASP 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K SER* 5.6 0.7 + - - -
205K PHE* 4.4 15.7 - - + -
206K THR 2.8 9.4 + - - +
207K GLU* 3.3 27.1 - - + +
208K SER 3.4 16.5 + - - +
209K PRO 4.4 1.9 - - - +
235K ILE* 1.3 72.1 - - - +
237K GLY* 1.3 56.4 + - - +
238K THR* 2.5 34.2 + - - -
239K PHE* 5.8 0.2 - - - -
256K LEU* 3.0 28.5 - - + +
500K PLP 3.3 31.6 + - - +
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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