Contacts of the strand formed by residues 226 - 232 (chain B) in PDB entry 3KXK
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 ARG 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B ASN 4.2 21.8 + - - +
180B PRO* 4.1 28.9 - - - +
222B PRO* 3.6 2.8 - - - +
223B ILE* 2.8 38.1 + - - +
224B ASN 3.4 0.4 + - - -
225B ASN* 1.3 85.8 - - + +
227B LYS* 1.3 62.6 + - - +
228B ILE* 3.9 8.7 + - + +
349B TYR* 3.5 33.7 - - + +
352B ALA* 4.4 12.4 + - - +
353B THR* 4.0 21.9 + - - +
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Residues in contact with LYS 227 (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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179B ILE* 3.4 50.6 - - + +
180B PRO* 3.5 12.6 - - - +
220B ALA* 3.6 34.2 - - + +
221B ILE 4.0 6.7 - - - +
222B PRO* 4.4 10.8 - - + -
225B ASN 4.3 0.8 + - - -
226B ARG* 1.3 73.7 + - - +
228B ILE* 1.3 61.8 + - - +
229B MET* 5.2 3.2 - - - +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 4.3 0.2 - - - -
180B PRO* 4.0 13.7 - - + +
182B ILE* 3.8 28.7 - - + -
220B ALA* 3.1 3.9 - - - -
221B ILE* 2.8 47.9 + - + +
223B ILE* 3.7 20.4 - - + -
226B ARG* 4.2 11.7 - - + +
227B LYS* 1.3 80.0 - - - +
229B MET* 1.3 64.1 + - - +
230B LEU* 3.5 9.8 + - + -
348B ILE* 3.7 24.2 - - + +
349B TYR* 4.6 2.0 - - - -
352B ALA* 3.6 30.7 - - + -
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Residues in contact with MET 229 (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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179B ILE* 3.8 12.5 - - + +
180B PRO 3.0 17.8 + - - +
181B SER* 4.2 9.4 + - - +
182B ILE* 2.8 30.3 + - - +
218B ARG* 3.5 31.6 - - + +
219B TYR 3.8 12.3 - - - -
220B ALA* 3.5 22.0 - - + +
227B LYS* 5.2 3.6 - - - +
228B ILE* 1.3 70.4 - - - +
230B LEU* 1.3 64.6 + - - +
231B VAL* 4.1 15.5 - - + -
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Residues in contact with LEU 230 (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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182B ILE* 3.5 21.5 - - + +
184B ILE* 4.7 7.0 - - + -
196B PHE* 3.5 17.5 - - + -
199B LEU* 3.7 31.2 - - + -
200B THR* 4.2 5.6 - - + -
218B ARG* 3.3 4.3 - - - -
219B TYR 2.9 41.3 + - - +
221B ILE* 3.5 42.2 - - + -
228B ILE* 4.3 11.7 - - + +
229B MET* 1.3 78.4 - - - +
231B VAL* 1.3 62.1 + - - +
262B ILE* 5.1 3.4 - - + -
348B ILE* 5.0 7.2 - - + -
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Residues in contact with VAL 231 (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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97B HIS 5.9 0.7 - - - +
181B SER* 3.9 21.8 - - - +
182B ILE 2.8 14.0 + - - +
183B GLY* 3.5 5.4 - - - -
184B ILE* 2.8 28.5 + - - +
196B PHE* 4.5 2.2 - - - -
217B LYS 4.0 5.4 - - - +
218B ARG* 4.0 41.5 - - + +
229B MET* 4.1 5.8 - - + -
230B LEU* 1.3 78.1 - - - +
232B ASP* 1.3 60.8 + - - +
233B THR* 3.0 23.7 + - + +
254B GLU* 6.1 2.2 - - + +
258B SER* 4.8 4.3 - - - +
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Residues in contact with ASP 232 (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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97B HIS* 2.8 37.9 + - - +
184B ILE* 4.0 6.0 - - - +
192B LYS* 3.3 27.7 - - - +
193B THR* 3.4 28.6 + - - +
196B PHE* 3.8 34.5 - - + +
217B LYS* 3.1 41.2 + - + +
231B VAL* 1.3 68.5 - - - +
233B THR* 1.3 54.5 + - - +
235B PRO* 5.6 0.3 - - - +
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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