Contacts of the strand formed by residues 233 - 239 (chain B) in PDB entry 4KPF
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 LYS 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LYS* 3.3 9.1 - - - +
228B ALA* 3.1 15.4 + - - -
231B THR* 3.1 21.9 + - - +
232B GLY* 1.3 78.7 - - - +
234B GLY* 1.3 58.9 + - - +
327B PHE 3.3 9.9 - - - +
328B ASN* 3.2 36.4 + - - +
339B GLN* 3.6 30.0 + - - +
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Residues in contact with GLY 234 (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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224B GLU* 3.6 15.5 - - - -
227B LYS* 4.9 1.8 - - - -
228B ALA* 3.9 11.9 - - - -
233B LYS* 1.3 76.1 - - - +
235B ARG* 1.3 59.4 + - - -
326B ASN* 3.2 7.8 - - - +
327B PHE* 2.7 37.3 + - - +
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Residues in contact with ARG 235 (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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221B GLY* 5.9 0.2 - - - -
224B GLU* 2.9 43.0 + - - +
234B GLY* 1.3 72.2 - - - -
236B VAL* 1.3 61.1 + - - +
237B VAL* 5.8 1.1 - - + +
324B ASN* 4.2 22.7 - - + +
325B TYR 3.6 2.9 - - - -
326B ASN* 3.5 25.6 - - - +
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Residues in contact with VAL 236 (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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211B PRO* 5.9 1.1 - - + -
213B PHE* 5.7 2.5 - - + -
219B ILE* 3.4 30.1 - - + -
220B GLN 3.0 27.6 - - - +
221B GLY* 4.1 2.5 - - - +
224B GLU* 4.6 2.7 - - + -
225B ILE* 4.1 16.8 - - + -
234B GLY 4.1 0.8 - - - -
235B ARG* 1.3 74.9 - - - +
237B VAL* 1.3 66.9 + - - +
238B VAL* 4.7 2.2 - - + -
324B ASN* 3.4 8.5 - - - +
325B TYR* 2.9 53.6 + - + +
327B PHE* 4.1 21.3 - - + -
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Residues in contact with VAL 237 (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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218B ILE 3.7 0.9 - - - +
219B ILE* 3.4 4.7 - - - +
220B GLN* 2.8 60.3 + - + +
235B ARG* 5.8 0.9 - - + +
236B VAL* 1.3 75.9 - - - +
238B VAL* 1.3 67.2 + - - +
239B ARG* 4.5 1.1 - - + +
322B GLN* 2.8 42.8 - - + +
323B ILE 3.5 3.4 - - - +
324B ASN* 3.7 18.4 - - - +
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Residues in contact with VAL 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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213B PHE* 3.5 34.5 - - + -
217B ALA* 4.2 12.6 - - + -
218B ILE 3.3 8.5 - - - +
219B ILE* 4.6 5.8 - - + -
236B VAL* 4.2 2.9 + - + -
237B VAL* 1.3 76.2 - - - +
239B ARG* 1.3 63.2 + - - +
260B PRO* 3.6 29.9 - - + +
261B TYR* 4.6 3.1 - - + +
322B GLN* 3.1 5.6 - - - +
323B ILE* 2.8 51.7 + - + +
325B TYR* 4.3 16.4 - - + -
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Residues in contact with ARG 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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217B ALA* 3.4 4.7 - - - +
218B ILE* 2.8 55.6 + - + +
220B GLN* 4.4 22.9 + - - +
237B VAL* 4.2 2.9 - - + -
238B VAL* 1.3 74.8 - - - +
240B SER* 1.3 70.3 + - - +
260B PRO* 5.0 0.7 - - - -
313B ASN* 5.0 6.1 + - - -
316B PHE* 3.2 49.5 - - + +
321B LEU 3.9 3.1 - - - -
322B GLN* 3.2 32.2 + - + +
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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