Contacts of the strand formed by residues 295 - 300 (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 ILE 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B LEU* 3.4 22.7 - - + +
263B LEU* 4.0 24.7 - - + +
282B PHE* 4.4 4.7 - - + -
285B LEU* 3.7 28.7 - - + -
290B VAL* 4.5 6.1 - - + -
293B LYS* 3.5 12.6 - - + +
294B PRO* 1.3 74.4 - - - +
296B LEU* 1.3 63.1 + - - +
297B VAL* 3.8 12.6 + - + -
324B TYR* 3.4 34.5 - - + +
326B PRO 3.2 7.1 + - - -
327B ILE* 3.6 16.5 - - + +
328B PHE* 3.1 22.1 + - - +
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Residues in contact with LEU 296 (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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261B LEU 2.9 12.4 + - - +
262B ILE* 3.3 13.0 - - + +
263B LEU 2.9 23.5 + - - -
294B PRO 4.2 0.4 - - - -
295B ILE* 1.3 71.6 - - - +
297B VAL* 1.3 67.0 + - - +
298B THR* 4.3 7.6 - - + -
328B PHE* 4.3 13.7 - - + -
329B ASP* 3.1 42.8 - - + +
330B VAL 4.2 0.4 - - - +
331B ILE* 4.6 9.6 - - + -
344B LEU* 3.8 16.2 - - + -
347B LYS* 4.1 15.7 - - + -
348B ILE* 3.7 30.1 - - + -
351B LEU* 4.8 9.3 - - + +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.4 21.8 - - + +
265B ILE* 4.4 14.8 - - + -
278B LEU* 4.9 0.7 - - + -
282B PHE* 4.5 2.5 - - + -
295B ILE* 4.2 18.6 - - + +
296B LEU* 1.3 75.6 - - - +
298B THR* 1.3 68.3 + - - +
299B LEU* 4.1 1.1 - - - +
316B VAL* 3.8 26.5 - - + -
320B SER* 4.1 19.7 - - - +
327B ILE* 4.6 4.0 - - + -
329B ASP 3.0 7.0 + - - +
330B VAL* 3.3 21.4 - - + +
331B ILE 3.1 23.9 + - - -
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Residues in contact with THR 298 (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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195B LEU* 3.7 5.0 - - + +
262B ILE* 3.8 20.6 - - + -
263B LEU 2.9 15.6 + - - -
264B VAL* 3.6 20.1 - - - +
265B ILE 3.1 21.8 + - - -
296B LEU* 4.3 4.7 - - + +
297B VAL* 1.3 79.7 - - - +
299B LEU* 1.3 59.8 + - - +
300B ASN 3.1 4.3 + - - -
331B ILE* 3.3 11.9 - - + -
333B ILE* 3.6 21.3 - - + +
344B LEU* 3.9 24.5 - - + -
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Residues in contact with LEU 299 (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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265B ILE* 3.8 18.8 - - + -
267B SER* 3.5 31.2 - - - -
274B LEU* 4.6 2.5 - - + -
297B VAL* 4.1 2.6 + - - +
298B THR* 1.3 67.4 - - - +
300B ASN* 1.3 60.2 + - - +
302B ILE* 3.2 7.2 - - + +
309B LEU* 4.3 15.0 - - + -
312B LYS* 4.2 12.6 - - + +
313B LEU* 4.1 35.9 - - + +
316B VAL* 3.8 27.4 - - + -
330B VAL* 5.5 2.4 - - + +
331B ILE 2.9 10.3 + - - +
332B PRO* 4.0 10.5 - - + -
333B ILE 2.8 26.2 + - - +
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Residues in contact with ASN 300 (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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190B SER 3.0 28.1 + - - +
191B GLY* 3.2 23.8 + - - -
195B LEU* 5.2 0.8 - - - +
264B VAL* 3.9 10.7 - - + +
265B ILE 2.9 11.3 + - - +
266B ASP* 4.1 0.4 - - - -
267B SER* 2.7 33.1 + - - -
298B THR 3.1 2.2 + - - +
299B LEU* 1.3 70.6 - - - +
301B LYS* 1.3 83.0 + - - +
302B ILE 3.3 2.7 - - - -
333B ILE* 3.4 16.5 - - + +
334B SER* 3.3 3.3 - - - -
335B ALA* 2.9 35.4 + - - +
336B LEU* 5.8 1.4 - - - +
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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