Contacts of the helix formed by residues 327 - 338 (chain B) in PDB entry 1CK4
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 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B PHE* 3.9 16.4 - - + -
283B ILE* 3.9 17.3 - - + -
316B PHE* 3.9 39.7 - - + -
317B ASN 5.8 2.0 - - - +
318B VAL* 3.9 32.5 - - + -
324B LEU* 3.0 16.8 + - + +
326B THR* 1.3 85.8 + - - +
328B VAL* 1.3 66.5 + - - +
329B LYS 3.2 3.4 + - - -
330B ALA* 3.3 8.2 + - + +
331B LEU* 3.0 26.3 + - + +
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Residues in contact with VAL 328 (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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168B PHE* 4.0 21.8 - - + +
171B ASP* 3.8 45.8 - - + +
172B LEU* 4.1 11.0 - - - +
175B ARG* 4.5 5.0 + - - +
324B LEU 3.6 4.8 + - - +
325B VAL* 3.5 33.0 - - + +
326B THR 3.4 1.0 - - - -
327B ILE* 1.3 78.3 - - - +
329B LYS* 1.3 76.3 + - - +
331B LEU* 4.1 2.5 - - - +
332B GLY* 3.1 21.8 + - - -
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Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 3.3 25.4 + - - +
325B VAL* 4.6 7.7 + - - +
326B THR 4.7 4.8 + - - +
327B ILE 3.2 1.0 - - - -
328B VAL* 1.3 95.2 - - - +
330B ALA* 1.3 58.5 + - - +
333B GLU* 3.0 36.1 + - - +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE* 4.0 18.4 - - + -
326B THR 5.3 1.3 + - - +
327B ILE* 3.3 11.4 + - + +
329B LYS* 1.3 75.3 - - - +
331B LEU* 1.3 61.2 + - - +
333B GLU* 3.2 14.0 - - - +
334B ARG* 2.9 48.3 + - - +
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 4.2 16.2 - - + -
172B LEU* 3.6 34.8 - - + -
253B VAL* 5.0 11.0 - - + -
281B PHE* 3.9 36.1 - - + -
283B ILE* 4.5 11.7 - - + -
316B PHE* 3.8 23.5 - - + -
327B ILE* 3.0 21.4 + - + +
328B VAL* 4.1 2.7 - - - +
330B ALA* 1.3 77.2 - - - +
332B GLY* 1.3 58.2 + - - +
334B ARG* 3.2 0.6 + - - -
335B ILE* 2.9 38.4 + - + +
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Residues in contact with GLY 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 4.2 14.1 - - - +
175B ARG* 4.2 17.6 + - - -
176B MET* 5.5 0.4 - - - -
328B VAL 3.1 15.7 + - - -
329B LYS 4.0 0.9 - - - -
330B ALA 3.3 0.2 - - - -
331B LEU* 1.3 80.0 - - - +
333B GLU* 1.3 58.7 + - - +
335B ILE* 2.7 22.7 - - - +
336B PHE* 3.4 14.7 - - - +
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Residues in contact with GLU 333 (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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175B ARG* 4.0 19.4 + - - +
329B LYS* 3.0 27.0 + - - +
330B ALA* 3.2 18.2 - - - +
332B GLY* 1.3 75.1 - - - +
334B ARG* 1.3 64.2 + - + +
336B PHE* 3.4 5.0 + - - +
337B ALA* 3.0 31.8 + - + +
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Residues in contact with ARG 334 (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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281B PHE* 3.5 14.5 - - + -
312B GLU 4.0 8.3 + - - -
313B LYS* 3.1 58.2 + - + +
315B PHE 4.9 1.0 + - - -
316B PHE* 3.1 31.5 - - - -
330B ALA* 2.9 30.4 + - - +
331B LEU* 3.9 3.4 - - - +
333B GLU* 1.3 77.6 + - + +
335B ILE* 1.3 66.3 + - - +
336B PHE 3.1 2.0 - - - -
337B ALA* 4.6 1.6 - - + -
338B LEU* 3.0 46.4 + - + +
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Residues in contact with ILE 335 (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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147B LEU* 3.8 12.2 - - + +
149B ILE* 3.7 21.5 - - + -
172B LEU* 5.3 0.7 - - + -
176B MET* 4.6 7.0 - - + -
251B VAL* 3.5 41.1 - - + -
253B VAL* 5.4 1.3 - - + -
279B GLN* 4.8 8.0 + - - +
281B PHE* 3.6 16.5 - - + -
331B LEU* 2.9 23.2 + - + +
332B GLY* 2.7 35.4 - - - +
334B ARG* 1.3 75.2 - - - +
336B PHE* 1.3 80.0 + - + +
337B ALA 3.7 0.3 + - - -
338B LEU 4.7 1.4 + - - -
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Residues in contact with PHE 336 (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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145B THR* 2.6 53.1 + - + +
147B LEU* 3.5 21.9 - - + +
149B ILE* 4.2 5.2 - - + -
176B MET* 3.8 27.6 - - + -
183B THR* 3.5 29.2 - - + -
332B GLY* 3.4 19.5 - - - +
333B GLU* 3.4 6.8 + - - +
334B ARG 3.1 0.4 - - - -
335B ILE* 1.3 95.2 - - + +
337B ALA* 1.3 58.0 + - - +
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Residues in contact with ALA 337 (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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333B GLU* 3.0 17.9 + - + +
334B ARG* 3.3 1.8 + - + -
336B PHE* 1.3 79.7 - - - +
338B LEU* 1.3 68.8 + - - +
339B GLU 3.2 1.6 + - - -
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLN* 3.7 11.5 - - - +
281B PHE* 3.8 6.5 - - + -
310B PRO* 4.6 9.9 - - + -
313B LYS* 3.3 53.4 - - + +
314B HIS* 3.4 31.0 - - + +
334B ARG* 3.0 27.1 + - + +
337B ALA* 1.3 79.0 - - - +
339B GLU 1.3 48.2 + - - +
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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