Contacts of the helix formed by residues 337 - 349 (chain B) in PDB entry 4PKO
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 GLY 337 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294B THR 3.7 13.2 - - - -
295B LEU 3.0 15.8 + - - -
296B THR 4.0 2.8 - - - -
297B GLY* 4.2 9.0 - - - -
336B VAL* 1.3 74.7 - - - +
338B GLU* 1.3 80.6 + - - +
340B ALA* 4.4 0.5 - - - +
341B ALA* 3.4 22.5 + - - +
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Residues in contact with GLU 338 (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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295B LEU 4.4 1.2 + - - -
335B GLY 4.2 7.4 + - - -
336B VAL* 3.1 9.5 - - - +
337B GLY* 1.3 94.9 - - - +
339B GLU* 1.3 73.7 + - - +
340B ALA* 3.6 20.2 - - + +
342B ILE* 3.0 31.0 - - - +
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Residues in contact with GLU 339 (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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338B GLU* 1.3 91.1 - - - +
340B ALA* 1.3 62.3 + - - +
341B ALA 3.5 0.4 - - - -
342B ILE* 4.0 7.4 - - + +
343B GLN* 3.1 40.3 + - + +
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Residues in contact with ALA 340 (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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337B GLY 4.4 0.4 - - - +
338B GLU* 3.5 23.4 - - + +
339B GLU* 1.3 81.4 - - - +
341B ALA* 1.3 62.7 + - - +
343B GLN* 5.1 0.2 - - - +
344B GLY* 3.6 13.2 + - - -
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Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR* 3.4 34.5 - - + +
297B GLY* 5.9 0.7 - - - -
337B GLY* 3.4 13.3 + - - +
340B ALA* 1.3 78.8 - - - +
342B ILE* 1.3 64.6 + - - +
344B GLY* 3.5 1.9 + - - -
345B ARG* 3.2 27.4 + - - +
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Residues in contact with ILE 342 (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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294B THR* 4.4 3.6 - - - +
295B LEU* 4.0 42.4 - - + +
335B GLY* 6.0 1.6 - - - -
338B GLU* 3.0 25.7 + - - +
339B GLU* 3.8 6.5 + - + +
340B ALA 3.4 0.6 - - - -
341B ALA* 1.3 75.9 - - - +
343B GLN* 1.3 64.5 + - - +
345B ARG* 2.9 10.0 + - - +
346B VAL* 2.7 44.5 + - + +
372B LEU* 3.8 31.6 - - + +
373B ALA* 5.0 2.5 - - + +
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Residues in contact with GLN 343 (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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339B GLU* 3.1 30.0 + - + +
342B ILE* 1.3 87.9 - - - +
344B GLY* 1.3 59.8 + - - +
346B VAL* 3.5 21.5 - - + +
347B ALA* 2.8 31.1 + - + +
350B ARG* 5.7 2.2 - - - +
373B ALA* 4.7 11.8 - - - +
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Residues in contact with GLY 344 (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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340B ALA 3.6 11.9 + - - -
341B ALA 3.5 6.6 + - - -
342B ILE 3.1 1.0 - - - -
343B GLN* 1.3 78.8 - - - +
345B ARG* 1.3 62.1 + - - +
347B ALA* 3.5 4.5 + - - +
348B GLN* 3.2 23.9 + - - +
209C GLU* 5.5 1.4 - - - +
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Residues in contact with ARG 345 (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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287B ALA* 3.7 4.0 + - - +
290B GLN* 2.9 51.1 + - - +
291B ASP* 2.6 30.9 + - - +
294B THR* 3.6 28.0 - - + +
341B ALA 3.2 13.0 + - - +
342B ILE* 2.9 11.1 + - - +
344B GLY* 1.3 76.7 - - - +
346B VAL* 1.3 58.8 + - - +
348B GLN* 3.0 37.8 + - - +
349B ILE* 3.1 30.8 + - - +
352B GLN* 5.9 0.2 - - - +
368B ARG* 5.7 4.4 - - - +
372B LEU* 5.2 9.9 - - + +
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Residues in contact with VAL 346 (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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342B ILE* 2.7 36.8 + - + +
343B GLN* 3.6 24.2 - - + +
344B GLY 3.3 0.2 - - - -
345B ARG* 1.3 78.9 - - - +
347B ALA* 1.3 59.1 + - - +
349B ILE* 2.9 25.2 - - + +
350B ARG* 3.0 49.4 + - - +
369B VAL* 4.6 8.3 - - + +
372B LEU* 4.6 17.3 - - + -
373B ALA* 4.9 9.0 - - + -
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Residues in contact with ALA 347 (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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343B GLN* 2.8 17.3 + - + +
344B GLY* 3.5 5.4 + - - +
345B ARG 3.4 0.2 - - - -
346B VAL* 1.3 78.2 - - - +
348B GLN* 1.3 59.2 + - - +
350B ARG* 3.1 28.8 - - + +
351B GLN* 4.3 1.4 + - - +
209C GLU* 4.4 9.1 - - + +
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Residues in contact with GLN 348 (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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344B GLY 3.2 15.0 + - - +
345B ARG* 3.0 66.0 + - - +
347B ALA* 1.3 76.9 - - - +
349B ILE* 1.3 68.0 + - - +
350B ARG 3.2 2.8 + - - -
351B GLN* 3.8 14.2 + - - +
352B GLN* 3.9 22.0 + - - +
368B ARG* 6.0 0.2 - - - +
205C ILE* 5.3 9.1 - - + +
209C GLU* 3.3 33.5 - - + +
210C THR 4.9 2.1 + - - -
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ASP* 5.1 2.2 - - - +
345B ARG* 3.1 18.1 + - - +
346B VAL* 2.9 27.4 - - + +
348B GLN* 1.3 83.9 - - - +
350B ARG* 1.3 61.5 + - - +
351B GLN 3.2 1.3 - - - -
352B GLN* 2.9 28.4 + - + +
353B ILE* 2.9 13.5 + - - +
365B LEU* 4.2 4.5 - - + -
368B ARG* 3.1 51.8 - - - +
369B VAL* 3.6 33.0 - - + +
372B LEU* 5.0 6.5 - - + -
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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