Contacts of the helix formed by residues 342 - 353 (chain B) in PDB entry 3K6G
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 GLU 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336B PHE* 4.3 0.2 - - - -
339B ASN 3.1 21.0 + - - +
340B SER* 4.2 5.1 - - - +
341B GLY* 1.3 73.9 - - - +
343B LEU* 1.3 58.2 + - - +
344B GLU 4.8 0.4 - - - +
345B ALA* 3.7 18.0 - - + +
346B THR* 2.6 37.2 + - - -
355B ARG* 3.0 28.4 + - - -
389B ASN* 4.4 1.2 - - - +
392B ARG* 3.4 41.2 + - - -
281E THR 3.9 7.0 - - - +
282E THR* 4.4 8.5 - - + +
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Residues in contact with LEU 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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317B ILE* 3.7 41.7 - - + -
321B LEU* 4.4 11.2 - - + -
336B PHE* 3.9 16.6 - - + -
341B GLY 3.3 3.4 + - - +
342B GLU* 1.3 71.3 - - - +
344B GLU* 1.3 61.4 + - - +
346B THR* 3.7 0.3 - - - -
347B SER* 2.9 33.3 + - - -
281E THR* 3.3 44.0 + - + +
282E THR* 5.6 0.2 - - - -
283E ILE* 5.7 2.2 - - + -
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Residues in contact with GLU 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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342B GLU* 3.5 0.6 - - - +
343B LEU* 1.3 80.4 - - - +
345B ALA* 1.3 57.5 - - - +
347B SER* 3.7 7.2 - - - -
348B ALA* 2.9 38.7 + - + +
281E THR* 4.9 1.8 + - - -
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Residues in contact with ALA 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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339B ASN* 4.3 5.2 - - + +
342B GLU* 3.7 36.0 + - + +
343B LEU 3.4 0.6 - - - -
344B GLU* 1.3 76.0 - - - +
346B THR* 1.3 61.0 + - - +
348B ALA* 3.4 6.3 + - - +
349B PHE* 2.9 31.2 + - - +
355B ARG* 4.0 24.0 - - + +
356B ALA* 5.7 6.5 - - + +
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Residues in contact with THR 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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321B LEU* 4.3 1.3 - - + -
335B ALA* 4.0 27.1 - - + -
336B PHE* 3.4 38.1 - - + +
339B ASN* 3.3 26.0 - - - +
342B GLU 2.6 26.4 + - - -
343B LEU 3.7 2.7 - - - -
345B ALA* 1.3 76.3 - - - +
347B SER* 1.3 63.9 + - - +
349B PHE* 3.1 4.0 + - - +
350B LEU* 2.9 33.0 + - + +
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Residues in contact with SER 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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321B LEU* 3.9 28.1 - - - +
324B LYS* 4.0 17.2 + - - -
325B PHE* 3.6 5.8 - - - -
343B LEU* 2.9 22.4 + - - -
344B GLU* 3.7 11.1 + - - -
346B THR* 1.3 77.6 - - - +
348B ALA* 1.3 61.6 + - - +
350B LEU* 3.3 3.9 + - - -
351B ALA* 3.1 23.4 + - - +
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Residues in contact with ALA 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 GLU* 2.9 26.1 + - + +
345B ALA* 3.8 6.3 - - - +
347B SER* 1.3 76.7 - - - +
349B PHE* 1.3 62.3 + - - +
351B ALA* 3.3 7.1 + - - +
352B SER* 3.0 28.7 + - - +
354B GLN 3.9 3.1 - - - +
356B ALA* 4.6 23.6 - - + +
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Residues in contact with PHE 349 (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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335B ALA* 4.8 1.3 - - + -
339B ASN* 3.9 22.7 - - - +
345B ALA 2.9 19.1 + - - +
346B THR 3.1 4.5 + - - +
348B ALA* 1.3 77.2 - - - +
350B LEU* 1.3 64.4 + - + +
353B GLY* 2.6 65.0 + - - -
354B GLN* 3.5 19.4 + - - +
355B ARG* 4.0 3.4 - - + -
361B ILE* 3.7 34.8 - - + -
313E LEU* 3.4 28.5 - - + -
315E LEU* 3.9 22.9 - - + +
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Residues in contact with LEU 350 (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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321B LEU* 4.2 17.5 - - + -
325B PHE* 3.8 38.3 - - + +
327B LEU* 3.6 27.2 - - + +
331B THR* 5.1 1.3 - - + +
332B VAL* 4.7 6.3 - - + -
335B ALA* 3.8 25.1 - - + -
346B THR* 2.9 32.7 + - + +
347B SER 3.3 4.0 + - - +
349B PHE* 1.3 80.7 - - + +
351B ALA* 1.3 62.2 + - - +
353B GLY 4.3 1.6 + - - -
315E LEU* 3.9 25.1 - - + +
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Residues in contact with ALA 351 (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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324B LYS* 5.9 1.8 - - - +
325B PHE* 3.5 22.2 - - + -
347B SER 3.1 17.1 + - - +
348B ALA* 3.7 6.7 - - - +
349B PHE 3.2 0.2 - - - -
350B LEU* 1.3 79.3 - - - +
352B SER* 1.3 59.0 + - - +
306D ALA* 4.9 13.2 - - - +
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Residues in contact with SER 352 (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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348B ALA* 3.0 16.5 + - - +
351B ALA* 1.3 77.0 - - - +
353B GLY* 1.3 60.6 + - - +
354B GLN* 3.1 34.4 + - - +
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Residues in contact with GLY 353 (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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349B PHE* 2.6 43.4 + - - -
350B LEU 4.3 1.8 + - - -
351B ALA 3.8 1.0 - - - -
352B SER* 1.3 72.7 - - - +
354B GLN* 1.3 58.6 + - - +
315E LEU* 4.6 12.1 - - - -
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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