Contacts of the helix formed by residues 342 - 353 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336C PHE* 4.3 0.2 - - - -
339C ASN 3.1 13.2 + - - +
340C SER* 3.2 11.1 - - - +
341C GLY* 1.3 74.5 - - - +
343C LEU* 1.3 59.7 + - - +
344C GLU 3.6 0.4 - - - +
345C ALA* 3.4 19.7 - - + +
346C THR* 2.7 37.5 + - - -
355C ARG* 3.1 33.9 + - - -
389C ASN* 4.4 1.0 - - - +
392C ARG* 3.3 39.2 + - + -
281F THR 3.7 6.5 - - - +
282F THR* 4.4 9.0 - - - +
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C ILE* 3.4 39.7 - - + -
321C LEU* 4.7 7.8 - - + +
336C PHE* 4.1 13.9 - - + -
341C GLY 3.2 3.4 + - - +
342C GLU* 1.3 72.4 - - - +
344C GLU* 1.3 67.4 + - + +
346C THR* 3.8 1.0 - - - -
347C SER* 2.8 35.2 + - - -
281F THR* 2.8 51.6 + - + +
283F ILE* 5.4 2.9 - - + -
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Residues in contact with GLU 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C GLU* 3.6 0.4 - - - +
343C LEU* 1.3 86.9 - - + +
345C ALA* 1.3 58.4 + - - +
347C SER* 3.2 11.4 + - - -
348C ALA* 2.8 32.8 + - - +
281F THR* 4.6 7.0 + - - +
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Residues in contact with ALA 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C ASN* 4.6 2.9 - - - +
342C GLU* 3.4 40.1 + - + +
343C LEU 3.3 0.2 - - - -
344C GLU* 1.3 77.8 - - - +
346C THR* 1.3 58.0 + - - +
348C ALA* 3.4 5.6 + - - +
349C PHE* 2.9 28.8 + - - +
355C ARG* 3.9 21.6 - - + +
356C ALA* 5.3 4.0 + - - +
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Residues in contact with THR 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C LEU* 4.8 1.1 - - + -
332C VAL 4.9 0.2 - - - +
335C ALA* 4.0 15.5 - - + +
336C PHE* 3.4 51.6 - - + +
339C ASN* 3.3 21.5 - - - +
342C GLU 2.7 28.3 + - - -
343C LEU 3.8 2.0 - - - -
345C ALA* 1.3 71.1 - - - +
347C SER* 1.3 67.7 + - - +
349C PHE* 3.1 6.5 + - - +
350C LEU* 3.1 32.3 + - + +
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Residues in contact with SER 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C LEU* 4.0 28.0 - - - +
324C LYS* 4.7 6.8 - - - -
325C PHE* 3.6 17.2 - - - -
343C LEU* 2.8 22.4 + - - -
344C GLU* 3.5 15.3 + - - -
346C THR* 1.3 78.9 - - - +
348C ALA* 1.3 61.4 + - - +
350C LEU 3.6 0.5 + - - -
351C ALA* 3.5 15.1 + - - +
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Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C GLU* 2.8 18.3 + - - +
345C ALA* 3.8 5.4 - - - +
347C SER* 1.3 77.1 - - - +
349C PHE* 1.3 62.1 + - - +
351C ALA* 3.4 19.6 + - - +
352C SER* 3.4 13.5 + - - -
354C GLN 3.7 2.5 - - - +
356C ALA* 4.1 26.2 - - + +
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Residues in contact with PHE 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C ALA* 4.4 12.6 - - + -
339C ASN* 3.5 26.5 - - - +
345C ALA 2.9 17.6 + - - +
346C THR 3.1 4.5 + - - +
348C ALA* 1.3 75.1 - - - +
350C LEU* 1.3 78.7 + - + +
353C GLY* 2.8 50.9 + - - -
354C GLN* 3.5 26.9 - - - +
355C ARG* 3.9 3.5 - - + +
361C ILE* 3.6 39.9 - - + -
313F LEU 5.9 4.7 - - - -
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Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C LEU* 4.7 11.2 - - + -
325C PHE* 3.9 41.0 - - + -
327C LEU* 3.6 27.8 - - + +
331C THR* 4.9 5.6 - - + +
332C VAL* 4.6 14.8 - - + -
335C ALA* 3.8 25.4 - - + -
346C THR* 3.1 30.4 + - + +
347C SER 4.1 0.2 - - - +
348C ALA 3.4 0.2 - - - -
349C PHE* 1.3 85.4 - - + +
351C ALA* 1.3 65.4 + - - +
353C GLY* 4.1 3.1 + - - -
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C PHE* 3.7 19.4 - - + -
347C SER 3.5 9.9 + - - +
348C ALA* 3.4 13.2 + - - +
349C PHE 3.1 0.8 - - - -
350C LEU* 1.3 83.8 - - - +
352C SER* 1.3 62.7 + - - +
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Residues in contact with SER 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C ALA 3.4 6.1 + - - -
351C ALA* 1.3 78.2 - - - +
353C GLY* 1.3 60.1 + - - +
354C GLN* 3.3 30.6 + - - +
356C ALA* 6.0 0.5 - - - -
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Residues in contact with GLY 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349C PHE* 2.8 36.8 + - - -
350C LEU 4.1 2.8 + - - -
351C ALA 3.5 1.8 + - - -
352C SER* 1.3 72.0 - - - +
354C GLN* 1.3 67.4 + - - +
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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