Contacts of the helix formed by residues 386 - 398 (chain A) 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 GLY 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A TYR* 3.7 18.6 - - - -
382A VAL* 2.6 25.7 + - - -
385A PHE* 1.3 77.8 - - - +
387A ALA* 1.3 66.1 + - - -
388A GLN 3.3 3.5 + - - -
389A ASN 3.4 0.6 + - - -
390A VAL* 3.2 21.1 + - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A VAL* 3.7 24.6 - - + +
386A GLY* 1.3 71.9 - - - -
388A GLN* 1.3 66.6 + - + +
390A VAL* 3.4 6.1 + - - +
391A ALA* 3.0 24.1 + - - +
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Residues in contact with GLN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A GLY 3.3 0.6 - - - -
387A ALA* 1.3 81.2 - - + +
389A ASN* 1.3 64.0 - - - +
391A ALA* 3.1 11.3 + - - +
392A ARG* 3.0 54.5 + - - +
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Residues in contact with ASN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A SER* 5.3 0.2 + - - -
342A GLU* 4.4 0.7 - - - +
355A ARG* 3.1 27.7 + - - +
357A ASP* 2.8 23.0 + - - -
359A TYR* 3.5 10.7 - - - +
362A TRP* 3.9 8.8 + - - +
385A PHE* 3.1 33.4 + - + +
386A GLY 3.4 2.2 + - - +
388A GLN* 1.3 78.4 - - - +
390A VAL* 1.3 57.7 + - - +
392A ARG* 3.0 34.5 + - - +
393A ARG* 2.9 29.1 + - - +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A TRP* 4.1 10.5 - - + -
370A LEU* 3.8 22.0 - - + -
378A ARG* 4.1 18.8 - - - +
381A LEU* 3.8 33.0 - - + +
382A VAL* 4.0 8.3 - - + -
385A PHE* 4.1 7.6 - - + -
386A GLY 3.2 16.5 + - - +
387A ALA* 3.7 9.6 - - - +
389A ASN* 1.3 76.4 - - - +
391A ALA* 1.3 62.8 + - - +
393A ARG* 3.1 3.1 + - - +
394A ILE* 3.1 30.2 + - + +
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Residues in contact with ALA 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A ALA 3.0 14.0 + - - +
388A GLN* 3.4 16.2 - - - +
390A VAL* 1.3 78.5 - - - +
392A ARG* 1.3 62.2 + - + +
394A ILE* 3.5 12.9 + - - +
395A GLU* 3.2 22.2 + - - +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A SER* 4.5 7.0 + - - -
342A GLU* 3.2 30.6 + - - +
355A ARG* 4.5 2.4 - - - +
357A ASP* 4.9 3.0 + - - +
388A GLN* 3.0 40.8 + - - +
389A ASN* 3.0 29.4 + - - +
390A VAL 3.2 0.2 - - - -
391A ALA* 1.3 75.1 - - + +
393A ARG* 1.3 61.0 + - - +
395A GLU* 3.5 7.1 + - - +
396A PHE* 2.8 30.2 + - - +
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LEU 2.8 30.7 + - - -
338A LYS* 4.2 5.5 - - - +
340A SER* 2.8 41.9 + - - +
362A TRP* 3.5 49.4 - - + +
367A ASP* 2.8 34.5 + - - +
370A LEU* 3.5 18.8 - - + -
389A ASN 2.9 16.8 + - - +
390A VAL 3.1 6.0 + - - +
392A ARG* 1.3 74.9 - - - +
394A ILE* 1.3 60.5 + - - +
396A PHE* 3.2 6.5 + - - +
397A ARG* 2.8 57.4 + - + +
309D ASP* 4.8 0.8 + - - -
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU* 3.8 23.1 - - + +
371A GLN* 5.5 6.7 - - - +
378A ARG* 3.9 30.7 - - - +
390A VAL* 3.1 19.9 + - + +
391A ALA* 3.7 10.3 - - - +
393A ARG* 1.3 76.8 - - - +
395A GLU* 1.3 59.8 + - - +
397A ARG* 3.7 3.6 - - - +
398A LYS* 2.9 29.1 + - + +
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ALA 3.2 14.3 + - - +
392A ARG* 3.6 8.7 - - - +
394A ILE* 1.3 81.4 - - - +
396A PHE* 1.3 57.6 + - - +
398A LYS* 2.8 72.4 - - - +
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Residues in contact with PHE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A PHE 4.3 4.5 - - - -
337A LEU* 3.8 25.8 - - + -
340A SER* 3.3 35.0 - - - +
341A GLY* 3.6 9.6 - - - -
392A ARG 2.8 18.8 + - - +
393A ARG* 3.5 21.1 - - - +
395A GLU* 1.3 79.6 - - - +
397A ARG* 1.3 69.9 + - - +
398A LYS* 3.6 5.2 + - - +
282D THR* 5.2 2.9 - - + -
283D ILE 3.3 25.1 - - - -
284D GLY* 4.6 2.5 - - - -
285D MSE 3.6 58.2 + - + +
288D LEU* 4.7 3.8 - - + -
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Residues in contact with ARG 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ARG* 4.6 3.0 - - - +
367A ASP* 3.5 15.0 + - - +
370A LEU* 4.4 5.4 - - + -
371A GLN* 5.0 7.2 - - - +
393A ARG* 2.8 71.6 + - + +
394A ILE* 3.9 4.3 - - - +
396A PHE* 1.3 79.1 - - - +
398A LYS* 1.3 70.6 + - - +
285D MSE 3.7 22.4 - - - +
309D ASP* 2.7 42.8 + - - -
316E PRO* 2.8 50.5 + - - +
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Residues in contact with LYS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ILE 2.9 13.3 + - - +
395A GLU* 2.8 49.1 - - - +
396A PHE* 4.2 4.4 + - - +
397A ARG* 1.3 87.1 - - - +
285D MSE 5.7 1.7 - - - +
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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