Contacts of the helix formed by residues 374 - 386 (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 ASP 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A LYS* 2.8 17.3 + - + +
373A ASP* 1.3 74.7 - - - +
375A GLU* 1.3 65.7 + - - +
376A ASP* 3.7 14.3 + - - +
377A THR* 2.6 40.1 + - - +
378A ARG* 3.1 22.8 + - - +
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Residues in contact with GLU 375 (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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374A ASP* 1.3 74.6 + - - +
376A ASP* 1.3 65.1 + - - +
378A ARG* 3.3 7.7 + - - +
379A GLU* 3.0 34.7 + - + +
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Residues in contact with ASP 376 (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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374A ASP* 3.4 14.8 + - - +
375A GLU* 1.3 77.6 - - - +
377A THR* 1.3 61.6 + - - +
379A GLU* 3.5 8.0 + - - +
380A ALA* 3.2 23.0 + - - +
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Residues in contact with THR 377 (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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369A ASP* 3.5 48.7 - - + +
372A LYS* 4.2 16.3 + - + +
374A ASP* 2.6 35.0 + - - +
375A GLU 3.2 0.2 - - - -
376A ASP* 1.3 76.3 - - - +
378A ARG* 1.3 63.6 + - - +
380A ALA* 3.2 9.1 + - + +
381A LEU* 3.1 22.1 + - + +
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Residues in contact with ARG 378 (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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369A ASP 5.4 0.4 + - - -
370A LEU* 2.9 35.6 + - - +
372A LYS 4.6 10.7 + - - +
374A ASP 3.1 16.0 + - - +
375A GLU* 3.8 6.7 - - - +
377A THR* 1.3 76.5 - - - +
379A GLU* 1.3 64.0 + - - +
381A LEU* 3.3 9.9 + - - +
382A VAL* 3.0 39.2 + - + +
390A VAL* 4.1 20.3 - - - +
394A ILE* 3.9 27.2 - - - +
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Residues in contact with GLU 379 (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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375A GLU* 3.0 26.6 + - + +
376A ASP* 3.8 8.7 - - - +
377A THR 3.3 0.2 - - - -
378A ARG* 1.3 81.8 - - - +
380A ALA* 1.3 58.6 + - - +
382A VAL* 3.2 14.5 + - - +
383A LYS* 2.9 29.5 + - - +
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Residues in contact with ALA 380 (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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376A ASP 3.2 10.9 + - - +
377A THR* 3.2 12.1 + - + +
379A GLU* 1.3 80.4 - - - +
381A LEU* 1.3 57.3 - - + +
383A LYS* 3.5 7.1 + - - +
384A LYS* 3.1 27.9 + - - +
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Residues in contact with LEU 381 (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* 4.4 3.1 - - + -
366A ASP* 4.1 31.4 - - - +
369A ASP* 3.9 17.3 - - + +
370A LEU* 3.5 48.0 - - + +
377A THR 3.1 17.1 + - - +
378A ARG* 3.6 16.8 - - - +
379A GLU 3.2 0.2 - - - -
380A ALA* 1.3 76.7 - - + +
382A VAL* 1.3 60.2 + - - +
384A LYS* 3.1 4.5 + - + -
385A PHE* 2.8 48.0 + - + +
390A VAL* 4.0 11.4 - - + -
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Residues in contact with VAL 382 (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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378A ARG* 3.0 27.8 + - + +
379A GLU* 3.5 17.7 - - - +
381A LEU* 1.3 76.2 - - - +
383A LYS* 1.3 58.9 + - - +
386A GLY* 2.6 30.2 + - - +
387A ALA* 3.7 28.5 - - + +
390A VAL* 4.0 18.6 - - + -
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Residues in contact with LYS 383 (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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359A TYR* 4.6 6.6 - - - -
379A GLU 2.9 15.7 + - - +
380A ALA* 3.8 7.9 - - - +
382A VAL* 1.3 78.0 - - - +
384A LYS* 1.3 63.1 + - - +
386A GLY 4.6 0.7 + - - -
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Residues in contact with LYS 384 (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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359A TYR* 3.4 8.1 - - - -
360A PRO* 3.4 35.0 - - + +
361A ILE 5.3 0.9 - - - -
363A SER* 4.5 2.2 + - - -
366A ASP* 2.8 36.0 + - - +
380A ALA 3.1 18.0 + - - +
381A LEU* 3.1 5.8 + - + +
383A LYS* 1.3 79.2 - - - +
385A PHE* 1.3 81.2 + - + +
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Residues in contact with PHE 385 (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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355A ARG* 4.9 4.0 - - - -
359A TYR* 3.1 17.7 - - + -
360A PRO* 3.3 37.5 - - + -
361A ILE 3.5 12.1 - - - -
362A TRP* 3.6 47.8 - + + -
366A ASP* 3.4 37.0 - - + -
381A LEU* 2.8 27.7 + - + +
384A LYS* 1.3 90.1 - - + +
386A GLY* 1.3 63.2 + - - +
389A ASN* 3.1 32.3 + - + +
390A VAL* 4.1 5.4 - - + -
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Residues in contact with GLY 386 (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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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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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