Contacts of the helix formed by residues 384 - 395 (chain A) in PDB entry 4KPE
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 ILE 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A ARG* 3.6 19.1 - - + +
381A VAL* 2.7 18.6 + - - +
383A SER* 1.3 83.8 - - - +
385A LEU* 1.3 64.1 + - - +
386A ASP 3.3 2.7 - - - -
387A GLU* 3.3 26.3 + - + +
388A VAL* 3.0 40.3 + - + +
409A TYR* 3.4 38.8 - - + -
411A PHE* 4.3 12.1 - - + -
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Residues in contact with LEU 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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381A VAL* 2.7 30.7 + - + +
382A ILE* 3.6 17.2 + - + +
383A SER 3.9 0.2 - - - -
384A ILE* 1.3 72.5 - - - +
386A ASP* 1.3 65.3 + - - +
388A VAL* 3.0 5.4 + - + +
389A ILE* 2.9 44.2 + - + +
427A LEU* 4.0 33.7 - - + +
429A ASN 4.7 8.5 - - - +
430A THR* 6.1 0.2 - - + -
393B ARG* 3.5 44.2 - - - +
424B LEU* 6.2 0.9 - - + -
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Residues in contact with ASP 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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384A ILE 3.3 0.8 - - - -
385A LEU* 1.3 80.0 - - - +
387A GLU* 1.3 65.4 + - - +
389A ILE* 3.7 7.6 + - - +
390A ALA* 3.1 26.0 + - - +
393B ARG* 2.7 42.0 + - - -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A SER 4.9 0.3 - - - +
384A ILE* 3.3 41.4 - - + +
386A ASP* 1.3 83.9 + - - +
388A VAL* 1.3 60.4 + - - +
390A ALA* 3.6 9.8 - - + +
391A LEU* 3.1 25.8 + - - +
409A TYR* 3.3 30.1 + - + +
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A VAL* 4.5 16.2 - - + -
384A ILE* 3.0 42.8 + - + +
385A LEU* 3.0 7.8 + - + +
387A GLU* 1.3 75.8 - - - +
389A ILE* 1.3 66.4 + - + +
390A ALA 3.2 0.2 - - - -
391A LEU* 3.4 6.7 + - - +
392A ILE* 3.0 43.7 + - + +
405A LEU* 4.0 24.2 - - + -
409A TYR* 4.8 4.9 - - + -
411A PHE* 4.5 5.8 - - + -
419A ILE* 4.1 14.8 - - + -
424B LEU* 5.6 2.9 - - + -
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Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 2.9 36.1 + - + +
386A ASP* 3.9 7.0 - - - +
388A VAL* 1.3 76.2 - - + +
390A ALA* 1.3 57.3 + - - +
392A ILE* 3.3 9.6 + - - +
393A ARG* 2.9 28.8 + - + +
427A LEU* 3.4 32.3 - - + -
389B ILE* 3.9 32.3 - - + -
393B ARG* 4.1 23.1 - - + -
424B LEU* 5.7 5.4 - - + -
427B LEU* 4.6 9.4 - - + +
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Residues in contact with ALA 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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386A ASP 3.1 17.5 + - - +
387A GLU* 3.6 12.3 - - + +
389A ILE* 1.3 81.9 - - - +
391A LEU* 1.3 55.8 + - - +
393A ARG* 3.4 8.3 - - - +
394A ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 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 GLU 3.1 15.0 + - - +
388A VAL* 3.6 4.9 - - - +
389A ILE 3.2 0.2 - - - -
390A ALA* 1.3 75.0 - - - +
392A ILE* 1.3 66.4 + - + +
394A ALA* 3.2 6.7 + - - +
395A SER* 2.8 29.8 + - - -
401A ALA* 3.8 5.8 - - - +
404A ASN* 3.5 43.3 + - + +
405A LEU* 3.7 29.4 - - + +
408A SER* 3.9 8.1 - - - -
409A TYR* 3.8 29.2 - - + -
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A VAL* 3.0 37.7 + - + +
389A ILE* 3.7 7.0 - - - +
391A LEU* 1.3 78.9 - - + +
393A ARG* 1.3 65.4 + - - +
394A ALA 3.0 1.1 - - - -
395A SER* 2.9 15.4 + - - -
401A ALA* 4.3 15.7 - - + -
405A LEU* 4.7 3.4 - - + -
419A ILE* 4.6 8.1 - - + -
420A VAL* 4.4 9.0 - - + -
424B LEU* 3.6 50.7 - - + +
425B TYR* 4.5 2.2 - - - -
427B LEU* 4.0 14.8 - - + +
428B THR* 3.1 28.4 - - + +
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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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389A ILE* 2.9 20.8 + - + +
390A ALA* 3.4 11.9 - - - +
392A ILE* 1.3 79.2 - - - +
394A ALA* 1.3 58.6 + - - +
395A SER 3.6 4.0 + - - +
385B LEU* 3.3 33.7 - - - +
386B ASP* 2.5 48.7 + - - +
389B ILE* 4.5 11.9 - - + -
427B LEU* 4.2 18.1 + - + +
428B THR* 5.4 0.2 - - - -
430B THR* 4.8 14.3 + - - +
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Residues in contact with ALA 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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390A ALA 3.0 18.5 + - - +
391A LEU* 3.4 7.9 - - - +
392A ILE 3.0 0.4 - - - -
393A ARG* 1.3 76.8 - - - +
395A SER* 1.3 62.0 + - - +
396A GLU* 4.0 2.9 + - - +
400A ASP* 5.0 0.9 - - - +
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Residues in contact with SER 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A LEU 2.8 15.8 + - - -
392A ILE* 2.9 9.4 + - - +
393A ARG 4.1 2.9 - - - +
394A ALA* 1.3 82.0 - - - +
396A GLU* 1.3 63.7 + - - +
397A ASN 3.4 0.4 - - - -
400A ASP* 3.8 4.7 - - - -
401A ALA* 3.4 40.6 - - - -
404A ASN* 3.9 9.4 - - - +
428B THR* 3.3 18.6 - - - +
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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