Contacts of the helix formed by residues 383 - 392 (chain A) in PDB entry 4WIK
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 SER 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A TYR 3.3 3.1 + - - -
382A VAL* 1.3 76.5 - - - +
384A ASN* 1.4 58.8 + - - +
385A GLU* 4.0 1.5 + - - -
386A LEU* 3.4 9.6 + - - +
387A LEU* 3.0 28.8 + - - +
402A VAL* 3.7 4.3 - - - +
459B LEU* 3.4 24.9 - - - -
461B GLU* 2.9 44.2 + - - -
464B ALA* 4.8 0.7 - - - -
474B ARG* 2.9 13.9 + - - +
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Residues in contact with ASN 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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383A SER* 1.4 71.7 - - - +
385A GLU* 1.3 67.7 + - - +
387A LEU* 3.3 5.8 + - - +
388A GLU* 3.0 29.6 + - - +
400A ALA 3.7 18.5 - - - +
401A VAL* 3.4 9.2 - - - +
402A VAL* 2.7 35.8 + - - +
457B ASP 3.1 26.7 + - - -
458B GLY* 3.8 0.2 - - - -
459B LEU 2.9 37.2 + - - +
460B PRO* 3.5 5.7 - - - +
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Residues in contact with GLU 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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383A SER* 3.3 0.6 - - - +
384A ASN* 1.3 85.1 + - - +
386A LEU* 1.4 58.8 + - - +
388A GLU* 3.6 10.8 - - - +
389A GLU* 3.2 27.9 + - - +
460B PRO* 3.3 13.5 - - - +
461B GLU* 2.7 52.2 + - + +
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Residues in contact with LEU 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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381A TYR 4.9 0.2 - - - +
382A VAL* 3.8 31.9 - - + -
383A SER* 3.4 19.6 + - - +
384A ASN 3.3 0.6 - - - -
385A GLU* 1.4 76.2 - - - +
387A LEU* 1.3 58.9 + - - +
389A GLU* 3.3 11.3 + - + +
390A ALA* 2.9 30.7 + - - +
438A LEU* 4.2 22.2 - - + +
439A THR* 4.6 5.8 - - + -
461B GLU* 4.5 1.0 + - - -
474B ARG* 3.5 37.7 - - - +
478B PRO* 3.8 28.0 - - + -
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Residues in contact with LEU 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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375A VAL* 3.9 18.8 - - + -
378A LEU* 4.0 17.3 - - + -
382A VAL* 4.4 2.9 - - + +
383A SER 3.0 16.5 + - - +
384A ASN 3.5 5.6 - - - +
386A LEU* 1.3 76.6 - - - +
388A GLU* 1.4 59.7 + - - +
390A ALA* 3.6 3.3 + - - -
391A PHE* 3.2 56.2 + - + +
400A ALA* 4.4 3.0 - - + +
401A VAL 3.4 36.3 - - - +
402A VAL* 4.0 9.2 - - + -
416A VAL* 3.8 21.3 - - + -
438A LEU* 4.2 11.9 - - + -
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Residues in contact with GLU 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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384A ASN* 3.0 18.2 + - - +
385A GLU* 3.6 12.2 - - - +
387A LEU* 1.4 74.3 - - - +
389A GLU* 1.4 57.4 + - - +
391A PHE 3.3 1.9 + - - -
392A SER* 2.9 33.7 + - - -
397A ILE* 3.7 40.0 - - + +
398A GLU 5.1 3.1 - - - +
399A ARG* 5.3 0.9 - - - -
400A ALA* 3.8 21.3 + - + +
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Residues in contact with GLU 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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385A GLU 3.2 15.5 + - - +
386A LEU* 3.3 12.5 + - + +
388A GLU* 1.4 77.3 - - - +
390A ALA* 1.3 59.5 + - - +
392A SER* 2.8 21.1 + - - +
393A GLN* 4.4 5.4 + - - +
478B PRO* 5.2 11.7 - - + +
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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 LEU 2.9 16.7 + - - +
387A LEU 3.8 3.6 - - - +
388A GLU 3.3 0.2 - - - -
389A GLU* 1.3 77.5 - - - +
391A PHE* 1.3 60.9 + - + +
392A SER 3.5 0.2 - - - -
393A GLN* 3.2 27.2 - - - +
394A PHE* 3.7 0.3 - - - -
436A PHE* 3.3 10.6 - - + -
438A LEU* 2.6 48.9 - - + -
478B PRO* 3.7 10.1 - - + +
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Residues in contact with PHE 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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373A LEU* 5.9 1.3 - - + -
375A VAL* 3.7 20.2 - - + -
387A LEU* 3.2 49.4 + - + +
390A ALA* 1.3 76.6 - - + +
392A SER* 1.4 62.8 + - - +
393A GLN 3.2 2.9 - - - -
394A PHE* 3.3 37.2 + + - -
395A GLY 3.8 0.2 + - - -
397A ILE* 3.5 13.3 - - + +
416A VAL* 3.9 26.7 - - + -
418A PHE* 3.6 10.8 - + + -
427A ALA* 4.4 10.8 - - + -
431A CYS* 4.1 10.3 - - - -
436A PHE* 3.7 26.7 - + - -
438A LEU* 4.2 7.6 - - + -
445A VAL* 3.8 16.6 - - + -
447A VAL* 4.2 9.4 - - + -
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Residues in contact with SER 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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388A GLU* 2.9 15.9 + - - -
389A GLU* 2.8 29.2 + - - +
391A PHE* 1.4 72.1 - - - +
393A GLN* 1.4 59.9 + - - +
394A PHE 3.1 4.9 - - - -
395A GLY* 2.9 24.6 + - - +
397A ILE* 3.8 10.3 - - - -
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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