Contacts of the helix formed by residues 384 - 392 (chain A) in PDB entry 4DKK
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 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A ILE* 3.5 21.8 - - - +
377A GLU* 2.6 21.9 + - - -
378A LEU* 4.2 10.5 - - - +
383A THR* 1.3 78.1 - - - +
385A PRO* 1.3 66.4 - - - +
387A ALA* 3.0 29.6 + - - +
388A GLU* 2.9 28.4 + - - +
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Residues in contact with PRO 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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377A GLU* 3.3 20.4 - - + +
383A THR* 4.0 12.1 - - - +
384A SER* 1.3 84.5 - - - +
386A THR* 1.3 55.8 + - - +
388A GLU* 3.3 15.1 + - + +
389A THR* 2.9 33.8 + - - +
406A THR* 6.3 2.2 - - + -
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Residues in contact with THR 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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370A VAL* 4.2 20.6 - - + +
373A MET 5.2 1.4 - - - -
374A ILE* 3.7 19.7 - - + +
377A GLU* 2.7 30.7 + - - -
384A SER* 3.9 1.6 - - - -
385A PRO* 1.3 78.6 - - - +
387A ALA* 1.3 61.1 + - - +
389A THR* 3.2 7.3 + - - -
390A ILE* 3.2 26.8 + - + +
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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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374A ILE* 4.1 14.3 - - + +
384A SER* 3.0 27.9 + - - +
386A THR* 1.3 76.5 - - - +
388A GLU* 1.3 64.6 + - + +
390A ILE* 3.1 20.5 + - - +
391A LEU* 3.2 30.7 + - + +
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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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383A THR* 4.4 9.2 - - - +
384A SER 2.9 27.5 + - - +
385A PRO* 3.5 15.3 - - + +
386A THR 3.2 0.2 - - - -
387A ALA* 1.3 79.4 - - + +
389A THR* 1.3 55.8 + - - +
391A LEU* 3.8 6.1 - - + +
392A LYS* 2.9 30.9 + - - +
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Residues in contact with THR 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 PRO* 2.9 20.5 + - - +
386A THR* 3.6 8.4 - - - -
387A ALA 3.2 0.2 - - - -
388A GLU* 1.3 77.8 - - - +
390A ILE* 1.3 61.6 + - + +
392A LYS* 2.8 48.3 - - - +
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Residues in contact with ILE 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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367A LYS* 4.1 24.2 - - - +
370A VAL* 3.9 27.6 - - + -
374A ILE* 4.0 15.0 - - + -
386A THR* 3.2 19.2 + - + +
387A ALA* 3.1 8.2 + - - +
389A THR* 1.3 80.5 - - + +
391A LEU* 1.3 65.9 + - + +
392A LYS 4.3 3.3 - - - +
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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 ALA* 3.2 26.4 + - + +
388A GLU* 4.1 5.2 - - + +
390A ILE* 1.3 80.1 - - + +
392A LYS* 1.3 65.0 + - - +
393A ASN* 3.7 7.8 + - - +
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Residues in contact with LYS 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 16.0 + - - +
389A THR* 2.8 45.5 - - - +
390A ILE 4.3 3.1 - - - +
391A LEU* 1.3 78.6 - - - +
393A ASN* 1.3 63.2 + - - +
394A ASN* 5.5 10.4 + - - +
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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