Contacts of the helix formed by residues 392 - 401 (chain D) in PDB entry 5UQ9
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 392 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379D ALA* 3.6 16.6 - - + +
382D ARG* 2.3 36.6 + - - +
386D LEU* 4.2 15.2 - - + +
388D ASN 4.1 1.0 + - - -
389D LEU 3.4 14.0 + - - +
390D LEU 3.2 1.4 - - - -
391D LEU* 1.3 78.6 - - - +
393D ASP* 1.3 57.4 + - - +
394D PHE* 3.1 24.1 + - - +
395D PHE* 3.5 16.4 - - + -
396D LYS* 2.8 37.3 + - - +
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Residues in contact with ASP 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C LYS* 5.3 6.2 + - - -
382D ARG* 6.0 1.6 - - - +
391D LEU 4.0 2.6 + - - +
392D ASP* 1.3 78.0 + - - +
394D PHE* 1.3 64.0 + - - +
396D LYS* 3.3 24.1 + - - +
397D SER* 2.9 26.2 + - - -
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Residues in contact with PHE 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D GLU* 5.8 4.9 - - + -
328D TYR* 3.7 22.9 - - - -
375D LYS* 3.8 46.0 - - + -
382D ARG* 4.3 14.1 - - - +
392D ASP* 3.1 12.2 + - - +
393D ASP* 1.3 78.2 - - - +
395D PHE* 1.3 73.3 + + + +
397D SER* 3.0 10.3 + - - -
398D ALA* 2.9 32.2 + - + +
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Residues in contact with PHE 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D ILE* 4.0 24.9 - - + -
372D PHE* 3.4 31.2 - + - -
375D LYS* 3.5 40.8 - - + -
376D ILE* 3.6 5.4 - - + -
379D ALA* 3.5 15.3 - - + -
382D ARG* 5.5 0.2 - - - -
389D LEU* 3.5 44.0 - - + +
390D LEU* 4.9 3.4 - - - -
392D ASP* 3.4 21.5 + - + +
393D ASP 3.3 0.4 - - - -
394D PHE* 1.3 88.9 - + - +
396D LYS* 1.3 59.7 - - - +
398D ALA* 3.7 3.3 - - - +
399D VAL* 3.0 34.1 + - - +
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Residues in contact with LYS 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C LYS* 3.3 47.3 + - + +
304C LEU* 3.8 20.0 - - + +
390D LEU* 3.9 12.9 + - - +
391D LEU* 5.3 2.7 - - - +
392D ASP 2.8 22.3 + - - +
393D ASP* 3.7 25.5 + - - +
395D PHE* 1.3 75.1 - - - +
397D SER* 1.3 64.8 + - - +
399D VAL* 3.7 3.4 + - - +
400D GLU* 3.0 43.7 + - - +
430D TYR* 5.6 1.2 + - - -
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Residues in contact with SER 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D ASP 2.9 12.8 + - - -
394D PHE* 3.0 20.6 + - - -
396D LYS* 1.3 79.9 - - - +
398D ALA* 1.3 58.9 + - - +
400D GLU* 3.5 13.8 - - - +
401D ASN* 2.9 45.5 + - - -
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Residues in contact with ALA 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D TYR* 3.8 29.4 - - + +
332D ILE* 3.8 9.2 - - + -
394D PHE* 2.9 25.8 + - + +
395D PHE* 3.7 6.5 - - - +
396D LYS 3.3 0.4 - - - -
397D SER* 1.3 75.3 + - - +
399D VAL* 1.3 65.3 + - - +
401D ASN* 3.4 5.4 + - - +
402D CYS* 3.2 31.1 + - - -
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Residues in contact with VAL 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LEU* 6.1 0.9 - - + -
329D ALA* 4.7 11.8 - - + +
332D ILE* 4.0 30.3 - - + -
333D ILE* 5.1 2.0 - - + -
390D LEU* 4.2 12.1 - - + -
395D PHE 3.0 16.5 + - - +
396D LYS* 4.1 4.7 - - - +
398D ALA* 1.3 75.7 - - - +
400D GLU* 1.3 63.8 + - - +
402D CYS* 3.3 5.3 + - - +
403D GLN* 3.2 23.1 + - - +
406D TRP* 4.3 15.4 - - + -
430D TYR* 3.6 42.0 - - + +
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Residues in contact with GLU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C LYS* 3.4 45.0 + - + +
396D LYS* 3.0 35.4 + - + +
397D SER* 3.5 11.1 - - - +
398D ALA 3.2 0.2 - - - -
399D VAL* 1.3 79.0 - - - +
401D ASN* 1.3 67.8 + - - +
402D CYS 3.1 1.4 + - - -
403D GLN* 3.4 13.1 + - - +
404D ASP* 5.1 2.6 + - - +
430D TYR* 5.4 1.1 + - - -
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Residues in contact with ASN 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D LYS* 3.5 18.9 - - - +
397D SER* 2.9 33.1 + - - +
398D ALA* 4.1 5.1 - - - +
399D VAL 3.4 0.2 - - - -
400D GLU* 1.3 83.4 - - - +
402D CYS* 1.3 60.4 + - - +
403D GLN 3.6 0.4 - - - -
404D ASP* 5.6 3.3 - - - +
405D SER* 5.3 0.5 + - - -
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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