Contacts of the helix formed by residues 466 - 472 (chain A) in PDB entry 4TVJ
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 MET 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A SER 5.1 0.4 - - - +
389A THR* 3.1 41.3 - - - +
390A HIS 4.1 1.3 - - - +
391A ALA* 3.6 26.7 - - + -
392A PRO* 4.8 1.8 - - + -
427A TRP* 3.6 3.3 - - - -
464A ALA* 3.3 6.1 - - + +
465A ASP* 1.3 87.6 + - - +
467A SER* 1.3 67.4 + - - +
468A SER 3.2 0.9 - - - +
469A LYS* 3.0 30.6 + - + +
470A SER 3.5 4.0 + - - -
521A MET 5.0 0.7 - - - +
522A ALA* 5.0 0.4 - - - -
523A PRO* 3.5 28.7 - - + -
541A ALA* 3.8 22.2 - - + +
556A TYR* 4.0 28.3 - - + -
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Residues in contact with SER 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 2.7 39.5 + - - -
389A THR* 3.0 17.8 + - - -
390A HIS 3.6 2.1 + - - -
399A MET* 3.5 7.8 - - - +
427A TRP* 3.4 37.6 - - - +
466A MET* 1.3 70.7 - - - +
468A SER* 1.3 59.3 + - - +
470A SER* 3.3 6.1 + - - -
471A ALA* 2.8 27.5 + - - +
485A LEU* 4.3 3.6 - - - +
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Residues in contact with SER 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR 4.0 0.5 + - - -
390A HIS* 3.5 27.6 - - - -
391A ALA* 2.8 23.3 + - - +
394A HIS* 2.6 27.3 + - - -
397A TYR* 3.3 16.6 + - - -
399A MET* 4.2 1.6 - - - -
467A SER* 1.3 78.1 + - - +
469A LYS* 1.3 66.4 + - - +
471A ALA* 4.0 3.6 - - - -
472A ASN* 2.9 28.2 + - - -
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Residues in contact with LYS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A HIS* 3.6 18.8 + - + -
464A ALA* 4.0 10.8 - - + -
466A MET* 3.0 17.6 + - + +
468A SER* 1.3 80.4 + - - +
470A SER* 1.3 61.7 - - - +
472A ASN* 3.7 7.9 + - - +
473A TYR* 3.2 28.9 - - + -
554A LEU* 4.5 5.3 - - - +
556A TYR* 2.9 33.1 + - + +
557A ASN 2.8 29.0 + - - +
558A GLU* 2.6 29.9 + - - +
601A 09L 4.0 18.2 - - + -
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Residues in contact with SER 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A TRP* 3.1 38.8 + - - +
428A HIS 3.9 1.1 - - - -
429A GLY* 3.3 27.2 - - - -
464A ALA* 3.3 11.1 + - - +
466A MET 3.5 1.4 + - - -
467A SER 3.3 5.5 + - - -
468A SER 3.2 0.2 - - - -
469A LYS* 1.3 78.9 - - - +
471A ALA* 1.3 60.2 + - - +
473A TYR* 2.9 19.8 + - - +
474A CYS 3.8 0.2 + - - -
485A LEU* 4.0 2.5 - - - -
601A 09L 2.7 27.0 + - - -
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Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A TYR* 3.6 12.1 - - - +
399A MET* 3.6 28.9 - - - -
467A SER 2.8 18.0 + - - +
468A SER* 3.2 0.6 + - - -
470A SER* 1.3 73.1 - - - +
472A ASN* 1.3 62.5 + - - +
474A CYS* 3.0 21.0 + - - +
485A LEU* 3.9 9.8 - - + +
577A PHE* 3.7 11.0 - - + -
602A GOL 2.8 18.2 + - - -
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Residues in contact with ASN 472 (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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394A HIS* 3.3 37.4 + - - +
396A ASP* 5.2 0.3 - - - +
397A TYR* 2.9 29.5 + - - -
468A SER 2.9 17.0 + - - +
469A LYS* 3.8 9.0 + - - +
470A SER 3.2 0.2 - - - -
471A ALA* 1.3 75.0 - - - +
473A TYR* 1.3 62.3 + - + +
474A CYS 3.2 0.2 - - - -
475A PHE* 3.2 19.4 + - - -
602A GOL 3.1 32.3 + - - +
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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