Contacts of the helix formed by residues 471 - 481 (chain A) in PDB entry 6DEE
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 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A LYS* 4.2 14.7 - - + +
434A LYS* 3.3 31.8 + - - +
467A MET 3.8 1.9 + - - +
468A CYS 3.7 6.0 - - - +
469A SER 3.8 0.2 - - - -
470A LEU* 1.3 81.1 - - - +
472A ALA* 1.3 65.1 + - - +
473A ALA* 2.8 33.4 + - - +
474A ILE* 3.7 16.5 + - + +
475A ILE* 3.6 15.2 + - - +
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Residues in contact with ALA 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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471A ASP* 1.3 76.8 + - - +
473A ALA* 1.3 59.3 + - - +
474A ILE 3.2 0.4 - - - -
475A ILE* 3.1 18.7 + - + +
476A SER* 2.9 26.3 + - - -
514A MET* 5.6 6.9 - - + +
606A HIS* 3.7 29.5 - - + +
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Residues in contact with ALA 473 (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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434A LYS* 4.2 10.1 - - - +
438A PHE* 3.9 19.8 - - + -
471A ASP* 2.8 14.9 + - - +
472A ALA* 1.3 76.9 - - - +
474A ILE* 1.3 60.4 + - - +
476A SER* 3.2 9.1 + - - -
477A THR* 2.9 30.7 + - - -
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Residues in contact with ILE 474 (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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430A LYS* 5.1 3.1 - - - -
433A CYS* 4.0 22.7 - - + -
434A LYS* 4.3 14.1 - - + -
438A PHE* 4.1 18.4 - - + -
441A VAL* 4.4 20.2 - - + -
467A MET* 3.6 40.8 - - + +
468A CYS 5.0 0.2 - - - +
470A LEU* 4.1 19.5 - - + -
471A ASP* 3.8 13.2 - - + +
472A ALA 3.2 0.6 - - - -
473A ALA* 1.3 73.5 - - - +
475A ILE* 1.3 60.4 + - - +
477A THR* 3.3 2.8 + - - -
478A LEU* 2.9 37.7 + - + +
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Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A CYS* 3.7 38.8 - - + +
471A ASP 3.6 13.2 - - - +
472A ALA* 3.1 16.8 + - + +
474A ILE* 1.3 76.4 - - - +
476A SER* 1.3 59.0 + - - +
478A LEU* 3.4 7.8 + - - +
479A VAL* 2.9 30.0 + - + +
510A MET* 4.1 8.7 - - + +
511A VAL* 3.6 32.2 - - - +
513A SER* 6.3 0.4 - - - -
514A MET* 3.9 21.5 - - + +
604A PHE* 5.2 11.9 - - + -
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Residues in contact with SER 476 (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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472A ALA 2.9 13.8 + - - -
473A ALA* 3.2 12.1 + - - -
475A ILE* 1.3 76.5 - - - +
477A THR* 1.3 54.6 + - - +
479A VAL* 3.2 10.2 - - - +
480A SER* 2.7 38.5 + - - -
514A MET* 5.7 1.5 - - - +
516A GLU* 5.4 13.0 - - - -
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Residues in contact with THR 477 (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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438A PHE* 3.2 46.1 - - + -
441A VAL* 4.3 10.1 - - + -
442A LEU* 3.7 27.2 - - + +
473A ALA 2.9 16.1 + - - -
474A ILE* 3.5 8.3 - - - -
476A SER* 1.3 77.6 - - - +
478A LEU* 1.3 57.8 + - - +
480A SER* 3.2 7.1 + - - -
481A SER* 2.9 27.2 + - - -
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Residues in contact with LEU 478 (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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441A VAL* 3.6 26.7 - - + -
445A VAL* 3.6 22.7 - - + -
464A PHE* 4.3 21.5 - - + +
467A MET* 5.0 1.1 - - + -
468A CYS* 3.8 28.0 - - - -
474A ILE* 2.9 29.5 + - + +
475A ILE* 3.8 3.1 - - - +
477A THR* 1.3 76.3 - - - +
479A VAL* 1.3 61.3 + - - +
481A SER* 2.6 20.9 + - - -
483A LEU* 3.7 20.7 - - + +
484A PRO* 3.3 15.0 - - - +
511A VAL* 4.1 12.8 - - + -
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Residues in contact with VAL 479 (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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475A ILE* 2.9 17.8 + - + +
476A SER* 3.2 24.0 - - - +
478A LEU* 1.3 76.7 - - - +
480A SER* 1.3 61.8 + - - +
481A SER 3.3 4.6 - - - +
484A PRO* 4.1 11.0 - - + +
511A VAL* 3.7 24.9 - - + +
512A PHE* 3.7 31.4 - - + -
514A MET* 6.2 2.2 - - + -
516A GLU* 5.9 2.0 - - + -
517A ALA* 4.5 29.6 - - + +
519A PRO* 4.9 10.9 - - - +
564A HIS* 5.6 0.4 - - - +
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Residues in contact with SER 480 (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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476A SER* 2.7 24.8 + - - -
477A THR* 3.5 7.0 - - - -
478A LEU 3.2 0.4 - - - -
479A VAL* 1.3 79.3 - - - +
481A SER* 1.3 65.1 + - - +
517A ALA* 4.8 9.5 - - - +
519A PRO* 5.6 3.8 - - - -
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Residues in contact with SER 481 (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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442A LEU* 3.9 22.0 - - - -
445A VAL* 3.8 12.1 - - - +
477A THR 2.9 13.6 + - - -
478A LEU* 2.6 25.4 + - - -
479A VAL 3.9 2.8 - - - +
480A SER* 1.3 83.8 - - - +
482A VAL* 1.3 62.5 + - - +
483A LEU* 3.2 16.2 + - - +
484A PRO* 3.6 9.5 - - - +
485A VAL* 5.4 2.4 - - - +
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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