Contacts of the helix formed by residues 472 - 489 (chain A) in PDB entry 1D0N
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 THR 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A GLY 4.6 2.9 + - - +
470A GLN 4.5 6.1 - - - +
471A SER* 1.3 74.6 + - - +
473A GLN* 1.3 66.2 + - - +
474A ASP* 2.7 25.1 + - - -
475A GLU* 3.0 20.4 + - - +
476A VAL* 2.9 19.1 + - - +
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Residues in contact with GLN 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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471A SER 3.6 6.9 + - - -
472A THR* 1.3 70.6 - - - +
474A ASP* 1.3 57.5 + - - +
476A VAL* 3.2 16.1 + - - +
477A ALA* 2.8 35.0 + - - +
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Residues in contact with ASP 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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427A GLY* 4.9 7.4 - - - +
472A THR* 2.7 28.6 + - - -
473A GLN* 1.3 75.4 + - - +
475A GLU* 1.3 74.3 + - - +
477A ALA* 3.7 5.3 - - - +
478A ALA* 2.8 30.0 + - - +
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Residues in contact with GLU 475 (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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425A VAL* 3.5 21.2 - - + +
427A GLY* 3.0 29.8 + - - +
444A GLY 4.4 3.3 - - - +
445A ASP* 4.8 1.9 - - - -
446A SER* 4.1 4.3 + - - +
471A SER* 4.0 12.3 + - - +
472A THR* 3.0 19.0 + - - +
474A ASP* 1.3 91.5 - - - +
476A VAL* 1.3 62.4 + - - +
478A ALA* 3.7 6.6 - - - +
479A SER* 2.9 29.3 + - - -
526A ARG* 2.8 42.0 + - - -
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A SER* 3.8 5.6 - - - +
467A GLN* 3.4 35.0 - - + +
468A GLY 4.8 3.6 - - - +
471A SER* 3.5 32.5 - - - +
472A THR 2.9 18.5 + - - +
473A GLN* 3.6 20.2 - - - +
475A GLU* 1.3 74.8 - - - +
477A ALA* 1.3 66.3 + - - +
479A SER* 2.6 24.4 + - - -
480A ALA* 3.2 8.4 + - + +
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Residues in contact with ALA 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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473A GLN* 2.8 18.9 + - - +
474A ASP* 3.7 5.6 - - - +
476A VAL* 1.3 80.3 - - - +
478A ALA* 1.3 61.3 + - - +
480A ALA* 3.4 6.9 + - - +
481A ILE* 3.3 31.1 + - + +
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Residues in contact with ALA 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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425A VAL* 4.1 5.6 - - + -
427A GLY 3.6 22.9 - - - +
428A SER* 4.7 7.9 - - - -
474A ASP 2.8 19.2 + - - +
475A GLU* 3.7 6.1 - - - +
476A VAL 3.2 0.2 - - - -
477A ALA* 1.3 75.2 - - - +
479A SER* 1.3 59.0 + - - +
481A ILE* 3.4 8.8 + - - +
482A LEU* 2.9 37.1 + - + +
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Residues in contact with SER 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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425A VAL* 3.7 25.5 - - - +
446A SER* 3.7 11.8 + - - -
447A TYR 5.1 0.7 - - - -
448A ILE* 5.4 2.1 - - - +
465A ASN* 3.4 24.0 + - - -
467A GLN* 4.2 3.5 - - - +
475A GLU 2.9 14.3 + - - -
476A VAL* 2.6 24.8 + - - -
478A ALA* 1.3 74.5 - - - +
480A ALA* 1.3 54.3 + - - +
482A LEU* 3.3 3.5 + - - +
483A THR* 2.7 38.2 + - - -
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Residues in contact with ALA 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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465A ASN* 3.5 14.8 - - - +
467A GLN* 4.8 6.1 - - - +
476A VAL* 3.2 7.0 + - + +
477A ALA* 3.7 11.7 - - - +
479A SER* 1.3 80.4 + - - +
481A ILE* 1.3 65.5 + - + +
483A THR* 3.2 5.3 + - - -
484A ALA* 3.0 22.7 + - - +
496A GLN* 5.2 1.9 + - - -
697A LEU* 6.1 5.6 - - + -
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Residues in contact with ILE 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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477A ALA* 3.3 20.3 + - + +
478A ALA* 3.7 9.0 - - - +
480A ALA* 1.3 79.5 - - + +
482A LEU* 1.3 59.5 + - + +
484A ALA* 3.1 9.0 + - + +
485A GLN* 2.8 48.9 + - + +
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Residues in contact with LEU 482 (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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425A VAL* 4.1 22.2 - - + -
428A SER* 4.0 25.6 - - - +
429A ASN* 4.1 19.3 - - - -
430A LYS* 4.1 28.8 + - + +
448A ILE* 4.3 6.1 - - + +
478A ALA* 2.9 21.7 + - + +
479A SER* 3.8 4.7 - - - +
481A ILE* 1.3 77.8 - - + +
483A THR* 1.3 57.1 + - - +
485A GLN* 3.4 21.3 + - + +
486A LEU* 2.9 28.9 + - - +
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Residues in contact with THR 483 (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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448A ILE* 4.0 17.9 - - - +
463A ILE* 4.0 17.1 - - + +
465A ASN* 3.4 29.9 + - + +
479A SER 2.7 20.3 + - - -
480A ALA* 3.2 12.1 - - - -
482A LEU* 1.3 74.1 - - - +
484A ALA* 1.3 66.8 + - - +
486A LEU* 3.2 3.3 + - - +
487A ASP* 3.0 22.3 + - - +
496A GLN* 3.6 33.7 - - + +
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Residues in contact with ALA 484 (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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480A ALA 3.0 12.4 + - - +
481A ILE* 3.5 11.2 - - + +
483A THR* 1.3 78.5 - - - +
485A GLN* 1.3 57.6 + - + +
487A ASP* 3.4 4.7 + - - +
488A GLU* 3.0 27.5 + - - +
496A GLN* 4.2 17.0 - - - +
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Residues in contact with GLN 485 (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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481A ILE* 2.8 34.9 + - + +
482A LEU* 3.7 20.3 - - + +
484A ALA* 1.3 75.8 - - - +
486A LEU* 1.3 59.0 + - - +
488A GLU* 3.7 10.1 - - + +
489A GLU* 2.9 32.3 + - - +
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Residues in contact with LEU 486 (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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423A TRP* 4.1 21.3 - - + -
430A LYS* 5.1 13.7 - - - +
448A ILE* 3.4 27.4 - - + -
450A LEU* 4.6 13.0 - - + -
463A ILE* 3.8 22.2 - - + -
482A LEU 2.9 17.6 + - - +
483A THR 3.2 4.9 + - - +
485A GLN* 1.3 72.2 - - - +
487A ASP* 1.3 67.0 + - - +
489A GLU* 3.3 25.7 + - + +
490A LEU* 3.1 40.7 + - + +
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Residues in contact with ASP 487 (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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463A ILE* 3.7 14.0 - - + +
483A THR 3.0 12.8 + - - +
484A ALA* 3.5 9.3 - - - +
486A LEU* 1.3 77.4 - - - +
488A GLU* 1.3 61.7 + - - +
490A LEU* 3.1 11.5 + - - +
491A GLY 3.2 0.7 + - - -
492A GLY* 2.8 37.2 + - - -
494A PRO* 3.5 21.6 - - - +
496A GLN* 3.6 20.6 - - - +
721A LYS* 2.8 27.8 + - - -
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Residues in contact with GLU 488 (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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484A ALA 3.0 16.6 + - - +
485A GLN* 3.7 11.4 - - - +
486A LEU 3.2 0.2 - - - -
487A ASP* 1.3 77.1 + - - +
489A GLU* 1.3 59.0 + - - +
490A LEU 2.9 9.3 + - - -
491A GLY* 3.1 12.8 + - - -
492A GLY* 4.2 4.4 + - - +
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Residues in contact with GLU 489 (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* 4.5 10.7 + - - -
485A GLN* 2.9 17.5 + - - +
486A LEU* 3.6 31.2 - - + +
488A GLU* 1.3 75.9 - - + +
490A LEU* 1.3 63.8 + - + +
491A GLY 3.5 0.2 - - - -
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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