Contacts of the helix formed by residues 464 - 479 (chain A) in PDB entry 6EBT
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 GLY 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A LEU 3.9 0.2 + - - -
460A ASN* 3.0 20.4 + - - +
461A PRO 4.9 0.2 - - - -
462A HIS 3.7 0.8 - - - -
463A ILE* 1.3 81.8 - - - +
465A TYR* 1.3 66.8 + - - -
466A ASP 3.4 2.7 - - - -
467A LYS 4.8 0.4 - - - -
468A ALA* 3.1 21.8 + - - +
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Residues in contact with TYR 465 (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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460A ASN* 4.2 28.5 + - + +
464A GLY* 1.3 71.6 - - - -
466A ASP* 1.3 81.0 + - - +
468A ALA* 2.9 18.1 + - + +
469A ALA* 2.9 27.1 + - + +
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Residues in contact with ASP 466 (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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464A GLY 3.4 0.6 - - - -
465A TYR* 1.3 94.6 - - - +
467A LYS* 1.3 61.8 + - - +
469A ALA* 3.4 5.6 + - - +
470A LYS* 3.2 21.1 + - - +
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Residues in contact with LYS 467 (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* 3.1 39.5 - - + +
464A GLY* 3.4 1.6 + - - -
465A TYR 3.3 0.4 - - - -
466A ASP* 1.3 79.7 - - - +
468A ALA* 1.3 60.8 + - - +
470A LYS* 3.5 8.2 + - - +
471A ILE* 3.3 26.3 + - - +
491A TYR* 3.8 18.2 - - + -
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Residues in contact with ALA 468 (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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456A VAL* 3.4 31.2 - - + +
459A LEU* 4.6 8.7 - - + -
460A ASN* 3.7 20.9 - - - +
463A ILE* 4.3 1.1 - - - +
464A GLY 3.1 13.1 + - - +
465A TYR* 2.9 10.4 + - + +
467A LYS* 1.3 75.2 - - - +
469A ALA* 1.3 65.6 + - - +
471A ILE* 3.1 10.5 + - - +
472A ALA 2.9 18.5 + - - -
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Residues in contact with ALA 469 (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 TYR* 2.9 29.3 + - + +
466A ASP* 3.4 8.7 + - - +
468A ALA* 1.3 75.8 - - - +
470A LYS* 1.3 57.3 + - - +
472A ALA* 3.6 7.8 - - - +
473A LYS* 2.8 49.0 + - + +
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Residues in contact with LYS 470 (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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466A ASP 3.2 12.7 + - - +
467A LYS* 3.6 11.2 - - - +
468A ALA 3.1 0.6 - - - -
469A ALA* 1.3 74.7 - - - +
471A ILE* 1.3 57.8 + - - +
473A LYS* 4.8 4.7 - - - -
474A THR* 2.4 40.1 + - - +
489A LEU* 4.7 4.3 - - + -
491A TYR* 3.9 21.5 - - + +
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Residues in contact with ILE 471 (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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456A VAL* 4.8 2.7 - - + -
459A LEU* 3.8 13.5 - - + -
463A ILE* 3.4 32.3 - - + -
467A LYS 3.3 9.6 - - - +
468A ALA* 3.1 7.7 + - - +
470A LYS* 1.3 76.0 - - - +
472A ALA* 1.3 58.1 + - - +
474A THR* 4.5 0.2 - - - -
475A ALA* 2.9 30.0 + - - +
482A LEU* 3.5 38.6 - - + +
485A THR* 3.5 10.4 - - + +
486A ALA* 3.6 30.1 - - + +
489A LEU* 5.0 1.1 - - + -
491A TYR* 3.4 19.5 - - + -
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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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453A LEU* 4.5 11.4 - - + +
456A VAL* 4.2 21.3 - - + -
468A ALA 2.9 13.4 + - - +
469A ALA* 3.6 11.2 - - - +
471A ILE* 1.3 77.3 - - - +
473A LYS* 1.3 60.5 + - + +
475A ALA* 3.3 1.2 + - - +
476A HIS* 2.9 31.8 + - - +
482A LEU* 4.2 12.1 - - + +
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Residues in contact with LYS 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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469A ALA* 2.8 35.7 + - + +
470A LYS* 4.2 4.5 - - - +
472A ALA* 1.3 73.3 - - + +
474A THR* 1.3 56.4 + - - +
476A HIS* 3.8 8.0 - - - +
477A LYS* 3.0 28.4 + - - +
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Residues in contact with THR 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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470A LYS* 2.4 26.2 + - - +
473A LYS* 1.3 75.5 - - - +
475A ALA* 1.3 60.6 + - - +
477A LYS* 3.2 4.9 + - + +
478A ASN* 2.8 49.8 + - - +
485A THR* 3.7 19.7 - - + -
489A LEU* 4.1 20.5 - - + +
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Residues in contact with ALA 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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453A LEU* 4.2 11.7 - - + -
471A ILE 2.9 16.5 + - - +
472A ALA 3.9 2.5 - - - +
474A THR* 1.3 75.6 - - - +
476A HIS* 1.3 54.3 + - - +
479A GLY* 2.6 36.0 + - - -
480A SER* 3.3 16.0 + - - +
481A THR 3.5 17.7 - - - +
482A LEU* 4.5 2.7 - - + +
485A THR* 3.3 23.9 + - - +
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Residues in contact with HIS 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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453A LEU* 3.9 28.5 - - + +
472A ALA 2.9 17.5 + - - +
473A LYS* 3.8 7.9 - - - +
475A ALA* 1.3 78.6 - - - +
477A LYS* 1.3 63.3 + - - +
479A GLY* 3.6 7.0 + - - -
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Residues in contact with LYS 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 LYS 3.0 20.0 + - - +
474A THR* 3.6 6.5 - - + +
476A HIS* 1.3 80.1 - - - +
478A ASN* 1.3 71.3 + - - +
479A GLY 3.8 0.2 + - - -
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Residues in contact with ASN 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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474A THR* 2.8 42.4 + - - +
477A LYS* 1.3 84.4 - - - +
479A GLY* 1.3 61.0 + - - +
480A SER* 3.5 17.4 + - - +
485A THR* 5.2 1.0 + - - -
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Residues in contact with GLY 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 ALA 2.6 16.9 + - - -
476A HIS* 3.6 5.5 + - - -
477A LYS 3.5 2.8 - - - -
478A ASN* 1.3 73.7 - - - +
480A SER* 1.3 59.1 + - - -
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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