Contacts of the helix formed by residues 464 - 479 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460B ASN* 2.7 27.3 + - - -
461B PRO 4.6 0.4 - - - -
462B HIS 3.8 0.6 - - - -
463B ILE* 1.3 73.6 - - - +
465B TYR* 1.3 67.4 + - - -
466B ASP* 3.2 4.0 - - - -
467B LYS 3.1 2.8 + - - -
468B ALA* 3.1 21.0 + - - +
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Residues in contact with TYR 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B ASN* 3.6 35.1 + - + +
464B GLY* 1.3 70.9 - - - -
466B ASP* 1.3 76.5 + - - +
467B LYS 3.1 0.3 + - - -
468B ALA* 3.1 1.1 + - + +
469B ALA* 2.9 39.2 + - + +
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Residues in contact with ASP 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B GLY 3.2 1.3 - - - -
465B TYR* 1.3 90.2 - - - +
467B LYS* 1.3 61.3 + - - +
469B ALA* 3.9 3.7 + - - +
470B LYS* 3.4 17.8 + - - +
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Residues in contact with LYS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ILE* 3.3 38.8 + - + +
464B GLY 3.1 2.0 + - - -
465B TYR 3.1 0.6 - - - -
466B ASP* 1.3 79.6 - - - +
468B ALA* 1.3 64.3 + - - +
470B LYS* 3.1 16.4 + - - +
471B ILE* 3.1 17.0 + - - +
491B TYR* 4.0 15.4 - - + -
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Residues in contact with ALA 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B VAL* 3.4 28.7 - - + +
459B LEU* 4.4 8.7 - - + -
460B ASN* 3.1 26.9 - - - +
463B ILE* 3.8 2.7 - - - +
464B GLY 3.1 9.8 + - - +
465B TYR 3.7 4.5 - - - +
467B LYS* 1.3 76.5 - - - +
469B ALA* 1.3 62.8 + - - +
471B ILE* 2.9 25.4 + - - +
472B ALA 3.0 10.2 + - - -
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Residues in contact with ALA 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B VAL* 6.0 0.9 - - - -
465B TYR* 2.9 36.1 + - + +
466B ASP* 4.1 4.7 - - - +
468B ALA* 1.3 74.9 - - - +
470B LYS* 1.3 62.1 + - - +
472B ALA* 3.3 7.5 + - - +
473B LYS* 3.0 27.4 + - - +
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Residues in contact with LYS 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B ASP 3.4 12.0 + - - +
467B LYS* 3.1 13.9 + - - +
469B ALA* 1.3 78.0 - - - +
471B ILE* 1.3 56.7 + - - +
473B LYS* 4.1 5.5 - - + -
474B THR* 2.6 42.4 + - - +
489B LEU* 4.2 5.6 - - + -
491B TYR* 3.5 26.9 - - + +
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B VAL* 4.6 2.9 - - + -
459B LEU* 3.9 12.1 - - + -
463B ILE* 3.5 32.1 - - + -
467B LYS 3.1 8.3 + - - +
468B ALA* 2.9 9.0 + - - +
470B LYS* 1.3 74.7 - - - +
472B ALA* 1.3 61.6 + - - +
474B THR 3.1 1.2 + - - -
475B ALA* 2.8 28.6 + - - +
482B LEU* 3.6 37.9 - - + +
485B THR* 3.6 17.3 - - + +
486B ALA* 3.7 23.6 - - + +
489B LEU* 4.3 1.8 - - + -
491B TYR* 3.7 20.2 - - + -
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Residues in contact with ALA 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU* 4.5 11.9 - - + +
456B VAL* 4.1 23.9 - - + +
468B ALA 3.0 12.0 + - - +
469B ALA* 3.8 9.0 - - - +
471B ILE* 1.3 76.2 - - - +
473B LYS* 1.3 57.6 + - - +
475B ALA* 3.8 0.9 - - - +
476B HIS* 2.8 33.0 + - - +
482B LEU* 4.1 13.9 - - + -
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Residues in contact with LYS 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B ALA 3.0 17.7 + - - +
470B LYS* 4.2 6.7 - - + +
472B ALA* 1.3 75.3 - - - +
474B THR* 1.3 58.0 + - - +
476B HIS* 3.8 7.2 + - - +
477B LYS* 3.1 26.5 + - - +
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Residues in contact with THR 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B LYS* 2.6 34.1 + - - +
471B ILE 3.1 3.7 + - - -
473B LYS* 1.3 76.6 - - - +
475B ALA* 1.3 61.2 + - - +
477B LYS* 3.0 5.8 + - + +
478B ASN* 2.8 55.4 + - - +
485B THR* 3.7 18.2 - - + -
488B GLU* 6.1 0.9 - - - +
489B LEU* 4.4 14.7 - - + +
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Residues in contact with ALA 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU* 3.8 17.0 - - + -
471B ILE 2.8 20.1 + - - +
472B ALA 3.8 0.4 - - - +
474B THR* 1.3 71.3 - - - +
476B HIS* 1.3 54.7 + - - +
479B GLY* 2.7 32.1 + - - -
480B SER* 3.1 29.7 + - - +
481B THR 3.9 8.5 - - - +
482B LEU* 4.2 5.4 - - + -
485B THR* 3.5 21.4 + - - +
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Residues in contact with HIS 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU* 3.8 26.6 - - + +
472B ALA 2.8 22.4 + - - +
473B LYS* 3.9 7.0 - - - +
475B ALA* 1.3 73.0 - - - +
477B LYS* 1.3 67.0 + - - +
479B GLY* 3.6 6.5 + - - -
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Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B LYS 3.1 18.9 + - - +
474B THR* 3.0 8.3 + - - +
476B HIS* 1.3 80.0 - - - +
478B ASN* 1.3 66.5 + - - +
479B GLY 3.4 0.3 + - - -
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Residues in contact with ASN 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B THR* 2.8 43.2 + - - +
477B LYS* 1.3 77.8 + - - +
479B GLY* 1.3 61.2 + - - +
480B SER* 3.6 15.8 + - - +
485B THR* 5.2 0.3 + - - -
488B GLU* 5.6 2.5 - - - +
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Residues in contact with GLY 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B ALA 2.7 16.4 + - - -
476B HIS* 3.6 5.9 + - - -
477B LYS 3.3 4.4 + - - -
478B ASN* 1.3 76.1 - - - +
480B SER* 1.3 57.6 + - - -
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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