Contacts of the helix formed by residues 493 - 501 (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 THR 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487B ILE* 4.5 2.0 - - - -
492B LEU* 1.3 84.5 - - - +
494B ALA* 1.3 64.5 + - - +
495B GLU* 3.7 13.6 + - - +
496B GLN* 2.7 50.9 + - - +
497B PHE 2.9 11.1 + - - -
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Residues in contact with ALA 494 (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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483B LYS* 4.0 15.0 - - - +
487B ILE* 3.8 28.5 - - + +
493B THR* 1.3 72.7 - - - +
495B GLU* 1.3 73.0 + - - +
497B PHE* 3.3 3.9 + - - +
498B ASP* 3.2 29.6 + - - +
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Residues in contact with GLU 495 (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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493B THR* 3.2 11.8 + - - +
494B ALA* 1.3 90.0 + - - +
496B GLN* 1.3 60.4 - - - +
498B ASP* 3.7 8.0 + - - +
499B GLU* 3.3 21.5 + - - +
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Residues in contact with GLN 496 (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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491B TYR 5.7 0.2 + - - -
492B LEU* 3.2 10.4 - - + -
493B THR* 2.7 54.3 + - - +
495B GLU* 1.3 75.0 - - - +
497B PHE* 1.3 66.7 + - - +
499B GLU* 3.3 3.2 + - - -
500B TRP* 3.1 72.0 + - + +
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Residues in contact with PHE 497 (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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459B LEU* 4.1 12.1 - - + -
482B LEU* 4.0 22.9 - - + -
483B LYS* 3.7 58.8 - - + -
486B ALA* 4.6 1.8 - - + -
492B LEU* 3.7 32.6 - - + +
493B THR 2.9 5.6 + - - +
494B ALA 3.3 8.9 + - - +
496B GLN* 1.3 77.7 - - - +
498B ASP* 1.3 61.9 + - - +
500B TRP* 4.9 1.1 - - - -
501B VAL* 2.8 73.0 + - + +
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Residues in contact with ASP 498 (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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483B LYS* 3.2 35.8 + - - +
494B ALA 3.2 13.6 + - - +
495B GLU* 4.1 7.0 - - - +
496B GLN 3.3 0.2 - - - -
497B PHE* 1.3 80.6 - - - +
499B GLU* 1.3 59.8 + - - +
501B VAL 3.7 13.8 - - - +
502B LYS* 3.8 12.1 - - - +
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Residues in contact with GLU 499 (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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495B GLU 3.3 14.7 + - - +
496B GLN* 3.3 6.2 + - - +
497B PHE 3.2 0.6 - - - -
498B ASP* 1.3 81.5 - - - +
500B TRP* 1.3 71.7 + - + +
502B LYS* 3.8 23.0 - - - +
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Residues in contact with TRP 500 (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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458B ALA* 3.6 16.4 - - - +
459B LEU* 3.8 23.8 - - + -
462B HIS* 3.2 67.9 + + + +
463B ILE* 3.9 12.3 - - + -
491B TYR 5.3 0.9 - - - -
492B LEU* 3.9 25.4 - - + -
496B GLN* 3.1 56.4 + - + +
497B PHE 4.2 1.1 - - - +
499B GLU* 1.3 90.9 - - + +
501B VAL* 1.3 59.8 + - - +
502B LYS* 3.5 5.6 + - - +
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Residues in contact with VAL 501 (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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455B LEU* 4.0 42.4 - - + +
456B VAL* 6.2 0.2 - - - -
458B ALA* 4.1 10.8 - - + -
459B LEU* 3.7 28.3 - - + -
497B PHE* 2.8 52.4 + - + +
498B ASP* 3.7 12.3 - - - +
500B TRP* 1.3 73.2 - - - +
502B LYS* 1.3 60.9 + - - +
503B PRO* 3.7 6.8 - - + +
506B MET* 5.8 0.9 - - - -
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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