Contacts of the helix formed by residues 545 - 553 (chain B) in PDB entry 1KEK
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 545 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513B ASN* 4.3 1.1 + - - +
514B SER 3.2 14.3 + - - +
515B PRO* 3.6 30.3 - - + +
517B SER* 4.4 12.2 + - - +
543B ASN* 4.2 1.4 - - - +
544B ILE* 1.3 74.2 - - - +
546B ALA* 1.3 61.3 + - - +
547B VAL* 3.7 8.5 + - - +
548B LYS* 3.2 44.0 + - + +
549B ILE* 3.3 16.8 + - + +
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Residues in contact with ALA 546 (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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513B ASN* 3.2 16.9 - - - +
544B ILE* 2.9 9.2 + - - +
545B ASP* 1.3 71.9 - - - +
547B VAL* 1.3 57.0 + - - +
549B ILE* 3.5 1.2 + - - +
550B ALA* 3.0 31.4 + - - +
559B ILE* 3.6 20.4 - - + -
562B ILE* 3.6 34.4 - - + +
563B MET* 3.7 15.7 - - - -
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Residues in contact with VAL 547 (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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513B ASN* 4.1 9.6 - - - +
545B ASP* 3.3 7.2 + - - +
546B ALA* 1.3 75.7 - - - +
548B LYS* 1.3 55.0 + - - +
550B ALA* 3.5 1.7 + - - +
551B THR* 2.7 44.6 + - - +
557B GLY* 4.1 19.1 - - - +
559B ILE* 3.7 17.9 - - + -
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Residues in contact with LYS 548 (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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545B ASP* 3.2 34.0 + - + +
547B VAL* 1.3 77.3 - - - +
549B ILE* 1.3 62.2 + - + +
551B THR* 3.4 5.7 + - - -
552B ASP* 2.9 57.7 + - - +
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Residues in contact with ILE 549 (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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544B ILE* 3.8 35.9 - - + -
545B ASP* 3.3 10.9 + - + +
546B ALA 4.0 5.8 - - - +
548B LYS* 1.3 77.2 - - + +
550B ALA* 1.3 65.0 + - - +
552B ASP* 3.0 4.1 + - - +
553B VAL* 3.0 27.5 + - + +
562B ILE* 3.8 22.0 - - + -
605B ALA* 4.5 6.5 - - - +
608B GLN* 3.5 43.1 - - + +
609B ALA* 4.5 4.3 - - - -
612B SER* 4.1 18.8 - - - +
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Residues in contact with ALA 550 (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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546B ALA 3.0 18.3 + - - +
547B VAL 3.7 0.2 - - - +
549B ILE* 1.3 78.0 - - - +
551B THR* 1.3 60.1 + - - +
553B VAL* 3.4 6.9 + - - +
554B GLY 3.3 3.1 + - - -
555B LEU* 2.8 34.3 + - + -
557B GLY* 3.6 19.5 - - - -
558B ARG 3.1 29.8 - - - +
562B ILE* 3.9 9.8 - - + +
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Residues in contact with THR 551 (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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547B VAL* 2.7 27.1 + - - +
548B LYS* 3.6 7.0 - - - -
549B ILE 3.3 0.2 - - - -
550B ALA* 1.3 74.3 - - - +
552B ASP* 1.3 65.9 + - - +
554B GLY* 3.4 11.4 + - - -
556B GLY* 4.3 6.8 - - - +
557B GLY* 3.5 17.8 + - - +
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Residues in contact with ASP 552 (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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548B LYS* 2.9 55.6 + - - +
549B ILE* 3.0 5.2 + - - +
551B THR* 1.3 82.0 - - - +
553B VAL* 1.3 58.8 + - - +
554B GLY 3.2 1.4 + - - -
608B GLN* 3.6 25.3 + - - +
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Residues in contact with VAL 553 (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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549B ILE 3.0 21.9 + - - +
550B ALA* 3.5 10.3 - - - +
552B ASP* 1.3 76.3 - - - +
554B GLY* 1.3 55.1 + - - +
555B LEU* 3.8 17.0 - - + -
601B MET* 3.4 44.4 - - - +
604B ASP* 3.8 33.3 - - + +
605B ALA* 4.0 9.4 - - + +
608B GLN* 3.8 24.2 - - + +
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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