Contacts of the helix formed by residues 545 - 553 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A ASN* 4.4 0.8 + - - +
514A SER 3.3 11.8 + - - +
515A PRO* 3.1 38.3 - - + +
517A SER* 4.8 10.9 + - - +
543A ASN* 4.3 1.0 - - - +
544A ILE* 1.3 72.6 - - - +
546A ALA* 1.3 55.5 + - - +
547A VAL* 3.8 9.0 + - - +
548A LYS* 2.8 52.3 + - + +
549A ILE* 3.1 15.4 + - + +
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Residues in contact with ALA 546 (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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513A ASN* 3.2 20.4 - - - +
544A ILE* 3.0 6.3 + - - +
545A ASP* 1.3 73.8 - - - +
547A VAL* 1.3 58.5 + - - +
549A ILE* 3.8 3.8 - - - +
550A ALA* 3.1 30.0 + - - +
559A ILE* 3.5 24.3 - - + +
562A ILE* 3.9 31.1 - - + +
563A MET* 4.0 8.7 - - - -
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Residues in contact with VAL 547 (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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513A ASN* 4.3 13.0 - - - +
545A ASP* 3.1 8.3 + - - +
546A ALA* 1.3 78.2 - - - +
548A LYS* 1.3 57.6 + - - +
551A THR* 2.8 37.4 + - - +
557A GLY* 4.0 18.7 - - - +
559A ILE* 3.6 21.5 - - + -
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Residues in contact with LYS 548 (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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545A ASP* 2.8 34.5 + - + +
547A VAL* 1.3 77.3 - - - +
549A ILE* 1.3 64.6 + - + +
551A THR* 3.4 4.9 + - - +
552A ASP* 2.9 74.9 + - - +
608A GLN* 5.6 1.3 - - - +
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Residues in contact with ILE 549 (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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544A ILE* 3.5 38.6 - - + -
545A ASP* 3.1 12.0 + - + +
546A ALA 4.1 4.0 - - - +
548A LYS* 1.3 79.1 - - + +
550A ALA* 1.3 57.7 + - - +
552A ASP* 3.2 3.7 + - - +
553A VAL* 3.0 34.6 + - + +
562A ILE* 4.1 19.5 - - + -
605A ALA* 4.3 7.0 - - - +
608A GLN* 3.8 42.2 - - + +
609A ALA* 4.5 3.8 - - - +
612A SER* 3.6 20.6 - - - +
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Residues in contact with ALA 550 (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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546A ALA 3.1 17.9 + - - +
549A ILE* 1.3 76.1 - - - +
551A THR* 1.3 62.2 + - - +
553A VAL* 3.6 8.2 + - - -
554A GLY 3.1 3.5 + - - -
555A LEU* 2.6 34.8 + - + +
556A GLY 3.4 0.2 + - - -
557A GLY* 3.6 17.9 - - - +
558A ARG 3.1 30.1 - - - +
562A ILE* 4.2 6.9 - - + +
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Residues in contact with THR 551 (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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547A VAL* 2.8 27.3 + - - +
548A LYS* 3.8 6.1 - - - +
549A ILE 3.3 0.2 - - - -
550A ALA* 1.3 75.6 - - - +
552A ASP* 1.3 68.3 + - - +
554A GLY* 3.4 10.9 + - - -
556A GLY* 4.3 6.2 - - - +
557A GLY* 3.8 15.3 + - - +
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Residues in contact with ASP 552 (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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548A LYS* 2.9 58.2 + - - +
549A ILE* 3.2 6.3 + - - +
551A THR* 1.3 85.9 - - - +
553A VAL* 1.3 61.1 - - + +
554A GLY 3.2 1.3 + - - -
608A GLN* 4.1 17.6 + - - +
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Residues in contact with VAL 553 (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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549A ILE* 3.0 20.1 + - + +
550A ALA* 3.7 11.0 - - - +
552A ASP* 1.3 77.5 - - - +
554A GLY* 1.3 59.0 + - - +
555A LEU* 4.0 6.5 - - + +
601A MET* 3.7 39.2 - - - +
604A ASP* 4.3 23.1 - - + +
605A ALA* 3.9 23.1 - - + +
608A GLN* 3.8 23.1 - - - +
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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