Contacts of the helix formed by residues 491 - 497 (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 ASN 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A TRP 4.1 1.4 + - - -
425A LEU* 3.6 34.6 - - + +
428A ASP* 5.2 0.2 - - - +
489A CYS* 3.1 17.1 - - - -
490A HIS* 1.3 80.3 - - - +
492A PRO* 1.3 73.7 - - - +
493A ALA* 3.2 26.3 - - - +
494A TYR* 3.0 52.4 + - + +
513A ASN 4.5 0.4 - - - -
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Residues in contact with PRO 492 (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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489A CYS* 4.8 0.2 - - - -
491A ASN* 1.3 91.4 - - - +
493A ALA* 1.3 63.7 + - + +
494A TYR 2.9 1.2 + - - -
495A VAL* 3.0 24.4 + - - +
512A LEU* 4.3 9.2 - - + -
513A ASN* 3.1 39.3 - - - +
514A SER* 3.8 19.3 - - - -
515A PRO* 4.9 4.9 - - + -
516A TRP* 3.9 18.0 - - + -
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Residues in contact with ALA 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ASN* 3.2 20.1 + - - +
492A PRO* 1.3 79.3 - - + +
494A TYR* 1.3 63.0 + - + +
495A VAL 3.3 1.2 + - - -
496A GLY* 3.9 5.4 + - - -
497A ILE* 3.6 18.7 - - + +
516A TRP* 6.0 0.2 - - - -
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Residues in contact with TYR 494 (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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423A TRP* 4.1 20.9 - + + -
424A GLY 2.6 37.5 + - - -
425A LEU* 3.2 19.4 - - + +
463A ILE* 3.1 36.1 - - + +
489A CYS* 4.0 2.5 - - - -
491A ASN* 3.0 43.2 + - + +
492A PRO 2.9 0.6 + - - -
493A ALA* 1.3 78.3 - - + +
495A VAL* 1.3 65.9 + - - +
496A GLY 3.3 0.7 - - - -
497A ILE* 3.6 10.1 - - + -
498A TYR* 3.0 45.6 + + + +
500A ILE* 3.7 15.8 - - + +
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Residues in contact with VAL 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A CYS* 4.7 4.7 - - - -
491A ASN 4.4 0.4 + - - -
492A PRO 3.0 11.8 + - - +
494A TYR* 1.3 80.0 - - - +
496A GLY* 1.3 62.5 + - - +
497A ILE 3.5 0.9 + - - -
498A TYR 4.1 4.9 - - - +
500A ILE* 4.7 4.7 - - + -
510A PHE* 4.9 8.7 - - + -
512A LEU* 4.2 22.4 - - + -
516A TRP* 3.8 17.5 - - + -
525A HIS 3.6 12.1 - - - +
526A LEU* 3.9 19.3 - - + -
527A PRO* 3.5 24.9 - - + +
530A ILE* 3.3 31.1 - - + +
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Residues in contact with GLY 496 (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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493A ALA 3.9 4.6 + - - -
494A TYR 3.3 0.4 - - - -
495A VAL* 1.3 81.6 - - - +
497A ILE* 1.3 69.7 + - - +
527A PRO* 3.7 17.7 - - - -
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Residues in contact with ILE 497 (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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493A ALA* 3.6 23.8 - - + +
494A TYR* 3.0 9.8 + - + -
495A VAL 3.3 0.6 + - - -
496A GLY* 1.3 86.1 - - - +
498A TYR* 1.3 102.3 + - + +
648A THR* 4.5 16.5 - - + +
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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