Contacts of the helix formed by residues 496 - 504 (chain A) in PDB entry 5KYT
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 LYS 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A GLU* 1.3 80.2 - - + +
497A GLU* 1.3 57.2 + - - +
499A VAL* 4.1 9.9 - - - -
500A ASP* 3.0 46.2 + - - +
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Residues in contact with GLU 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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461A HIS* 6.0 4.4 + - - +
495A GLU 3.1 6.4 - - - +
496A LYS* 1.3 80.7 - - - +
498A ILE* 1.3 59.3 + - - +
500A ASP* 4.6 2.7 - - - +
501A TYR* 3.3 21.8 + - - +
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Residues in contact with ILE 498 (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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458A LEU* 4.8 14.4 - - + -
461A HIS* 5.9 7.9 - - + -
485A VAL* 6.1 2.0 - - + -
495A GLU* 2.8 13.9 + - - +
497A GLU* 1.3 77.2 - - - +
499A VAL* 1.3 55.3 + - - +
501A TYR* 3.0 9.9 + - - +
502A VAL* 2.8 38.8 + - - +
512A LEU* 5.1 0.4 - - - -
516A VAL* 4.2 18.8 - - + -
518A PHE* 5.9 2.5 - - + -
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Residues in contact with VAL 499 (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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495A GLU* 2.8 35.2 + - + +
496A LYS* 3.9 8.5 - - - +
498A ILE* 1.3 72.9 - - - +
500A ASP* 1.3 67.9 + - - +
502A VAL* 3.3 3.9 + - - +
503A ALA* 3.0 30.3 + - + +
511A LYS* 6.5 0.2 - - + -
512A LEU* 3.7 41.1 + - + +
515A GLY* 4.5 6.1 - - - -
516A VAL* 4.4 8.5 - - + -
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Residues in contact with ASP 500 (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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496A LYS* 3.0 31.0 + - - +
497A GLU* 4.6 2.6 - - - +
499A VAL* 1.3 82.2 - - - +
501A TYR* 1.3 65.3 + - - +
503A ALA* 3.6 7.9 + - - +
504A SER* 3.3 21.1 + - - -
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Residues in contact with TYR 501 (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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457A ILE* 3.4 25.7 + - + -
458A LEU* 4.9 4.9 - - + -
460A GLN* 3.4 26.5 + - - +
461A HIS* 4.1 34.0 + + + -
497A GLU 3.3 16.9 + - - +
498A ILE* 3.0 13.6 + - - +
500A ASP* 1.3 77.6 - - - +
502A VAL* 1.3 70.9 + - + +
504A SER* 2.5 25.8 + - - -
505A GLN* 3.4 32.3 + - + +
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Residues in contact with VAL 502 (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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454A LEU* 3.8 27.6 - - + -
457A ILE* 4.2 16.2 - - + -
458A LEU* 3.5 33.4 - - + -
498A ILE 2.8 13.2 + - - +
499A VAL 3.6 7.6 - - - +
501A TYR* 1.3 75.6 - - + +
503A ALA* 1.3 54.4 + - - +
504A SER 2.8 5.0 + - - -
505A GLN* 2.6 26.7 + - - +
506A VAL* 3.1 21.4 + - + -
512A LEU* 4.0 29.8 - - + +
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Residues in contact with ALA 503 (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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499A VAL* 3.0 20.3 + - + +
500A ASP* 3.9 9.6 - - - +
501A TYR 3.4 0.2 - - - -
502A VAL* 1.3 77.9 - - - +
504A SER* 1.3 56.6 + - - +
505A GLN 3.3 0.2 - - - -
506A VAL* 3.6 20.7 - - - +
511A LYS* 4.6 16.8 - - + -
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Residues in contact with SER 504 (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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500A ASP 3.3 11.2 + - - -
501A TYR* 2.5 26.6 + - - -
502A VAL 2.8 1.0 + - - -
503A ALA* 1.3 76.4 - - - +
505A GLN* 1.3 74.3 + - - +
506A VAL 3.8 0.7 - - - -
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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