Contacts of the helix formed by residues 564 - 569 (chain A) in PDB entry 2JKK
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 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A LYS* 2.7 38.2 + - + -
471A GLU 4.8 0.9 - - - +
475A MET* 3.3 24.7 - - - +
484A VAL* 3.6 10.0 - - - +
497A ILE* 5.7 0.3 - - - +
499A MET* 3.5 13.5 - - + +
563A GLY* 1.3 69.2 - - - -
565A PHE* 1.3 54.7 + - - +
566A GLY 3.1 5.4 + - - -
567A LEU* 3.0 27.1 + - + -
568A SER* 2.7 34.5 + - - -
1686A BI9 3.0 30.4 + - + +
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Residues in contact with PHE 565 (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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474A THR* 4.2 7.4 - - + -
475A MET* 3.5 22.6 - - + -
478A PHE* 3.4 29.2 - + - -
483A ILE* 4.0 20.4 - - + -
537A LEU* 3.9 15.3 - - + -
542A PHE* 3.4 36.1 - + - -
544A HIS* 3.7 30.3 - + - -
562A LEU* 4.3 6.7 - - + -
563A GLY 3.4 16.8 - - - -
564A ASP* 1.3 71.6 - - - +
566A GLY* 1.3 67.1 + - - +
568A SER* 3.3 10.2 + - - -
569A ARG* 2.9 42.2 + - - +
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Residues in contact with GLY 566 (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 LYS* 4.8 0.2 - - - +
471A GLU* 3.6 38.1 + - - +
475A MET* 5.2 1.0 - - - +
564A ASP* 3.1 9.1 + - - -
565A PHE* 1.3 78.3 - - - +
567A LEU* 1.3 61.8 + - - +
569A ARG* 3.3 24.5 + - - +
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Residues in contact with LEU 567 (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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430A GLU 4.1 4.9 - - - +
431A GLY* 3.7 30.1 - - - -
436A VAL* 3.8 26.0 - - + -
454A LYS* 3.9 23.6 - - + -
471A GLU* 5.6 0.2 - - - +
551A ASN* 4.2 4.3 - - - +
564A ASP* 3.0 22.1 + - + +
565A PHE 3.3 0.4 - - - -
566A GLY* 1.3 74.1 - - - +
568A SER* 1.3 62.2 + - - +
569A ARG 3.2 2.7 + - - -
1686A BI9 3.5 59.2 + - + +
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Residues in contact with SER 568 (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 HIS* 4.0 14.1 + - - -
546A ASP* 3.5 19.4 - - - +
550A ARG* 4.0 6.9 + - - -
551A ASN* 3.1 44.0 + - - +
563A GLY 4.1 4.0 + - - -
564A ASP 2.7 22.6 + - - -
565A PHE* 3.5 9.3 - - - -
566A GLY 3.2 0.4 - - - -
567A LEU* 1.3 77.3 - - - +
569A ARG* 1.3 61.6 + - - +
1686A BI9 3.4 11.3 - - - -
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Residues in contact with ARG 569 (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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474A THR* 4.5 6.1 - - - +
542A PHE* 3.9 19.2 - - - -
543A VAL 4.7 1.6 + - - -
544A HIS* 2.6 41.6 + - - +
545A ARG* 4.8 0.8 - - - +
546A ASP* 2.8 32.7 + - - +
550A ARG* 5.3 2.8 + - - -
565A PHE* 2.9 44.6 + - - +
566A GLY* 3.3 16.0 + - - +
567A LEU 3.2 5.2 - - - -
568A SER* 1.3 82.2 - - - +
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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