Contacts of the helix formed by residues 585 - 589 (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 PRO 585 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A ARG 4.5 3.1 - - - +
546A ASP* 4.5 15.9 - - - +
550A ARG* 3.4 29.6 - - - +
584A LEU* 1.4 82.2 - - + +
586A ILE* 1.3 62.9 + - - +
587A LYS 3.3 2.5 - - - -
588A TRP* 3.0 24.4 + - + -
589A MET* 3.3 31.1 + - + +
599A PHE* 6.3 1.1 - - + -
607A MET* 4.2 14.1 - - + -
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Residues in contact with ILE 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A LEU* 2.9 43.3 + - + +
585A PRO* 1.3 69.6 - - - +
587A LYS* 1.3 62.7 + - - +
588A TRP 3.1 1.7 + - - -
589A MET* 3.1 24.2 + - + +
594A ILE* 3.9 33.6 - - + +
628A ASN* 3.4 51.9 + - + +
631A VAL* 3.8 17.8 - - + +
632A ILE* 5.2 1.1 - - + +
635A ILE* 5.5 0.5 - - - +
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Residues in contact with LYS 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A PRO 3.1 1.4 + - - -
586A ILE* 1.3 74.9 - - - +
588A TRP* 1.3 81.4 + - + +
589A MET 5.3 0.2 - - - -
606A TRP* 5.3 1.2 + - - -
610A VAL* 4.2 6.9 - - - +
622A PRO* 3.5 23.0 + - + +
623A PHE* 2.8 55.5 + - + -
624A GLN* 4.5 1.4 - - - +
625A GLY 4.5 3.6 - - - +
626A VAL 2.7 30.7 + - - +
628A ASN* 3.6 21.9 + - - +
631A VAL* 3.8 20.2 - - + -
635A ILE* 5.8 1.7 - - - +
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Residues in contact with TRP 588 (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 ILE 3.8 6.3 - - - +
548A ALA* 3.5 22.2 - - + +
550A ARG* 3.7 31.2 - - + -
585A PRO* 3.0 18.6 + - + +
587A LYS* 1.3 102.4 - - + +
589A MET* 1.3 60.8 + - - +
606A TRP* 3.2 21.6 - - - -
607A MET* 3.3 32.9 - - + +
610A VAL* 3.4 26.5 - - + +
614A GLU* 2.8 33.7 + - - -
621A LYS* 4.7 17.9 - - + -
622A PRO* 3.5 25.6 - - + -
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Residues in contact with MET 589 (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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584A LEU* 4.0 22.7 - - + -
585A PRO* 3.3 48.7 - - + +
586A ILE* 3.1 18.1 + - + +
587A LYS 5.3 0.3 - - - -
588A TRP* 1.3 78.2 - - - +
590A ALA* 1.3 65.9 + - - +
591A PRO* 3.8 0.9 - - - +
593A SER* 3.8 37.5 - - - +
594A ILE* 3.7 24.7 - - + +
599A PHE* 4.0 20.0 - - + -
606A TRP* 3.3 12.6 + - - -
607A MET* 4.5 10.5 - - + -
635A ILE* 4.5 3.6 - - - +
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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