Contacts of the helix formed by residues 590 - 597 (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 ALA 590 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A TRP 4.0 0.2 + - - -
589A MET* 1.3 74.5 - - - +
591A PRO* 1.4 74.0 - - + +
592A GLU* 3.5 26.9 - - - +
593A SER* 3.0 15.8 + - - +
594A ILE* 3.1 11.9 + - - +
603A SER* 3.7 13.4 + - - -
606A TRP* 3.6 22.9 - - + +
607A MET* 4.9 2.8 - - - +
666A ARG* 3.6 12.6 - - - +
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Residues in contact with PRO 591 (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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589A MET 3.8 0.4 - - - +
590A ALA* 1.4 84.7 - - + +
592A GLU* 1.3 53.7 + - + +
594A ILE* 3.2 1.9 + - + +
595A ASN* 2.7 41.7 + - - +
606A TRP* 3.5 32.5 - - + -
632A ILE* 3.9 23.8 - - + -
635A ILE* 4.3 3.1 - - + -
661A TYR* 3.5 58.3 - - + +
666A ARG* 4.5 0.4 - - - +
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Residues in contact with GLU 592 (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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590A ALA* 3.9 12.1 - - + -
591A PRO* 1.3 75.7 - - + +
593A SER* 1.3 54.8 + - - +
595A ASN* 4.8 0.2 - - - -
596A PHE* 3.1 38.4 + - + +
598A ARG* 3.2 47.5 + - + +
600A THR* 4.3 5.8 + - - +
603A SER* 3.5 15.7 + - - -
661A TYR* 5.0 0.8 - - - +
663A PRO* 3.5 29.3 - - + +
666A ARG* 2.3 38.1 + - - +
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Residues in contact with SER 593 (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* 6.1 0.2 - - - +
589A MET* 3.8 15.1 - - - +
590A ALA* 3.0 16.7 + - - +
592A GLU* 1.3 75.1 - - - +
594A ILE* 1.3 67.1 + - - +
597A ARG* 3.1 22.7 + - - +
598A ARG 2.7 25.1 + - - +
599A PHE* 3.7 24.1 - - - -
603A SER* 3.4 22.3 + - - -
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Residues in contact with ILE 594 (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* 6.1 2.3 - - - +
586A ILE* 3.9 39.7 - - + +
589A MET* 3.7 39.0 - - + +
590A ALA 3.1 9.7 + - - +
591A PRO* 3.7 4.7 - - + +
593A SER* 1.3 80.5 - - - +
595A ASN* 1.3 64.4 + - - +
596A PHE 3.7 0.2 + - - -
597A ARG* 4.5 4.2 + - - +
631A VAL* 5.1 0.4 - - + -
632A ILE* 4.0 42.6 - - + -
635A ILE* 5.0 5.6 - - + -
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Residues in contact with ASN 595 (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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591A PRO 2.7 23.6 + - - +
594A ILE* 1.3 77.2 - - - +
596A PHE* 1.3 92.3 + - + +
597A ARG* 5.9 0.6 - - - -
632A ILE* 3.8 23.1 - - - +
636A GLU* 3.4 25.4 + - - +
661A TYR* 3.6 8.5 + - - -
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Residues in contact with PHE 596 (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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592A GLU* 3.1 22.9 + - + +
595A ASN* 1.3 103.8 - - + +
597A ARG* 1.3 75.1 + - - +
598A ARG* 3.1 20.9 + - + +
661A TYR* 5.9 1.8 - - - -
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Residues in contact with ARG 597 (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* 6.4 2.9 - - + -
593A SER 3.1 19.8 + - - +
594A ILE 5.3 3.8 - - - +
595A ASN 3.8 1.1 - - - -
596A PHE* 1.3 80.4 - - - +
598A ARG* 1.3 63.0 + - - +
599A PHE* 3.5 23.8 + - + -
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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