Contacts of the helix formed by residues 583 - 594 (chain A) in PDB entry 2JED
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 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581A GLY 4.0 1.8 - - - -
582A GLN* 1.3 80.0 - - - +
584A GLU* 1.3 63.7 + - - +
585A GLU* 3.5 27.1 + - - +
586A GLU* 2.8 28.1 + - - +
587A LEU* 3.0 20.9 + - - +
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Residues in contact with GLU 584 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A PHE* 6.4 0.2 - - - -
543A PRO* 3.7 25.5 - - + +
583A ASP* 1.3 73.7 - - - +
585A GLU* 1.3 63.8 + - + +
587A LEU* 3.3 9.5 + - - +
588A PHE* 2.9 71.8 + - + -
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Residues in contact with GLU 585 (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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583A ASP* 3.2 22.7 - - - +
584A GLU* 1.3 88.7 + - + +
586A GLU* 1.3 64.6 + - - +
588A PHE* 3.4 10.2 + - + +
589A HIS* 3.1 21.3 + - - +
592A ARG* 5.3 1.0 + - - -
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Residues in contact with GLU 586 (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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580A HIS* 4.4 11.3 + - - +
581A GLY* 3.6 9.3 - - - -
582A GLN* 2.7 39.6 + - - +
583A ASP* 2.8 21.7 + - - +
585A GLU* 1.3 72.6 - - - +
587A LEU* 1.3 56.6 + - - +
589A HIS* 3.4 11.1 + - + +
590A SER* 2.9 26.2 + - - -
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Residues in contact with LEU 587 (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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543A PRO* 3.7 39.7 - - + +
544A ASP* 3.8 17.5 - - - +
579A PHE* 3.6 39.5 - - + +
580A HIS* 3.7 12.1 - - - +
581A GLY* 3.8 7.7 - - - +
583A ASP 3.0 14.5 + - - +
584A GLU* 3.5 12.1 - - - +
586A GLU* 1.3 73.6 - - - +
588A PHE* 1.3 61.9 + - + +
590A SER* 3.2 2.8 + - - -
591A ILE* 2.9 36.7 + - + +
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Residues in contact with PHE 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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539A PHE* 3.9 29.6 - + - -
543A PRO* 4.2 15.5 - - + -
546A ILE* 3.9 20.2 - - + -
551A LEU* 3.6 28.8 - - + +
584A GLU* 2.9 58.6 + - + +
585A GLU* 3.7 8.3 - - - +
587A LEU* 1.3 80.0 - - + +
589A HIS* 1.3 60.1 + - - +
591A ILE* 3.4 5.9 + - + -
592A ARG* 3.1 36.0 + - - +
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Residues in contact with HIS 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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585A GLU 3.1 13.5 + - - +
586A GLU* 3.5 14.4 + - + +
588A PHE* 1.3 73.0 - - - +
590A SER* 1.3 62.9 + - - +
592A ARG* 3.3 27.2 + - - +
593A MET* 3.0 68.9 + - + +
594A ASP* 4.8 7.2 + - - -
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Residues in contact with SER 590 (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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579A PHE* 3.4 12.2 - - - +
580A HIS* 3.1 44.3 + - - -
586A GLU* 2.9 8.8 + - - -
587A LEU 3.2 7.6 + - - -
589A HIS* 1.3 77.9 + - - +
591A ILE* 1.3 62.7 + - - +
594A ASP* 2.6 56.2 + - - +
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Residues in contact with ILE 591 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543A PRO 3.1 27.1 - - - +
544A ASP 4.2 7.2 - - - +
546A ILE* 3.4 32.1 - - + +
548A PRO* 4.1 9.4 - - + +
551A LEU* 3.7 10.5 - - + -
563A TRP* 3.9 20.8 - - + +
579A PHE* 3.7 27.6 - - + -
587A LEU* 2.9 27.4 + - + +
588A PHE* 3.7 13.0 - - + +
589A HIS 3.4 0.2 - - - -
590A SER* 1.3 75.4 - - - +
592A ARG* 1.3 57.3 + - - +
616A ARG* 2.8 26.0 + - - -
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Residues in contact with ARG 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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548A PRO* 4.6 10.8 - - + +
551A LEU* 4.1 29.0 + - + +
552A LEU* 4.0 29.9 - - + +
585A GLU 5.3 0.8 + - - -
588A PHE* 3.1 22.0 + - - +
589A HIS* 3.6 35.4 - - - +
591A ILE* 1.3 76.3 - - - +
593A MET* 1.3 77.5 + - + +
616A ARG* 3.0 25.6 + - - +
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Residues in contact with MET 593 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A HIS* 3.0 49.5 + - + +
590A SER 3.2 0.2 + - - -
592A ARG* 1.3 99.7 - - + +
594A ASP* 1.3 69.7 + - - +
595A ASN* 4.1 5.4 + - - -
616A ARG* 3.8 7.4 + - - +
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Residues in contact with ASP 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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578A PRO 5.9 0.2 - - - +
579A PHE* 3.7 10.2 - - + -
580A HIS* 3.7 19.0 - - + +
589A HIS* 4.8 7.0 + - - -
590A SER* 2.6 50.2 + - - +
593A MET* 1.3 80.7 - - - +
595A ASN* 1.3 66.8 + - - +
596A PRO* 3.8 1.9 - - - +
616A ARG* 2.7 28.9 + - - -
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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