Contacts of the helix formed by residues 575 - 584 (chain A) in PDB entry 2JY5
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 575 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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572A THR* 2.8 31.8 + - - +
573A GLY 4.4 4.0 - - - +
574A GLY* 1.3 73.0 - - - +
576A ILE* 1.3 59.8 + - - +
577A ASN* 3.2 4.0 - - - +
578A ALA* 3.6 20.0 - - + +
579A ALA 2.8 21.1 + - - -
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Residues in contact with ILE 576 (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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550A GLN* 3.0 37.5 - - - +
553A GLN* 3.0 45.8 - - + +
554A LEU* 3.6 25.4 - - + +
569A LEU* 3.6 13.7 - - + -
574A GLY 2.7 14.5 + - - +
575A ASP* 1.3 69.7 - - - +
577A ASN* 1.3 60.2 + - - +
579A ALA* 3.0 8.2 + - - +
580A ILE* 2.7 40.5 + - + +
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Residues in contact with ASN 577 (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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553A GLN* 6.3 0.6 - - - +
575A ASP* 5.0 1.3 - - - +
576A ILE* 1.3 79.8 - - - +
578A ALA* 1.3 65.8 + - - +
579A ALA 3.0 1.3 - - - -
580A ILE* 3.0 32.0 + - - +
581A GLU* 3.2 21.7 + - - +
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Residues in contact with ALA 578 (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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572A THR* 4.3 6.5 - - + -
575A ASP* 3.3 30.2 + - + +
577A ASN* 1.3 79.6 - - - +
579A ALA* 1.3 59.6 + - - +
581A GLU* 3.7 13.1 + - - +
582A ARG* 3.2 23.7 + - - +
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Residues in contact with ALA 579 (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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554A LEU* 3.9 7.6 - - + -
568A ALA* 3.8 20.5 - - + +
569A LEU* 4.5 0.7 - - + -
572A THR* 3.5 24.0 - - + +
575A ASP 2.8 13.8 + - - +
576A ILE* 3.1 15.5 - - - +
578A ALA* 1.3 76.4 - - - +
580A ILE* 1.3 50.6 + - - +
582A ARG* 4.5 3.4 - - - +
583A LEU* 2.7 42.8 + - - +
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Residues in contact with ILE 580 (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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553A GLN* 5.1 5.4 - - + +
554A LEU* 3.4 16.8 - - + -
557A MET* 3.4 48.7 - - + -
559A PHE* 4.1 11.3 - - + -
576A ILE* 2.7 34.3 + - + +
577A ASN* 3.0 29.4 + - - +
579A ALA* 1.3 73.2 - - - +
581A GLU* 1.3 64.0 + - + +
583A LEU* 4.0 1.0 - - - +
584A LEU* 3.2 33.4 + - + +
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Residues in contact with GLU 581 (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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577A ASN* 3.2 18.1 + - - +
578A ALA* 3.9 13.8 - - - +
580A ILE* 1.3 80.4 - - + +
582A ARG* 1.3 58.9 + - - +
584A LEU* 3.6 16.7 - - + +
585A GLY* 3.4 14.9 + - - -
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Residues in contact with ARG 582 (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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568A ALA* 6.1 3.1 - - + -
571A ALA* 5.4 12.0 - - - +
572A THR* 5.4 8.7 - - + -
578A ALA 3.2 16.7 + - - +
579A ALA* 4.0 4.5 - - - +
581A GLU* 1.3 78.0 - - - +
583A LEU* 1.3 64.2 + - + +
585A GLY* 2.9 20.3 + - - -
586A SER 3.6 4.9 + - - -
587A SER* 4.1 29.1 + - - +
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Residues in contact with LEU 583 (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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554A LEU* 3.4 33.2 - - + -
559A PHE* 3.3 42.7 - - + -
561A ASN* 5.6 1.6 - - + +
564A ALA* 4.0 24.0 - - + +
565A ASN* 3.8 6.7 - - - +
568A ALA* 4.4 7.0 - - + -
579A ALA 2.7 22.0 + - - +
580A ILE 4.0 1.3 - - - +
582A ARG* 1.3 71.1 - - - +
584A LEU* 1.3 59.3 + - - +
585A GLY 3.0 5.1 + - - -
586A SER 3.8 6.6 + - - +
587A SER* 3.5 35.6 - - - +
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Residues in contact with LEU 584 (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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559A PHE* 3.8 20.0 - - + -
580A ILE* 3.2 23.1 + - + +
581A GLU* 3.6 18.8 - - + +
583A LEU* 1.3 77.8 - - - +
585A GLY* 1.3 72.1 + - - +
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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