Contacts of the helix formed by residues 501 - 509 (chain A) in PDB entry 2EZ9
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 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A ASP* 3.5 6.2 + - - +
500A ILE* 1.3 72.5 - - - +
502A PHE* 1.3 58.3 + - - +
503A SER* 2.6 32.3 + - - -
504A LYS* 3.1 51.7 + - + +
505A ILE* 3.1 14.2 + - - +
515A ARG* 3.4 30.0 + - - +
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Residues in contact with PHE 502 (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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447A ASP* 4.1 11.9 - - + -
450A ALA* 3.8 19.3 - - + -
451A SER* 3.5 35.4 - - - -
454A MET* 3.9 27.1 - - + -
457A LEU* 4.7 4.0 - - + -
471A VAL* 3.8 30.7 - - + -
473A THR* 4.2 3.8 - - - -
500A ILE* 3.3 24.2 + - + -
501A ASP* 1.3 70.1 - - - +
503A SER* 1.3 60.5 + - - +
505A ILE* 3.6 17.2 - - + +
506A ALA* 2.8 29.8 + - - +
539A LEU* 3.7 23.8 - - + +
541A ASP* 2.9 19.0 + - - +
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Residues in contact with SER 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ASP* 2.6 24.4 + - - -
502A PHE* 1.3 77.5 - - - +
504A LYS* 1.3 59.9 + - - +
506A ALA* 3.7 2.8 + - - +
507A ASP* 3.1 25.3 + - - +
513A ALA* 3.7 19.7 - - - +
514A PHE* 3.8 30.1 - - - -
515A ARG* 3.8 9.3 - - - +
539A LEU* 4.4 1.1 - - - -
541A ASP* 4.0 4.6 + - - +
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Residues in contact with LYS 504 (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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501A ASP* 3.1 38.1 + - + +
503A SER* 1.3 79.2 + - - +
505A ILE* 1.3 59.9 + - + +
506A ALA 3.3 0.2 - - - -
507A ASP* 3.3 9.7 + - + +
508A GLY* 2.9 24.9 + - - -
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Residues in contact with ILE 505 (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 MET* 4.1 37.0 - - + +
457A LEU* 4.1 20.4 - - + -
500A ILE* 3.7 23.8 - - + -
501A ASP 3.1 14.1 + - - +
502A PHE* 3.6 15.5 - - + +
504A LYS* 1.3 75.2 - - + +
506A ALA* 1.3 63.7 + - - +
508A GLY* 3.1 12.3 + - - -
509A VAL* 3.1 19.8 + - + +
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Residues in contact with ALA 506 (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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457A LEU* 5.0 3.1 - - - +
502A PHE 2.8 18.5 + - - +
503A SER 3.7 0.4 - - - +
505A ILE* 1.3 77.1 - - - +
507A ASP* 1.3 59.8 - - - +
509A VAL* 3.0 12.9 + - - +
510A HIS 3.0 5.2 + - - -
511A MET* 2.9 36.8 + - + +
513A ALA* 3.5 26.0 - - + -
539A LEU* 4.1 17.3 - - + -
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Residues in contact with ASP 507 (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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503A SER 3.1 16.2 + - - +
504A LYS* 3.3 13.3 + - + +
506A ALA* 1.3 73.1 - - - +
508A GLY* 1.3 58.4 + - - +
510A HIS* 3.0 27.9 + - - +
511A MET 3.7 8.4 + - - +
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Residues in contact with GLY 508 (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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504A LYS 2.9 14.2 + - - -
505A ILE* 3.1 6.7 + - - -
507A ASP* 1.3 76.9 - - - +
509A VAL* 1.3 59.7 + - - +
510A HIS* 3.3 16.8 + - - -
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Residues in contact with VAL 509 (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 MET 5.0 3.1 - - - +
455A GLN* 4.7 6.7 - - - +
457A LEU* 3.9 31.2 - - + +
458A ALA* 4.0 29.3 - - + +
461A VAL* 3.4 16.2 - - + +
505A ILE* 3.1 16.1 + - + +
506A ALA* 3.0 19.7 + - - +
508A GLY* 1.3 76.9 - - - +
510A HIS* 1.3 74.2 + - - +
511A MET* 4.1 9.4 - - + -
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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