Contacts of the strand formed by residues 468 - 473 (chain A) in PDB entry 2EZT
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 ILE 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A ILE* 4.1 13.2 - - + -
440A GLN* 3.7 35.2 - - + +
441A VAL 2.9 12.7 + - - +
442A PHE* 3.3 32.9 - - + +
443A ASN 2.9 24.3 + - - +
466A PRO 4.6 0.4 - - - +
467A VAL* 1.3 71.4 - - - +
469A ASN* 1.3 61.1 + - - +
470A VAL* 3.8 13.7 + - + +
526A PHE* 5.5 0.4 - - + -
529A ALA* 4.5 9.6 - - + +
530A LYS* 4.4 9.4 - - - +
533A ALA* 3.5 28.9 - - + -
538A VAL* 3.8 15.3 - - + -
540A ILE* 4.9 3.6 - - + -
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Residues in contact with ASN 469 (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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443A ASN* 2.9 34.8 + - - +
457A LEU* 3.6 9.9 - - - +
460A GLN* 2.7 39.6 + - - -
467A VAL* 3.6 8.4 + - - +
468A ILE* 1.3 71.8 - - - +
470A VAL* 1.3 57.4 + - - +
471A VAL* 4.1 1.3 - - + -
511A MET* 3.8 12.3 - - - -
538A VAL 2.9 24.8 + - - +
539A LEU* 3.3 20.0 - - + -
540A ILE* 2.7 33.4 + - - +
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Residues in contact with VAL 470 (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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376A VAL* 3.7 29.8 - - + -
380A VAL* 4.4 4.0 - - + -
442A PHE* 4.8 1.3 - - + -
443A ASN* 2.8 10.6 + - - +
444A LEU* 4.0 22.0 - - + -
445A ALA* 3.0 26.2 + - - +
468A ILE* 4.2 19.5 - - + +
469A ASN* 1.3 78.4 - - - +
471A VAL* 1.3 63.9 + - - +
472A PHE* 3.6 14.5 - - + -
526A PHE* 4.3 21.5 - - + -
540A ILE* 3.4 13.5 - - + +
542A ALA* 4.9 0.2 - - + -
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Residues in contact with VAL 471 (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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443A ASN* 5.7 3.1 - - - +
445A ALA* 3.2 7.2 - - + +
447A ASP* 3.8 19.3 - - - -
450A ALA* 4.0 17.3 - - + -
469A ASN* 5.2 1.8 - - + -
470A VAL* 1.3 77.0 - - - +
472A PHE* 1.3 62.4 + - - +
473A THR* 3.6 17.6 + - - +
502A PHE* 3.8 24.9 - - + -
539A LEU* 4.0 29.8 - - + -
540A ILE 2.8 10.9 + - - +
541A ASP* 3.9 8.5 - - - +
542A ALA* 2.8 35.2 + - - +
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Residues in contact with PHE 472 (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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373A ALA* 3.9 31.9 - - + -
376A VAL* 3.7 35.9 - - + -
377A LEU* 4.0 16.2 - - + -
380A VAL* 5.5 0.2 - - + -
397A ILE* 3.5 36.8 - - + -
400A ASN* 5.8 0.4 - - - -
444A LEU* 4.4 4.9 - - + -
445A ALA 2.8 25.3 + - - +
446A GLY* 3.8 6.4 - - - -
447A ASP* 3.2 19.2 + - - +
470A VAL* 3.6 25.1 - - + -
471A VAL* 1.3 70.2 - - - +
473A THR* 1.3 60.9 + - - +
474A ASN* 3.3 10.4 + - - +
542A ALA* 3.7 3.8 - - + -
544A ILE* 4.0 16.8 - - + -
1510A MG 4.1 0.3 - - - -
1611A TDM 4.8 5.3 + - - +
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Residues in contact with THR 473 (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* 3.5 18.2 - - + +
471A VAL* 3.7 12.3 - - - +
472A PHE* 1.3 69.8 - - - +
474A ASN* 1.3 57.1 + - - +
475A CYS* 4.1 10.3 - - - -
499A ASP* 3.7 22.9 - - - +
500A ILE 4.3 9.1 + - - +
502A PHE* 4.4 0.5 - - - -
515A ARG* 4.0 8.7 - - - +
541A ASP* 2.5 28.4 + - - -
542A ALA 2.8 12.3 + - - -
543A VAL* 3.4 13.7 - - + +
544A ILE* 2.9 26.6 + - - +
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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