Contacts of the strand formed by residues 451 - 456 (chain A) in PDB entry 2ZB5
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 VAL 451 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A SER* 2.6 40.1 + - - +
448A HIS* 3.2 22.9 + - + +
449A ASN 3.4 1.3 - - - +
450A ASN* 1.3 85.0 - - - +
452A TYR* 1.3 75.5 + - - +
469A THR* 4.2 19.3 - - + -
470A LEU 3.3 9.0 - - - +
471A GLU* 3.9 26.0 - - + +
472A TRP* 4.0 0.2 - - - -
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Residues in contact with TYR 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 4.3 13.8 + - + +
359A ALA* 3.7 23.4 - - - +
364A LYS* 3.7 23.6 - - + +
443A LEU* 4.3 18.2 - - + -
444A TYR 3.2 17.9 - - - +
445A LYS* 3.5 29.4 - - + -
446A SER* 4.5 0.7 - - - +
449A ASN 5.2 5.3 + - - -
451A VAL* 1.3 80.6 - - - +
453A TRP* 1.3 68.4 + - - +
469A THR* 3.2 9.4 - - - +
470A LEU* 2.8 46.6 + - + +
472A TRP* 3.1 49.5 - + - -
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Residues in contact with TRP 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ASP 3.6 0.9 - - - +
443A LEU* 3.2 8.6 - - - +
444A TYR* 2.7 32.7 + - + +
445A LYS 3.4 23.8 + - - -
446A SER* 3.5 23.6 - - - +
447A ASN 5.0 0.4 - - - +
452A TYR* 1.3 74.1 - - - +
454A LEU* 1.3 60.1 + - - +
455A THR* 4.0 2.7 - - + -
467A ILE* 3.6 21.3 - - + -
468A ASN 3.6 12.1 - - - -
469A THR* 3.6 22.2 - - + -
481A TYR* 3.6 46.2 - + - -
516A ILE* 3.6 39.3 - - + +
521A ASP* 5.3 1.1 - - - -
522A LEU* 3.6 30.4 - - + +
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Residues in contact with LEU 454 (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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366A ALA* 3.7 21.5 - - + -
410A TYR* 3.7 46.4 - - + -
412A VAL* 5.9 0.4 - - + -
441A MET* 3.8 23.6 - - + -
442A ASP 3.3 3.4 - - - +
443A LEU* 3.9 13.5 - - + -
452A TYR 4.0 0.2 + - - -
453A TRP* 1.3 74.3 - - - +
455A THR* 1.3 59.4 + - - +
456A ILE* 4.2 7.9 - - + -
466A VAL 3.8 0.9 - - - +
467A ILE* 3.7 0.5 - - - -
468A ASN* 2.9 48.9 + - + +
470A LEU* 4.7 12.3 - - + -
478A VAL* 4.7 11.9 - - + -
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Residues in contact with THR 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A MET* 3.4 7.1 - - - +
442A ASP* 2.9 44.7 + - - +
444A TYR* 4.6 3.8 - - + -
454A LEU* 1.3 78.1 - - - +
456A ILE* 1.3 68.1 + - - +
457A PRO* 4.5 1.3 - - - +
466A VAL 3.1 7.4 - - - -
467A ILE* 4.2 13.2 - - + -
514A LEU* 3.4 37.2 + - + +
516A ILE* 3.8 34.8 - - + -
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Residues in contact with ILE 456 (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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410A TYR* 4.3 13.9 - - + +
434A LEU 5.8 0.9 - - - +
435A ILE* 4.6 14.1 - - + -
437A HIS* 3.5 36.1 - - + +
440A GLY 3.7 14.6 - - - +
441A MET* 3.7 28.3 - - + -
454A LEU* 4.2 4.9 - - + -
455A THR* 1.3 80.7 - - - +
457A PRO* 1.3 71.1 - - - +
458A PRO* 4.2 0.2 - - - +
465A GLY* 3.4 2.3 - - - -
466A VAL* 2.9 56.9 + - + +
514A LEU* 4.4 5.5 - - - +
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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