Contacts of the strand formed by residues 524 - 531 (chain A) in PDB entry 5ZF6
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 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLN* 5.0 5.1 - - - +
515A THR* 3.9 26.7 - - + -
516A LYS 4.1 2.7 - - - +
517A THR* 4.1 15.3 - - + +
523A GLU* 1.3 79.8 - - - +
525A GLU* 1.3 63.5 + - - +
526A ASP 3.6 23.8 - - - +
527A TYR* 4.2 12.6 - - + -
563A LEU* 4.4 13.2 - - + -
565A GLY 4.5 5.8 - - - +
566A ILE* 4.5 4.7 - - + -
567A PRO* 3.7 34.5 - - + +
570A ILE* 4.3 4.7 - - + -
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Residues in contact with GLU 525 (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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516A LYS* 2.6 53.2 + - - +
518A ASP* 3.2 44.7 - - + +
523A GLU 3.7 1.4 + - - -
524A ILE* 1.3 73.7 - - - +
526A ASP* 1.3 61.3 + - + +
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Residues in contact with ASP 526 (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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353A LEU* 4.3 8.5 - - + +
515A THR* 3.3 1.2 - - - -
516A LYS* 2.9 42.4 + - + +
524A ILE* 3.6 4.2 - - - +
525A GLU* 1.3 81.1 - - + +
527A TYR* 1.3 71.6 + - - +
528A ARG* 2.8 46.8 + - - -
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Residues in contact with TYR 527 (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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353A LEU* 4.3 2.0 - - - -
513A LEU* 3.8 9.6 - - + -
514A VAL 3.1 12.8 - - - +
515A THR* 3.7 15.5 - - + -
524A ILE* 4.2 8.3 - - + -
526A ASP* 1.3 87.9 + - - +
528A ARG* 1.3 82.6 + - - +
529A LEU* 4.5 9.9 - - + -
569A LYS* 3.5 28.2 + - - +
570A ILE* 3.6 36.3 - - + +
573A GLU* 2.8 39.4 + - - -
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Residues in contact with ARG 528 (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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352A VAL* 3.6 25.0 + - + +
353A LEU* 2.6 47.8 + - + +
356A TYR* 3.2 44.5 + - - -
364A LEU* 3.6 24.5 - - + -
513A LEU* 3.5 3.6 - - - -
514A VAL* 2.9 29.7 + - + +
526A ASP* 2.8 43.4 + - - -
527A TYR* 1.3 85.4 + - - +
529A LEU* 1.3 64.2 + - - +
530A LEU* 3.8 4.1 + - + +
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Residues in contact with LEU 529 (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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364A LEU* 3.3 17.4 - - - +
511A ILE* 4.0 3.4 - - + -
512A GLY 3.4 14.6 - - - +
513A LEU* 3.9 15.7 - - + -
527A TYR* 4.5 9.6 - - + -
528A ARG* 1.3 73.8 - - - +
530A LEU* 1.3 60.0 + - - +
543A MET* 3.8 17.9 - - + -
570A ILE* 3.9 11.9 - - + +
573A GLU* 3.6 27.4 - - + +
574A ALA* 3.5 34.1 - - + +
577A GLN* 3.1 32.8 + - - +
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Residues in contact with LEU 530 (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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348A PHE* 5.6 0.9 - - + -
352A VAL* 3.7 20.9 - - + -
358A ARG* 4.0 12.3 - - + +
364A LEU* 3.7 31.4 - - + -
511A ILE* 3.1 8.7 - - - +
512A GLY* 2.5 39.4 + - - -
513A LEU 4.3 3.4 - - - +
514A VAL* 4.3 18.8 - - + -
528A ARG 4.1 10.1 - - - +
529A LEU* 1.3 75.5 - - - +
531A THR* 1.3 61.2 + - - +
532A ASP 3.9 0.2 + - - -
533A ILE* 3.5 17.7 - - + +
537A GLU* 3.8 36.3 - - + +
577A GLN* 4.0 1.1 - - - -
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Residues in contact with THR 531 (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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358A ARG* 2.6 31.3 + - - +
362A ARG* 3.3 2.8 + - - -
364A LEU 3.0 13.8 + - - -
365A THR* 3.4 24.9 + - - +
366A SER 3.3 1.8 - - - +
367A LEU* 3.9 12.8 - - + -
509A VAL* 4.7 0.7 - - + -
511A ILE* 3.8 7.9 - - + -
530A LEU* 1.3 69.6 - - - +
532A ASP* 1.3 64.6 + - - +
577A GLN* 2.5 37.1 + - - +
581A ALA* 3.8 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