Contacts of the strand formed by residues 469 - 478 (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 THR 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A THR 3.5 1.6 - - - +
399A PHE* 3.4 9.0 - - - -
400A ASP* 2.7 32.9 + - + +
401A SER 3.2 22.1 + - - +
402A LEU* 3.2 22.1 + - - +
404A SER* 4.7 9.6 + - - +
422A ASN* 3.7 23.6 + - - +
424A MET* 4.5 12.1 - - + -
468A PHE* 1.3 72.6 - - - +
470A ILE* 1.3 65.2 + - - +
471A ARG* 3.6 19.9 + - + -
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Residues in contact with ILE 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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397A VAL* 4.2 6.3 - - + -
398A THR 4.3 1.3 - - - -
399A PHE* 4.4 3.6 - - + -
421A LYS 5.5 1.1 - - - +
422A ASN 3.2 11.6 + - - +
423A PHE* 3.5 20.4 - - + -
424A MET* 2.9 31.0 + - - +
462A ILE* 4.2 20.9 - - + -
463A PRO* 5.1 0.2 - - + -
466A PHE* 3.8 35.4 - - + -
468A PHE 4.1 1.1 - - - +
469A THR* 1.3 73.4 - - - +
471A ARG* 1.3 62.1 + - - +
472A VAL* 4.0 5.2 - - + -
495A LEU* 3.5 27.1 - - + -
500A VAL* 3.8 31.2 - - + -
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Residues in contact with ARG 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A THR 3.6 0.9 - - - +
397A VAL* 3.5 2.9 - - - -
398A THR* 2.9 66.5 + - - +
400A ASP* 4.2 24.8 + - + +
404A SER* 6.1 0.4 - - - -
424A MET* 3.7 31.0 - - + -
426A HIS* 5.1 13.6 - - + -
469A THR* 4.1 11.0 - - + +
470A ILE* 1.3 75.0 - - - +
472A VAL* 1.3 62.6 + - - +
473A THR* 4.8 11.6 + - - +
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Residues in contact with VAL 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A CYS* 4.8 5.6 - - + -
396A THR 3.2 9.9 - - - +
397A VAL* 4.2 7.0 - - + -
423A PHE* 3.7 26.7 - - + -
424A MET 2.9 12.0 + - - +
425A LEU* 3.3 25.8 - - + -
426A HIS* 2.9 28.2 + - - +
470A ILE* 4.0 7.0 - - + -
471A ARG* 1.3 75.0 - - - +
473A THR* 1.3 70.3 + - - +
474A SER 4.9 0.2 - - - +
491A GLY* 4.2 18.2 - - - -
495A LEU* 4.0 21.1 - - + -
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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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394A LEU 3.5 2.1 - - - +
395A CYS* 3.2 3.7 - - - -
396A THR* 2.9 45.9 + - - +
426A HIS* 3.5 16.9 + - + +
427A TYR 5.9 1.6 - - - -
471A ARG* 4.1 13.3 + - - +
472A VAL* 1.3 77.4 + - - +
474A SER* 1.3 64.0 + - - +
475A GLU* 3.8 30.5 - - + +
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Residues in contact with SER 474 (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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393A VAL* 3.8 9.2 - - - +
394A LEU 3.5 3.1 - - - -
395A CYS* 3.3 21.6 - - - -
425A LEU* 4.9 10.5 - - - +
426A HIS 3.1 10.6 + - - +
427A TYR* 3.5 30.5 - - - -
472A VAL* 4.2 0.4 - - - +
473A THR* 1.3 73.5 - - - +
475A GLU* 1.3 61.7 + - - +
476A VAL* 4.0 2.3 + - - +
487A SER* 2.9 37.7 + - - -
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Residues in contact with GLU 475 (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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393A VAL* 3.5 1.1 - - - -
394A LEU* 2.9 42.3 + - + +
396A THR* 6.1 2.9 - - + +
427A TYR 5.6 1.3 - - - -
473A THR* 3.8 22.9 - - + +
474A SER* 1.3 73.9 - - - +
476A VAL* 1.3 63.4 + - - +
477A LEU* 3.4 10.2 + - + +
629B LYS* 3.3 40.5 - - + +
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Residues in contact with VAL 476 (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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392A GLN 3.8 5.2 - - - +
393A VAL* 3.8 11.2 - - + -
427A TYR* 3.2 41.9 - - + +
474A SER 4.0 2.0 + - - +
475A GLU* 1.3 70.0 - - - +
477A LEU* 1.3 62.3 + - - +
478A GLU 3.6 21.5 - - - +
479A SER* 3.8 20.6 - - - -
483A SER* 3.7 15.7 - - - -
487A SER* 4.7 0.4 - - - +
629B LYS* 4.9 3.5 + - - -
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Residues in contact with LEU 477 (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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385A LEU* 4.1 14.6 - - + -
392A GLN* 3.0 38.1 + - - +
394A LEU* 4.1 10.5 - - + +
475A GLU* 3.5 20.6 - - + +
476A VAL* 1.3 76.3 - - - +
478A GLU* 1.3 62.0 + - - +
623B PRO 4.2 1.8 - - - +
624B GLY* 3.7 31.8 - - - +
626B TYR* 4.0 26.5 - - + -
629B LYS* 3.4 34.8 - - + +
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Residues in contact with GLU 478 (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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306A LYS* 5.9 3.4 - - + +
387A GLN* 3.8 13.3 + - - -
390A GLN* 3.1 57.3 + - + +
391A THR* 3.3 3.5 - - - +
392A GLN* 2.8 40.5 + - + +
476A VAL* 3.6 6.1 - - - +
477A LEU* 1.3 78.7 - - - +
479A SER* 1.3 61.2 + - - +
624B GLY* 5.7 2.7 - - - -
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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