Contacts of the strand formed by residues 543 - 549 (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 MET 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A ILE* 3.3 22.7 - - + +
512A GLY* 3.4 38.0 - - - +
513A LEU* 3.5 21.2 + - + -
529A LEU* 3.8 13.7 - - + -
533A ILE* 3.8 5.9 - - - +
537A GLU 5.3 0.7 - - - +
538A ASP* 4.3 9.9 + - - +
541A GLY* 3.6 1.8 - - - -
542A ASP* 1.3 82.2 + - - +
544A ASP* 1.3 62.3 + - - +
545A PHE* 3.7 34.5 - - + +
560A ASP 3.2 11.2 - - - +
561A ILE* 4.1 13.7 - - + -
562A LYS* 4.9 1.6 - - - +
566A ILE* 3.9 23.8 - - - -
570A ILE* 5.1 0.7 - - - -
574A ALA* 4.5 3.6 - - + -
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Residues in contact with ASP 544 (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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482A SER* 5.1 6.5 + - - -
510A ALA* 3.8 13.9 - - - +
511A ILE 4.1 1.1 - - - -
533A ILE* 3.5 16.2 - - - +
538A ASP* 3.6 29.3 - - - +
543A MET* 1.3 71.8 - - - +
545A PHE* 1.3 60.5 - - - +
546A LYS* 3.2 32.9 + - - +
558A GLN 3.3 3.8 - - - +
560A ASP* 2.9 43.9 + - + +
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Residues in contact with PHE 545 (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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229A LEU* 4.4 4.0 - - + -
509A VAL 3.5 2.1 - - - +
510A ALA* 3.2 2.1 - - - -
511A ILE* 2.7 52.0 + - + +
543A MET* 3.7 27.1 - - + -
544A ASP* 1.3 68.5 + - - +
546A LYS* 1.3 61.3 + - - +
547A ILE* 4.2 14.8 - - + +
557A LEU* 3.5 25.4 - - + -
558A GLN 4.2 1.8 - - - -
559A ALA* 3.6 26.7 - - + +
561A ILE* 5.6 0.4 - - + -
571A VAL* 3.9 30.5 - - + -
574A ALA* 4.1 16.2 - - + -
575A ILE* 3.7 33.7 - - + -
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Residues in contact with LYS 546 (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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450A HIS* 6.1 1.6 + - - -
453A LEU* 4.2 12.1 - - + +
482A SER* 3.9 25.4 - - - +
484A SER* 5.1 7.6 - - - -
485A MET* 4.0 20.5 - - + +
509A VAL 3.6 4.0 - - - -
510A ALA* 3.9 12.1 - - + -
544A ASP* 3.5 25.8 + - - +
545A PHE* 1.3 70.3 - - - +
547A ILE* 1.3 58.4 + - - +
556A ALA 4.7 0.2 - - - -
557A LEU* 3.3 3.7 - - - +
558A GLN* 2.8 68.4 + - - +
560A ASP* 2.5 31.0 + - - -
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Residues in contact with ILE 547 (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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241A PHE* 4.8 2.5 - - + -
485A MET* 3.9 2.7 - - - -
508A GLY* 3.5 0.7 - - - -
509A VAL* 3.1 34.3 + - + +
545A PHE* 4.2 13.7 - - + +
546A LYS* 1.3 74.8 - - - +
548A ALA* 1.3 65.9 + - - +
554A ILE* 3.7 37.7 - - + -
556A ALA 3.4 13.7 - - - +
557A LEU* 3.8 16.6 - - + -
575A ILE* 4.1 25.6 - - + +
578A ALA* 3.5 31.2 - - + -
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Residues in contact with ALA 548 (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 ALA* 3.8 27.8 - - + -
485A MET* 3.8 10.5 - - + -
488A ALA* 4.9 1.6 - - + -
506A VAL* 4.6 2.2 - - + -
507A ALA 3.2 14.8 - - - +
508A GLY* 3.6 9.0 - - - -
547A ILE* 1.3 78.7 - - - +
549A GLY* 1.3 59.5 + - - +
554A ILE* 3.6 6.2 - - - +
555A THR* 2.9 20.7 + - - +
556A ALA* 2.9 16.2 + - + +
582A LYS* 4.8 4.0 - - - -
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Residues in contact with GLY 549 (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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506A VAL* 3.3 5.9 - - - +
507A ALA 2.9 32.4 + - - +
548A ALA* 1.3 76.2 - - - +
550A THR* 1.3 66.2 + - - -
553A GLY 3.4 11.7 - - - -
554A ILE* 4.0 0.4 - - - -
555A THR* 3.6 17.0 - - - -
582A LYS* 3.6 10.1 - - - +
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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