Contacts of the helix formed by residues 564 - 578 (chain E) in PDB entry 5ZCS
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 ASN 564 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727B MET* 6.4 1.3 - - - -
558E PRO* 4.9 13.0 - - + -
562E LEU 4.2 0.4 - - - -
563E ARG* 1.3 73.9 - - - +
565E TYR* 1.3 58.6 + - - +
566E LYS 3.5 2.0 - - - +
567E ASP* 3.9 19.1 - - + +
568E GLU* 3.1 26.3 + - - +
601E LEU* 6.1 5.6 - - + -
604E VAL* 5.5 10.8 - - + -
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Residues in contact with TYR 565 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563E ARG* 3.6 4.0 + - + +
564E ASN* 1.3 75.9 - - - +
566E LYS* 1.3 60.3 + - - +
568E GLU* 3.3 6.1 + - - +
569E GLN* 2.9 27.7 + - - +
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Residues in contact with LYS 566 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724B ALA 5.0 8.2 + - - +
725B PHE* 6.1 1.3 - - - -
727B MET* 3.7 32.8 - - + -
728B PRO* 4.4 17.9 - - + +
564E ASN* 4.5 0.2 - - - +
565E TYR* 1.3 75.8 - - - +
567E ASP* 1.3 60.9 + - - +
569E GLN* 3.3 7.9 + - - +
570E LEU* 2.9 29.5 + - - +
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Residues in contact with ASP 567 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B MET* 4.7 5.7 - - - -
554E ILE* 5.1 15.0 - - + -
564E ASN* 3.7 22.4 + - + +
565E TYR 3.3 0.4 - - - -
566E LYS* 1.3 78.5 - - - +
568E GLU* 1.3 58.0 + - - +
570E LEU* 3.5 4.8 + - - +
571E HIS* 2.9 30.2 + - - +
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Residues in contact with GLU 568 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486E GLY* 5.9 8.1 - - - -
564E ASN 3.1 20.1 + - - +
565E TYR* 3.7 6.3 - - - +
566E LYS 3.3 0.2 - - - -
567E ASP* 1.3 75.9 - - - +
569E GLN* 1.3 58.3 + - - +
571E HIS* 4.0 6.1 - - - +
572E ARG* 3.2 27.5 + - - +
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Residues in contact with GLN 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519E PHE* 5.1 15.7 - - + +
523E ASP* 4.2 21.7 - - + +
565E TYR 2.9 17.0 + - - +
566E LYS* 3.7 8.7 - - - +
568E GLU* 1.3 77.8 - - - +
570E LEU* 1.3 60.6 + - - +
572E ARG* 3.5 12.4 + - - +
573E PHE* 3.7 7.8 + - - +
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Residues in contact with LEU 570 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B PRO* 6.2 2.5 - - + -
523E ASP* 5.3 5.6 - - - +
526E GLU* 5.8 8.5 - - + -
566E LYS 2.9 17.4 + - - +
567E ASP* 3.9 6.1 - - - +
569E GLN* 1.3 75.8 - - - +
571E HIS* 1.3 62.0 + - - +
573E PHE* 3.5 16.8 + - - +
574E VAL* 4.0 5.0 + - - +
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Residues in contact with HIS 571 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567E ASP 2.9 18.8 + - - +
568E GLU* 4.1 6.3 - - - +
569E GLN 3.4 0.2 - - - -
570E LEU* 1.3 74.7 - - - +
572E ARG* 1.3 63.0 + - - +
573E PHE 3.3 0.2 - - - -
574E VAL* 3.4 20.7 + - - +
575E ARG* 4.4 1.6 + - - +
592E ASP* 5.6 10.3 - - + -
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Residues in contact with ARG 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482E MET* 6.4 2.9 - - - -
486E GLY* 5.0 12.1 - - - +
488E LYS* 5.7 7.1 - - + +
568E GLU 3.2 17.8 + - - +
569E GLN* 3.8 8.7 - - - +
570E LEU 3.3 0.6 - - - -
571E HIS* 1.3 76.5 - - - +
573E PHE* 1.3 60.0 + - - +
574E VAL 3.2 1.0 + - - -
575E ARG* 3.7 15.4 + - - +
576E ARG* 4.2 3.8 + - - +
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Residues in contact with PHE 573 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523E ASP* 4.8 19.1 - - + +
527E ALA* 4.8 12.8 - - + +
569E GLN 3.7 7.8 + - - +
570E LEU* 3.5 13.3 + - - +
571E HIS 3.3 1.0 - - - -
572E ARG* 1.3 76.3 - - - +
574E VAL* 1.3 59.4 + - - +
575E ARG 3.2 1.3 - - - -
576E ARG* 3.3 10.3 + - + +
577E LEU* 2.9 29.5 + - - +
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Residues in contact with VAL 574 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570E LEU 4.0 4.9 + - - +
571E HIS* 3.4 18.0 + - - +
572E ARG 3.2 1.2 - - - -
573E PHE* 1.3 78.0 - - - +
575E ARG* 1.3 62.0 + - - +
577E LEU* 3.6 7.0 + - - +
578E LEU* 3.2 24.1 + - - +
585E SER* 5.3 1.7 - - - -
588E TYR* 4.0 30.6 - - + +
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Residues in contact with ARG 575 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478E ARG* 6.4 2.2 - - + -
479E PHE* 5.8 8.5 - - + +
482E MET* 5.7 9.4 - - + -
488E LYS 5.9 1.3 - - - +
489E PRO* 5.7 10.3 - - + +
571E HIS 4.4 1.9 + - - +
572E ARG* 3.7 10.8 + - - +
573E PHE 3.2 0.4 - - - -
574E VAL* 1.3 79.3 - - - +
576E ARG* 1.3 60.2 + - - +
578E LEU* 3.6 16.9 + - - +
579E TYR* 4.5 1.7 + - - +
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Residues in contact with ARG 576 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492E LEU* 5.7 8.7 - - + -
496E HIS 5.7 0.3 - - - +
497E ILE* 5.9 2.8 - - - -
500E LYS* 3.9 29.4 - - + +
572E ARG 4.2 3.0 + - - +
573E PHE* 3.3 16.5 + - + +
575E ARG* 1.3 80.8 - - - +
577E LEU* 1.3 58.8 + - - +
578E LEU 3.2 1.0 + - - -
579E TYR* 3.8 17.3 + - - +
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Residues in contact with LEU 577 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527E ALA* 5.7 9.0 - - + +
530E ILE* 6.1 4.7 - - + -
573E PHE 2.9 17.7 + - - +
574E VAL* 3.9 7.4 - - - +
575E ARG 3.4 0.2 - - - -
576E ARG* 1.3 74.6 - - - +
578E LEU* 1.3 55.7 + - - +
579E TYR 3.2 6.8 + - - -
580E PHE 4.6 0.2 + - - -
581E TYR* 3.9 23.4 + - - +
584E SER* 4.8 12.7 - - - +
585E SER* 4.6 4.9 + - - -
588E TYR* 5.8 3.4 - - + -
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Residues in contact with LEU 578 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475E CYS* 5.7 9.0 - - + +
574E VAL 3.2 17.2 + - - +
575E ARG* 4.0 11.7 - - - +
576E ARG 3.2 2.0 - - - -
577E LEU* 1.3 75.9 - - - +
579E TYR* 1.3 59.4 + - - +
580E PHE 3.7 0.7 - - - -
581E TYR 4.4 2.9 - - - -
585E SER* 3.7 26.5 - - - -
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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