Contacts of the helix formed by residues 532 - 538 (chain C) in PDB entry 5ZX2
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 532 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C PHE 5.2 1.2 + - - -
374C GLY* 5.3 1.7 - - - -
482C ARG* 3.1 12.5 + - - +
507C ASN* 5.2 3.4 - - - -
511C PHE* 3.7 27.0 - - - +
512C ILE 3.9 5.5 + - - -
513C GLU* 4.0 16.4 - - - +
530C TYR 4.3 0.2 + - - -
531C LEU* 1.3 71.3 - - - +
533C ALA* 1.3 69.8 + - - +
534C ASP* 3.5 12.2 + - + +
535C GLU* 3.1 44.2 + - + +
536C GLU* 3.0 18.7 + - - +
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Residues in contact with ALA 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C HIS* 3.7 21.1 - - + -
373C PHE* 3.9 15.7 - - + -
374C GLY* 3.8 14.8 - - - +
478C SER* 4.2 4.9 - - - -
482C ARG* 3.2 26.8 - - - +
512C ILE 4.3 0.8 + - - +
532C THR* 1.3 79.1 + - - +
534C ASP* 1.3 63.6 + - - +
536C GLU* 3.3 10.2 + - - +
537C ASP* 3.3 20.6 + - - +
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Residues in contact with ASP 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LYS* 4.1 16.7 + - - +
318C LYS* 4.0 26.4 + - - +
372C HIS* 3.8 15.8 + - - -
374C GLY* 3.8 19.4 - - - +
375C ASN* 5.3 1.9 + - - +
532C THR* 3.3 11.1 + - + +
533C ALA* 1.3 77.3 - - - +
535C GLU* 1.3 65.1 + - + +
537C ASP* 3.1 22.3 + - - +
538C ARG* 3.8 13.1 + - - +
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Residues in contact with GLU 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C LYS* 5.9 1.1 - - - +
513C GLU* 5.0 4.4 - - - +
530C TYR 3.8 4.3 - - - +
531C LEU* 3.2 29.6 - - + +
532C THR* 3.1 38.5 + - + +
534C ASP* 1.3 76.8 - - + +
536C GLU* 1.3 59.7 + - - +
537C ASP 3.4 0.7 + - - -
538C ARG* 3.4 33.9 + - - +
539C HIS* 3.0 29.4 + - + +
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Residues in contact with GLU 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C PRO 5.9 1.1 - - - -
478C SER* 6.4 0.2 - - - -
480C TYR* 4.5 1.9 - - - +
482C ARG* 2.6 44.6 + - - +
516C TYR* 2.8 29.2 + - + -
531C LEU* 4.6 8.7 - - + +
532C THR 3.0 14.0 + - - +
533C ALA 3.5 6.1 - - - +
534C ASP 3.1 0.4 - - - -
535C GLU* 1.3 77.7 - - - +
537C ASP* 1.3 64.1 + - - +
539C HIS* 3.4 20.8 + - - +
541C VAL* 4.1 16.3 - - + +
562C ARG* 2.6 33.5 + - - +
563C ARG 4.3 1.9 - - - +
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Residues in contact with ASP 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C HIS* 3.0 30.2 + - - -
533C ALA 3.3 12.8 - - - +
534C ASP* 3.1 11.6 + - - +
536C GLU* 1.3 81.3 - - - +
538C ARG* 1.3 62.2 + - + +
563C ARG 3.4 18.1 - - - +
564C LYS* 3.5 21.2 - - + +
565C ALA* 4.4 21.1 + - - +
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Residues in contact with ARG 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C LYS* 3.6 30.3 - - - +
534C ASP* 4.2 12.7 + - - +
535C GLU* 3.4 40.1 + - - +
536C GLU 3.3 1.2 - - - -
537C ASP* 1.3 76.5 - - + +
539C HIS* 1.3 77.3 + - + +
540C VAL* 5.8 0.3 - - - +
564C LYS* 4.7 12.4 + - - +
577C ASP* 4.1 1.9 - - - +
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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