Contacts of the helix formed by residues 517 - 521 (chain A) in PDB entry 5ZE3
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 SER 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A VAL* 3.7 7.2 - - - +
479A GLN* 3.0 25.4 - - - -
515A GLU* 3.4 2.5 - - - +
516A LEU* 1.3 82.2 - - - +
518A LEU* 1.3 68.1 + - - +
519A ALA 3.8 1.1 + - - -
520A HIS* 2.6 54.1 + - - +
521A CYS 3.9 1.9 + - - -
434B LYS* 4.1 2.9 - - - -
802B SO4 3.5 25.0 + - - -
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Residues in contact with LEU 518 (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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435A LEU* 4.2 20.0 - - + -
448A VAL* 4.9 0.2 - - + -
450A VAL* 5.2 0.2 - - + -
463A VAL* 4.4 10.3 - - + -
468A TRP* 4.1 22.7 - - + -
472A GLU 4.7 2.2 - - - +
475A VAL* 3.7 9.2 - - + +
476A VAL* 3.9 21.1 - - + -
479A GLN* 2.8 14.5 + - - +
506A MET* 3.5 32.5 - - - +
509A VAL* 3.5 25.9 - - + +
511A CYS* 3.6 15.3 - - - -
517A SER* 1.3 71.1 - - - +
519A ALA* 1.3 61.7 + - - +
521A CYS* 3.1 15.8 + - - +
523A HIS* 4.6 2.6 - - - -
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLN* 5.8 0.4 - - - +
506A MET* 4.2 6.7 - - + +
517A SER* 2.9 2.4 + - - +
518A LEU* 1.3 78.4 - - - +
520A HIS* 1.3 55.7 + - - +
521A CYS 3.2 0.9 - - - -
523A HIS* 3.0 30.5 + - - -
519B ALA* 3.1 33.6 - - + +
520B HIS* 3.5 35.0 - - + +
523B HIS* 3.3 4.2 + - - -
802B SO4 3.9 9.2 - - - +
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Residues in contact with HIS 520 (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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515A GLU* 3.8 19.9 - - + +
516A LEU* 4.9 5.0 - - + +
517A SER* 2.6 41.6 + - - +
519A ALA* 1.3 68.6 - - - +
521A CYS* 1.3 63.4 + - - +
434B LYS* 4.6 23.3 + - + -
450B VAL* 4.7 14.6 - - + +
451B LEU 4.9 4.4 + - - -
452B VAL* 5.3 13.0 - - + -
505B VAL* 6.4 0.2 - - + -
506B MET* 4.6 19.4 - - + -
519B ALA* 3.8 21.0 - - + +
523B HIS* 3.8 14.4 - - - -
525B GLY* 4.3 8.8 - - - -
526B GLU* 4.6 2.5 + - - +
802B SO4 4.0 14.8 - - - -
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Residues in contact with CYS 521 (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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475A VAL* 4.3 2.7 - - - -
509A VAL* 4.3 2.9 - - + -
510A LYS 3.2 10.8 - - - +
511A CYS* 2.0 51.1 - - - -
515A GLU* 3.5 25.6 - - - -
518A LEU* 3.1 18.7 + - - +
519A ALA 3.4 1.0 - - - +
520A HIS* 1.3 83.8 - - - +
522A ARG* 1.3 68.3 + - - +
523A HIS* 3.1 17.7 - - - -
523B HIS* 3.8 5.0 + - - -
525B GLY* 4.4 2.7 - - - -
526B GLU* 5.5 0.7 - - - +
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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