Contacts of the helix formed by residues 539 - 546 (chain A) in PDB entry 1ZVR
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 539 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLY* 3.3 23.0 - - - -
206A TRP* 3.3 46.1 - - - +
450A GLU* 4.9 0.2 + - - -
517A PHE* 3.6 1.8 - - - -
519A THR* 3.5 8.3 + - - -
538A VAL* 1.3 80.9 - - - +
540A LEU* 1.3 61.8 + - - +
541A TRP* 3.3 16.6 + - - -
542A SER* 2.8 27.4 + - - -
543A TYR 3.6 0.3 + - - -
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Residues in contact with LEU 540 (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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507A THR* 4.7 1.1 - - + -
508A ILE* 4.3 13.9 - - + -
511A HIS* 3.9 21.1 - - + -
517A PHE* 3.5 43.3 - - + +
519A THR* 2.8 19.9 + - - +
520A PHE* 3.9 25.6 - - + -
539A SER* 1.3 71.2 - - - +
541A TRP* 1.3 85.7 + - + +
543A TYR* 3.1 8.0 + - + +
544A ILE* 3.0 41.2 + - + +
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Residues in contact with TRP 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLY* 3.6 17.0 - - - -
208A LEU* 3.8 18.2 - - + -
445A PHE* 5.6 0.2 - + - -
446A GLU* 3.4 54.3 - - + +
449A VAL* 4.2 26.0 - - + -
450A GLU* 2.6 33.4 + - - +
504A PHE* 4.5 1.3 - + - -
508A ILE* 4.1 20.4 - - + -
519A THR* 4.2 12.7 - - + +
520A PHE* 4.7 3.4 - + - -
539A SER* 3.0 18.8 - - - +
540A LEU* 1.3 97.6 - - + +
542A SER* 1.3 58.4 + - - +
544A ILE* 3.8 19.7 - - + -
545A ASN* 2.8 37.0 + - - +
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Residues in contact with SER 542 (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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201A PHE* 3.6 11.9 - - - +
203A GLU* 3.2 21.1 + - - +
204A ASN* 3.5 4.9 + - - -
205A GLY* 2.7 26.7 + - - +
206A TRP* 5.3 0.2 - - - -
538A VAL* 3.9 13.5 - - - +
539A SER* 2.8 21.4 + - - -
541A TRP* 1.3 79.5 - - - +
543A TYR* 1.3 61.2 + - - +
546A SER* 3.0 28.6 + - - -
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Residues in contact with TYR 543 (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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197A TYR* 5.6 0.4 - - - -
201A PHE* 3.6 30.3 - + + -
503A TYR* 4.5 10.0 + - - -
507A THR* 4.2 13.9 - - + +
511A HIS* 4.6 7.6 - + - -
517A PHE* 3.4 37.2 - + + -
539A SER 3.6 0.8 + - - -
540A LEU* 3.1 8.6 + - + +
542A SER* 1.3 82.1 - - - +
544A ILE* 1.3 72.9 + - + +
546A SER* 3.6 5.2 + - - -
547A GLN* 3.4 30.8 + - + +
550A ASP* 5.5 1.4 + - - -
551A PHE* 3.8 28.1 - + - -
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Residues in contact with ILE 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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442A ILE* 4.6 4.0 - - + -
446A GLU* 3.5 18.4 - - - +
504A PHE* 3.8 33.2 - - + +
507A THR* 4.5 7.4 - - + -
508A ILE* 4.5 6.5 - - + -
540A LEU* 3.0 31.1 + - + +
541A TRP* 3.8 22.2 - - + +
543A TYR* 1.3 84.5 - - + +
545A ASN* 1.3 62.1 + - - +
547A GLN* 3.1 8.5 + - - +
548A LEU* 3.0 24.2 + - + -
551A PHE* 3.7 33.5 - - + -
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Residues in contact with ASN 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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203A GLU* 4.6 13.0 - - + +
205A GLY* 5.5 1.7 - - - -
208A LEU* 4.5 5.4 - - - +
442A ILE* 4.1 1.2 - - - +
443A ARG* 3.2 41.3 + - - +
446A GLU* 2.4 43.5 + - - +
541A TRP* 2.8 25.9 + - - +
544A ILE* 1.3 71.5 - - - +
546A SER* 1.3 55.5 + - - +
547A GLN 2.8 10.2 + - - -
548A LEU* 3.3 27.9 + - - +
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Residues in contact with SER 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PHE* 4.1 7.8 - - - -
202A PRO* 3.3 34.4 - - - +
203A GLU* 3.3 21.5 + - - +
542A SER 3.0 20.9 + - - -
543A TYR 3.8 3.1 - - - +
544A ILE 3.3 0.8 - - - -
545A ASN* 1.3 72.4 - - - +
547A GLN* 1.3 69.7 + - - +
549A GLU* 5.2 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