Contacts of the helix formed by residues 542 - 553 (chain A) in PDB entry 5JZU
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 GLU 542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535A MET* 3.9 11.7 - - + -
540A ASN* 2.7 19.5 + - - +
541A LYS* 1.3 77.0 - - - +
543A ALA* 1.3 64.5 + - - +
544A TYR 3.3 2.0 - - - -
545A LYS* 3.1 27.9 + - + +
546A TRP* 3.4 11.8 - - + +
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Residues in contact with ALA 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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532A GLY* 3.4 27.6 - - - +
535A MET* 3.6 15.6 - - + -
536A GLN* 3.7 18.4 - - + -
540A ASN 3.4 15.5 + - - +
541A LYS* 3.1 2.3 - - - -
542A GLU* 1.3 78.7 - - - +
544A TYR* 1.3 62.2 + - + +
546A TRP* 3.0 20.4 + - - +
547A TYR* 3.2 16.2 + - + -
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Residues in contact with TYR 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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536A GLN* 3.5 23.3 - - + -
541A LYS 4.3 5.3 + - - +
542A GLU 3.3 0.4 - - - -
543A ALA* 1.3 79.7 - - + +
545A LYS* 1.3 59.6 + - - +
546A TRP 3.2 0.2 - - - -
547A TYR* 3.8 19.4 - + - +
548A GLU* 3.1 27.4 + - - +
559A VAL* 3.2 39.1 - - + +
560A TRP* 3.2 30.4 - + - -
562A ARG* 3.8 0.9 + - - -
724A GLU* 2.8 32.2 + - - -
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Residues in contact with LYS 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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541A LYS 5.1 0.6 + - - -
542A GLU* 3.1 22.9 + - + +
544A TYR* 1.3 79.3 - - - +
546A TRP* 1.3 63.2 + - + +
548A GLU* 3.8 6.0 - - - +
549A LEU* 3.3 23.4 + - - +
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Residues in contact with TRP 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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512A LYS* 3.7 28.9 - - + +
515A ILE* 4.1 21.3 - - + -
516A GLU* 3.8 31.2 - - + -
528A TYR* 3.7 37.8 - + + +
531A LEU* 3.5 26.0 - - + -
532A GLY* 4.9 3.4 - - - +
535A MET* 3.5 31.6 - - + +
542A GLU* 3.4 24.8 - - - +
543A ALA 3.0 7.4 + - - +
545A LYS* 1.3 82.2 - - + +
547A TYR* 1.3 60.4 + - - +
548A GLU 3.2 1.1 - - - -
549A LEU* 4.3 7.6 - - + +
550A GLY* 2.9 25.3 + - - -
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Residues in contact with TYR 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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528A TYR 4.1 4.5 - - - -
529A PHE* 3.8 13.7 + - - -
532A GLY* 3.7 18.6 - - - -
533A ASP* 3.0 21.1 + - - +
536A GLN* 2.8 36.0 + - + -
543A ALA 3.2 14.3 + - - -
544A TYR* 3.9 24.9 - + - +
545A LYS 3.5 0.2 - - - -
546A TRP* 1.3 80.1 - - - +
548A GLU* 1.3 56.4 + - - +
550A GLY 3.4 0.3 + - - -
551A HIS* 3.0 28.4 + - - +
556A PHE* 3.6 13.8 - + - -
559A VAL* 3.7 20.2 - - + +
562A ARG* 3.2 55.3 + - - -
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Residues in contact with GLU 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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544A TYR 3.1 20.4 + - - +
545A LYS* 3.8 7.9 - - - +
547A TYR* 1.3 77.4 - - - +
549A LEU* 1.3 56.7 + - - +
551A HIS* 3.2 15.2 + - - +
552A LYS* 2.9 27.6 + - + +
559A VAL* 4.0 23.7 - - + +
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Residues in contact with LEU 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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528A TYR* 4.3 13.0 - - + -
545A LYS 3.3 15.8 + - - +
546A TRP* 3.9 13.2 - - + +
547A TYR 3.4 0.2 - - - -
548A GLU* 1.3 76.1 - - - +
550A GLY* 1.3 66.5 + - - +
552A LYS* 3.0 8.7 + - - +
553A ARG* 3.0 32.4 + - + +
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Residues in contact with GLY 550 (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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528A TYR* 3.6 23.7 - - - -
546A TRP 2.9 18.1 + - - -
547A TYR 3.8 2.0 - - - -
549A LEU* 1.3 77.3 - - - +
551A HIS* 1.3 58.0 + - - +
553A ARG 3.5 0.9 + - - -
554A GLY 3.5 2.6 + - - -
555A HIS* 3.1 34.2 + - - +
556A PHE* 3.9 12.8 - - - -
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Residues in contact with HIS 551 (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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547A TYR 3.0 15.2 + - - +
548A GLU* 3.4 16.6 - - - +
550A GLY* 1.3 73.9 - - - +
552A LYS* 1.3 68.3 + - + +
553A ARG 3.1 0.4 - - - -
554A GLY* 3.1 14.0 + - - -
556A PHE* 3.1 32.0 + - + +
557A ALA 3.7 18.4 + - - -
558A SER* 3.8 9.9 - - - -
559A VAL* 4.2 20.4 - - + -
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Residues in contact with LYS 552 (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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548A GLU* 2.9 16.6 + - + +
549A LEU* 3.0 12.1 + - - +
551A HIS* 1.3 80.3 - - + +
553A ARG* 1.3 62.3 + - + +
554A GLY 3.3 1.5 + - - -
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Residues in contact with ARG 553 (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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523A ASP* 3.4 19.1 - - - +
528A TYR* 3.3 24.2 - - - +
549A LEU* 3.0 21.3 + - + +
550A GLY 3.5 0.2 + - - -
551A HIS 3.1 0.4 - - - -
552A LYS* 1.3 79.8 - - + +
554A GLY* 1.3 60.1 + - - +
555A HIS* 3.5 27.1 + - + +
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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