Contacts of the helix formed by residues 534 - 548 (chain A) in PDB entry 1ZM9
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 GLY 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A VAL* 3.4 19.1 - - - +
532A GLY 3.3 2.0 - - - -
533A THR* 1.3 81.3 - - - +
535A GLU* 1.3 67.5 + - - +
536A LEU 3.4 2.2 - - - -
537A HIS* 3.8 8.2 - - - +
538A LEU* 3.2 21.7 + - - +
729A PHE* 4.5 9.0 - - - -
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Residues in contact with GLU 535 (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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489A VAL* 4.1 10.8 - - - +
534A GLY* 1.3 72.6 - - - +
536A LEU* 1.3 61.2 + - + +
538A LEU* 3.8 3.6 - - - +
539A GLU* 3.0 28.4 + - + +
559A PRO* 6.0 3.3 - - + +
729A PHE* 5.6 1.4 - - - -
777A SER* 3.5 10.1 + - - +
778A PHE* 3.4 29.4 - - + +
779A GLY* 2.4 39.8 + - - -
780A PHE 4.1 0.7 + - - -
781A THR* 5.6 0.9 + - - -
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Residues in contact with LEU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A HIS* 6.3 0.7 - - + -
110A ASP* 3.9 38.8 - - + +
111A PHE* 4.1 32.5 - - + -
534A GLY 3.4 0.2 - - - -
535A GLU* 1.3 79.2 - - + +
537A HIS* 1.3 65.7 + - + +
539A GLU* 2.8 10.2 + - + +
540A ILE* 2.7 48.4 + - + +
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Residues in contact with HIS 537 (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 ASP* 3.5 30.0 + - - -
517A CYS* 3.5 19.2 + - + -
518A VAL* 4.2 2.0 + - - -
532A GLY* 3.4 9.6 - - - -
533A THR* 2.6 48.7 + - - -
534A GLY* 3.7 14.0 + - - +
535A GLU 3.5 0.4 - - - -
536A LEU* 1.3 86.6 - - + +
538A LEU* 1.3 60.1 + - - +
540A ILE* 3.6 5.5 + - - +
541A CYS* 3.1 35.2 + - - -
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Residues in contact with LEU 538 (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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489A VAL* 4.1 13.7 - - + +
490A GLN* 4.0 16.2 - - - +
491A VAL* 3.7 28.9 - - + -
518A VAL* 5.7 0.2 - - + -
530A VAL* 3.3 46.2 - - + +
531A ALA 4.2 0.2 - - - -
532A GLY* 3.9 15.0 - - - +
534A GLY 3.2 14.1 + - - +
535A GLU* 3.8 2.7 - - - +
536A LEU 3.1 0.4 - - - -
537A HIS* 1.3 78.8 - - - +
539A GLU* 1.3 69.8 + - - +
541A CYS* 2.8 8.6 + - + +
542A LEU* 2.8 34.9 + - + +
559A PRO* 5.3 4.9 - - + -
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Residues in contact with GLU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLU* 3.0 17.7 + - + +
536A LEU* 2.8 16.3 + - + +
538A LEU* 1.3 77.9 - - - +
540A ILE* 1.3 70.4 + - + +
542A LEU* 3.2 22.3 + - - +
543A GLN* 3.2 31.7 + - - +
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Residues in contact with ILE 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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111A PHE* 4.1 29.6 - - + -
536A LEU* 2.7 43.2 + - + +
537A HIS* 3.8 5.6 - - - +
539A GLU* 1.3 74.7 - - + +
541A CYS* 1.3 65.3 + - - +
543A GLN* 2.9 33.6 + - - +
544A ASP* 3.0 33.8 - - - +
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Residues in contact with CYS 541 (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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511A LEU* 3.9 23.8 - - + +
515A ASP* 4.7 5.6 - - - -
518A VAL* 3.7 33.9 - - + -
530A VAL* 4.7 5.2 - - + -
537A HIS* 3.1 33.3 + - - +
538A LEU* 2.8 17.5 + - - +
540A ILE* 1.3 76.8 - - - +
542A LEU* 1.3 61.1 + - - +
544A ASP* 3.6 6.3 + - - +
545A LEU* 3.2 22.2 + - - +
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Residues in contact with LEU 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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491A VAL* 3.6 30.1 - - + -
493A VAL* 4.2 17.0 - - + -
530A VAL* 4.3 13.7 - - + -
538A LEU* 2.8 32.5 + - + +
539A GLU* 3.5 18.8 - - - +
541A CYS* 1.3 70.8 - - - +
543A GLN* 1.3 64.8 + - - +
545A LEU* 3.2 10.4 + - + +
546A GLU* 3.1 23.6 + - - +
554A LEU* 5.7 0.3 - - - +
556A ILE* 3.9 35.4 - - + +
559A PRO* 6.5 0.7 - - + -
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Residues in contact with GLN 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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539A GLU* 3.2 33.5 + - - +
540A ILE* 2.9 23.4 + - - +
542A LEU* 1.3 75.2 - - - +
544A ASP* 1.3 68.3 + - - +
545A LEU 2.8 6.4 + - - -
546A GLU* 3.1 5.0 + - - -
547A HIS* 2.9 44.2 + - + +
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Residues in contact with ASP 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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511A LEU* 5.1 2.9 - - + -
540A ILE* 3.0 32.4 + - - +
541A CYS* 3.9 6.7 - - - +
543A GLN* 1.3 81.4 - - - +
545A LEU* 1.3 52.9 + - - +
547A HIS* 4.7 1.8 - - - -
548A ASP* 3.1 31.9 + - - +
549A HIS* 2.6 40.3 + - + +
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Residues in contact with LEU 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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493A VAL* 4.4 12.3 - - + -
504A LEU* 4.1 4.7 - - + -
507A GLY* 3.6 35.2 - - - +
508A LEU* 3.4 27.1 - - + +
511A LEU* 3.9 18.2 - - + -
530A VAL* 4.7 2.2 - - + -
541A CYS 3.2 12.4 + - - +
542A LEU* 3.2 14.3 + - + +
543A GLN 2.8 2.8 + - - -
544A ASP* 1.3 75.6 - - - +
546A GLU* 1.3 59.6 + - - +
547A HIS 3.0 5.3 + - - -
549A HIS* 3.7 10.3 - - + -
550A ALA* 3.0 34.1 + - + +
551A GLY 3.1 2.6 + - - -
554A LEU* 4.0 20.0 - - + -
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Residues in contact with GLU 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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542A LEU 3.1 10.3 + - - +
543A GLN* 3.1 5.2 + - - +
545A LEU* 1.3 78.0 - - - +
547A HIS* 1.3 76.6 + - + +
551A GLY* 3.2 18.4 - - - +
552A VAL 3.4 21.5 - - - +
553A PRO* 4.1 11.4 - - + +
554A LEU* 3.9 24.2 + - + +
556A ILE* 3.7 22.6 - - + +
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Residues in contact with HIS 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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543A GLN* 2.9 32.2 + - + +
544A ASP* 4.7 1.1 - - - -
546A GLU* 1.3 105.2 + - + +
548A ASP* 1.3 73.9 + - - +
551A GLY* 3.9 10.3 - - - -
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Residues in contact with ASP 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 ASP* 3.1 27.6 + - - +
547A HIS* 1.3 93.2 - - - +
549A HIS* 1.3 74.2 + - + +
550A ALA 2.9 4.6 + - - -
551A GLY* 3.6 5.7 + - - -
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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