Contacts of the helix formed by residues 529 - 540 (chain A) in PDB entry 4Z1H
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 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A CYS* 3.5 20.3 - - - -
502A ALA 4.2 0.6 + - - -
527A CYS 3.6 0.2 - - - -
528A PHE* 1.3 89.6 - - + +
530A GLN* 1.3 67.2 + - - +
531A PHE* 3.4 45.6 - - + -
532A ASP* 3.4 15.8 + - - +
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Residues in contact with GLN 530 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A CYS 5.8 0.7 - - - -
529A GLU* 1.3 75.7 + - - +
531A PHE* 1.3 59.1 + - - +
533A GLU* 3.1 14.3 + - - +
534A LEU* 2.9 55.5 + - + +
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Residues in contact with PHE 531 (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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449A ARG* 3.2 39.7 - - - +
529A GLU* 3.4 41.1 - - + -
530A GLN* 1.3 79.5 - - + +
532A ASP* 1.3 82.6 + - - +
534A LEU* 3.9 11.4 - - + +
535A THR* 2.5 39.5 + - - +
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Residues in contact with ASP 532 (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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441A PHE* 5.1 0.5 - - - -
449A ARG* 3.2 26.4 + - - +
470A TYR* 3.1 43.4 + - + +
501A CYS* 4.1 0.9 - - - -
527A CYS* 3.6 13.9 - - + +
528A PHE 4.3 2.3 + - - -
529A GLU* 3.4 28.5 + - - +
530A GLN 3.2 0.4 - - - -
531A PHE* 1.3 86.8 - - - +
533A GLU* 1.3 56.6 + - - +
535A THR* 3.4 3.6 + - - -
536A LEU* 2.9 31.2 + - - +
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Residues in contact with GLU 533 (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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499A TYR* 4.1 18.6 + - + +
501A CYS* 3.4 45.6 + - + +
527A CYS* 4.3 0.4 - - - -
529A GLU 4.3 1.6 - - - +
530A GLN* 3.1 16.3 + - - +
532A ASP* 1.3 77.1 - - - +
534A LEU* 1.3 65.7 + - + +
536A LEU* 3.3 6.8 + - - +
537A LEU* 2.8 39.2 + - + +
549A SER* 5.1 4.7 - - - -
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Residues in contact with LEU 534 (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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453A VAL* 5.5 2.2 - - + -
530A GLN* 2.9 49.3 + - + +
531A PHE* 3.9 8.3 - - + +
533A GLU* 1.3 78.8 - - + +
535A THR* 1.3 63.1 + - - +
537A LEU* 3.2 16.8 + - + +
538A HIS* 2.9 25.5 + - - +
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Residues in contact with THR 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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449A ARG* 3.3 43.0 - - + +
452A ILE* 4.1 31.7 - - + +
453A VAL* 4.5 13.3 - - + +
468A LEU* 4.6 9.4 - - + -
470A TYR* 5.0 1.1 - - - +
531A PHE* 2.5 23.5 + - - +
532A ASP* 3.5 5.8 - - - -
534A LEU* 1.3 76.3 - - - +
536A LEU* 1.3 57.0 + - - +
538A HIS* 3.3 3.8 + - - +
539A LEU* 2.9 28.4 + - + +
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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
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468A LEU* 5.2 4.7 - - + -
470A TYR* 4.7 19.1 - - + -
483A LEU* 4.2 17.5 - - + -
499A TYR* 3.7 35.4 - - + -
525A LEU* 4.9 7.9 - - + -
527A CYS* 3.7 28.9 - - - -
532A ASP 2.9 15.4 + - - +
533A GLU* 3.3 5.8 + - - +
535A THR* 1.3 76.8 - - - +
537A LEU* 1.3 62.8 + - - +
539A LEU* 3.3 9.3 - - + +
540A ARG* 3.3 5.5 + - - -
547A LEU* 3.3 50.3 - - + +
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Residues in contact with LEU 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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499A TYR* 3.2 24.9 - - + +
533A GLU* 2.8 28.5 + - + +
534A LEU* 3.5 17.0 - - + +
535A THR 3.2 0.2 - - - -
536A LEU* 1.3 74.7 - - - +
538A HIS* 1.3 60.0 + - - +
540A ARG* 2.9 27.3 + - - +
547A LEU 5.3 4.7 - - - +
548A ILE* 5.0 13.9 - - + -
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Residues in contact with HIS 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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452A ILE* 4.3 3.4 - - + -
453A VAL* 3.0 53.7 + - + +
458A GLN* 5.4 0.7 - - - +
461A LYS* 3.1 38.6 + - + +
534A LEU 2.9 16.5 + - - +
535A THR 3.7 4.3 - - - +
537A LEU* 1.3 75.5 - - - +
539A LEU* 1.3 63.6 + - - +
540A ARG* 3.1 14.6 + - - +
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Residues in contact with LEU 539 (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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452A ILE* 4.1 9.6 - - + +
458A GLN* 3.2 12.9 + - - +
461A LYS* 3.7 42.0 - - + +
462A GLU* 4.4 2.5 - - + +
465A ALA* 3.9 9.2 - - + -
468A LEU* 5.0 4.3 - - + -
483A LEU* 3.6 29.2 - - + -
535A THR* 2.9 14.0 + - + +
536A LEU* 3.3 17.5 - - + +
537A LEU 3.2 0.2 - - - -
538A HIS* 1.3 81.0 - - - +
540A ARG* 1.3 54.1 - - - +
541A GLU 2.4 37.8 + - - +
542A PHE* 4.0 6.1 - - + -
547A LEU* 3.6 19.3 - - + -
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Residues in contact with ARG 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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458A GLN* 4.4 11.7 + - - -
536A LEU 3.3 3.9 + - - -
537A LEU* 2.9 19.4 + - - +
538A HIS* 3.1 17.9 + - - +
539A LEU* 1.3 72.1 - - - +
541A GLU* 1.3 88.5 + - - +
546A LYS* 3.4 28.2 - - + +
547A LEU* 2.5 47.9 + - - +
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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