Contacts of the helix formed by residues 582 - 592 (chain A) in PDB entry 4B1H
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 582 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A VAL 3.6 3.7 + - - +
581A LEU* 1.3 75.4 - - - +
583A GLU* 1.3 68.0 + - - +
584A ALA* 4.4 7.6 - - + +
585A GLU* 3.0 29.9 + - + +
586A ALA* 2.9 20.8 + - - +
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Residues in contact with GLU 583 (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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581A LEU 4.0 0.4 + - - -
582A GLU* 1.3 72.8 - - - +
584A ALA* 1.3 58.3 - - - +
586A ALA* 3.2 7.0 + - + +
587A GLN* 2.8 57.0 + - + +
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Residues in contact with ALA 584 (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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582A GLU* 3.3 5.9 - - + +
583A GLU* 1.3 77.6 - - - +
585A GLU* 1.3 61.3 + - + +
587A GLN* 3.3 13.1 + - - +
588A HIS* 2.9 28.4 + - - +
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Residues in contact with GLU 585 (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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580A VAL 4.7 0.9 - - - +
581A LEU* 3.8 24.1 - - + +
582A GLU* 3.0 47.7 + - + +
584A ALA* 1.3 74.9 - - + +
586A ALA* 1.3 61.3 + - - +
588A HIS* 3.2 2.8 + - - -
589A LEU* 2.9 14.9 + - - +
677A LYS* 5.0 8.6 + - - -
1965A GOL 2.3 45.5 + - - +
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Residues in contact with ALA 586 (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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577A TRP* 3.9 37.0 - - + +
581A LEU* 3.9 12.2 - - + +
582A GLU 2.9 12.7 + - - +
583A GLU* 3.5 11.0 - - + +
585A GLU* 1.3 76.0 - - - +
587A GLN* 1.3 63.1 + - + +
589A LEU* 3.1 5.2 + - - +
590A TYR* 3.0 32.9 + - + -
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Residues in contact with GLN 587 (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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583A GLU* 2.8 44.8 + - + +
584A ALA* 3.6 9.5 - - - +
586A ALA* 1.3 76.0 - - - +
588A HIS* 1.3 56.9 + - - +
590A TYR* 3.6 27.0 + - + +
591A GLN* 2.9 54.2 + - - +
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Residues in contact with HIS 588 (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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584A ALA 2.9 16.6 + - - +
585A GLU* 3.2 1.8 + - - -
587A GLN* 1.3 75.7 - - - +
589A LEU* 1.3 63.6 + - - +
591A GLN* 5.0 0.9 - - - -
592A SER* 3.0 33.7 + - - +
593A ILE* 3.0 30.8 + - + +
684A ARG* 3.6 41.3 + - + +
1965A GOL 3.6 16.4 - - - +
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Residues in contact with LEU 589 (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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573A LEU* 5.9 2.2 - - + -
576A PHE* 4.6 5.4 - - + -
577A TRP* 4.1 29.8 - - + -
581A LEU* 4.0 19.3 - - + -
585A GLU 2.9 14.2 + - - +
586A ALA* 3.1 10.1 + - - +
588A HIS* 1.3 77.4 - - - +
590A TYR* 1.3 59.4 + - - +
593A ILE* 4.1 14.6 - - + -
594A LEU* 2.8 44.2 + - + +
680A PHE* 3.8 49.8 - - + -
1965A GOL 3.3 9.1 + - - +
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Residues in contact with TYR 590 (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 PHE* 3.1 35.3 + - + +
548A THR* 3.7 32.6 + - + +
577A TRP* 3.4 40.8 - + + -
586A ALA* 3.0 36.2 + - + -
587A GLN* 3.6 25.8 + - + +
589A LEU* 1.3 76.5 - - - +
591A GLN* 1.3 86.0 + - + +
592A SER 3.5 0.2 - - - -
594A LEU* 4.2 6.0 - - - +
595A PRO* 3.2 19.5 - - - +
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Residues in contact with GLN 591 (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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587A GLN* 2.9 38.2 + - - +
588A HIS* 5.0 0.4 - - - -
590A TYR* 1.3 101.9 + - + +
592A SER* 1.3 61.2 + - - +
595A PRO* 3.7 11.7 - - - +
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Residues in contact with SER 592 (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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588A HIS* 3.0 28.6 + - - -
590A TYR 3.5 0.4 - - - -
591A GLN* 1.3 82.1 - - - +
593A ILE* 1.3 67.1 + - - +
594A LEU 3.5 0.7 - - - -
595A PRO* 3.7 1.9 - - - +
596A ASP* 3.2 34.5 + - - +
684A ARG* 2.8 27.7 + - - -
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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