Contacts of the helix formed by residues 575 - 585 (chain A) in PDB entry 3OJW
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 TYR 575 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A ARG* 4.1 4.5 - - - -
292A LEU* 3.5 32.6 + - + +
302A HIS* 2.8 36.8 - + - -
459A ALA* 4.9 1.5 - - + +
472A THR* 2.6 38.9 + - + -
537A ILE* 4.1 10.8 - - + -
541A MET* 3.7 48.9 - - + -
573A TYR 3.6 0.4 + - - -
574A LEU* 1.3 81.0 - - + +
576A ARG* 1.3 62.5 + - - +
577A GLU* 4.5 2.1 + - - -
578A GLU* 3.0 36.1 - - + +
579A LEU* 3.0 25.0 + - + +
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Residues in contact with ARG 576 (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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569A SER* 2.6 37.0 + - - -
573A TYR* 3.1 67.7 + - + +
574A LEU 3.2 2.6 + - - -
575A TYR* 1.3 76.4 - - - +
577A GLU* 1.3 85.0 + - - +
579A LEU* 3.4 2.4 + - - +
580A ALA* 2.9 28.8 + - + +
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Residues in contact with GLU 577 (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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575A TYR* 4.1 1.2 + - - -
576A ARG* 1.3 99.9 + - + +
578A GLU* 1.3 79.1 + - + +
580A ALA* 3.3 6.2 + - - +
581A ARG* 3.0 24.8 + - - +
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Residues in contact with GLU 578 (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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290A ARG* 3.4 26.2 + - - -
541A MET* 3.9 18.6 - - + -
575A TYR* 3.0 38.1 - - + +
577A GLU* 1.3 87.3 - - + +
579A LEU* 1.3 63.1 + - - +
581A ARG* 3.2 12.8 + - - +
582A PHE* 3.0 35.7 + - + -
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Residues in contact with LEU 579 (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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537A ILE* 3.9 15.9 - - + -
541A MET* 3.8 23.3 - - + -
544A ILE* 4.1 13.2 - - + -
562A LEU* 3.9 24.9 - - + -
564A TYR* 5.4 2.5 - - + -
573A TYR* 4.4 14.4 - - + +
574A LEU 3.7 14.8 - - - +
575A TYR* 3.0 26.6 + - + +
576A ARG* 3.9 2.7 - - - +
578A GLU* 1.3 76.3 - - - +
580A ALA* 1.3 57.5 + - - +
582A PHE* 3.2 7.5 + - + +
583A HIS* 2.8 31.6 + - - +
588A LEU* 4.0 7.4 - - + +
591A LEU* 4.0 20.9 - - + -
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Residues in contact with ALA 580 (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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576A ARG* 2.9 21.7 + - + +
577A GLU* 3.6 7.0 - - - +
579A LEU* 1.3 76.2 - - - +
581A ARG* 1.3 57.9 + - - +
583A HIS* 3.4 8.1 + - - +
584A LYS* 2.8 31.3 + - - +
591A LEU* 4.7 5.3 - - + +
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Residues in contact with ARG 581 (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 ALA* 5.4 3.0 - - - +
552A GLU* 4.5 14.1 + - - -
577A GLU 3.0 13.2 + - - +
578A GLU* 3.2 15.1 + - - +
580A ALA* 1.3 77.8 - - - +
582A PHE* 1.3 92.0 + - - +
584A LYS* 3.4 8.9 + - - +
585A ASP* 3.0 52.4 + - - +
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Residues in contact with PHE 582 (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 MET* 4.2 19.5 - - + -
544A ILE* 3.6 29.2 - - + -
545A GLN* 3.9 34.1 - - + -
548A ALA* 4.0 26.5 - - + -
578A GLU* 3.0 34.8 + - + -
579A LEU* 3.6 10.8 - - + +
581A ARG* 1.3 110.1 - - - +
583A HIS* 1.3 64.0 + - - +
585A ASP* 3.4 3.2 + - + -
586A GLY 3.2 3.1 + - - -
587A ALA* 2.8 32.0 + - + +
588A LEU* 3.0 7.9 + - + -
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Residues in contact with HIS 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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579A LEU 2.8 17.5 + - - +
580A ALA* 3.7 7.4 - - - +
582A PHE* 1.3 75.4 - - - +
584A LYS* 1.3 68.1 + - - +
586A GLY* 3.0 13.5 + - - -
588A LEU* 2.9 33.8 + - + +
589A THR 3.5 19.9 - - - -
590A GLN* 4.5 6.1 - - - -
591A LEU* 4.5 21.6 + - + +
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Residues in contact with LYS 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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580A ALA 2.8 19.2 + - - +
581A ARG* 3.7 8.7 - - - +
583A HIS* 1.3 78.5 - - - +
585A ASP* 1.3 90.9 + - - +
586A GLY* 3.4 0.7 + - - -
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Residues in contact with ASP 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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551A ARG* 3.0 18.0 + - - -
552A GLU* 5.3 4.7 - - - +
581A ARG* 3.0 33.0 + - - +
582A PHE* 3.8 7.4 - - + +
583A HIS 3.2 0.4 - - - -
584A LYS* 1.3 115.6 + - - +
586A GLY* 1.3 58.6 + - - +
587A ALA* 4.3 6.5 - - + +
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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