Contacts of the helix formed by residues 577 - 588 (chain A) in PDB entry 5XA0
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 GLN 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573A TYR* 2.6 41.5 + - + +
576A LYS* 1.3 71.5 - - - +
578A PHE* 1.3 62.4 + - - +
579A GLY 3.1 0.4 - - - -
580A PHE* 2.9 28.0 + - + +
581A MET* 3.7 1.7 + - - +
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Residues in contact with PHE 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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573A TYR 3.6 1.0 + - - -
574A ILE* 2.7 35.7 + - + +
575A ALA 4.7 2.9 - - - +
576A LYS 3.2 1.0 - - - -
577A GLN* 1.3 75.4 - - - +
579A GLY* 1.3 67.3 + - - +
581A MET* 2.9 25.0 + - + +
582A GLN* 3.8 2.3 + - - +
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Residues in contact with GLY 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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575A ALA 5.3 0.6 + - - -
576A LYS* 3.5 10.5 + - - +
577A GLN 3.1 1.8 - - - -
578A PHE* 1.3 77.8 - - - +
580A PHE* 1.3 62.8 + - - +
581A MET 3.0 0.2 + - - -
582A GLN* 3.1 18.5 + - - +
583A LYS* 4.2 1.2 + - - +
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Residues in contact with PHE 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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523A LEU 6.1 0.9 - - - +
576A LYS 4.6 1.2 + - - -
577A GLN* 2.9 19.6 + - + +
579A GLY* 1.3 74.7 - - - +
581A MET* 1.3 50.1 + - - +
582A GLN 3.0 1.2 + - - -
583A LYS* 3.1 12.7 + - - +
584A GLN* 2.7 33.0 + - + +
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Residues in contact with MET 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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577A GLN 3.7 1.2 + - - +
578A PHE* 2.9 20.5 + - + +
580A PHE* 1.3 79.1 - - - +
582A GLN* 1.3 50.4 + - - +
584A GLN* 3.1 13.0 - - + +
585A ILE* 2.0 44.6 + - + +
591A ALA* 5.1 12.8 - - + -
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Residues in contact with GLN 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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578A PHE 3.8 1.8 + - - +
579A GLY* 3.1 12.4 + - - +
580A PHE 3.0 0.2 + - - -
581A MET* 1.3 73.3 - - - +
583A LYS* 1.3 70.3 + - - +
585A ILE* 2.9 16.8 + - - +
586A GLY* 3.2 7.8 + - - -
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Residues in contact with LYS 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 GLY 4.2 1.2 + - - +
580A PHE* 3.1 11.4 + - - +
582A GLN* 1.3 78.9 - - - +
584A GLN* 1.3 64.6 + - - +
586A GLY* 2.9 13.0 + - - -
587A TYR* 3.7 5.6 + - - +
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Residues in contact with GLN 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 PHE* 2.7 15.4 + - + +
581A MET* 3.1 23.8 - - + +
583A LYS* 1.3 71.1 - - - +
585A ILE* 1.3 61.3 + - - +
587A TYR* 3.0 19.5 + - - +
588A ASP 3.6 10.4 + - - +
591A ALA* 5.4 10.1 - - + -
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Residues in contact with ILE 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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581A MET* 2.0 30.1 + - + +
582A GLN* 2.9 12.7 + - - +
584A GLN* 1.3 69.3 - - - +
586A GLY* 1.3 61.4 + - - +
588A ASP* 3.4 17.4 + - - +
591A ALA* 6.1 3.8 - - - -
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Residues in contact with GLY 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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582A GLN 3.2 6.9 + - - -
583A LYS 2.9 10.4 + - - -
585A ILE* 1.3 78.7 - - - +
587A TYR* 1.3 59.7 + - - +
588A ASP 3.6 0.2 - - - -
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Residues in contact with TYR 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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553A CYS* 6.4 1.6 - - - -
583A LYS 3.7 6.5 + - - +
584A GLN* 3.0 12.7 + - - +
586A GLY* 1.3 79.9 - - - +
588A ASP* 1.3 65.1 + - + +
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Residues in contact with ASP 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 GLN 3.6 7.8 + - - +
585A ILE* 3.4 17.9 - - - +
586A GLY 3.6 1.2 - - - -
587A TYR* 1.3 82.0 - - + +
589A VAL* 1.3 60.5 + - - +
590A LEU* 3.3 16.7 + - + +
591A ALA* 5.0 2.4 + - - +
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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