Contacts of the helix formed by residues 579 - 588 (chain A) in PDB entry 6X70
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 THR 579 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A PHE* 4.4 3.4 - - + -
577A ARG 4.5 5.4 - - - +
578A TYR* 1.3 84.1 - - - +
580A LEU* 1.3 63.7 + - - +
581A ASP* 3.5 9.3 + - - +
582A ALA* 3.2 21.9 + - + +
583A LEU* 2.9 20.4 + - - +
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Residues in contact with LEU 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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578A TYR* 3.9 8.7 - - - -
579A THR* 1.3 71.8 - - - +
581A ASP* 1.3 56.8 + - - +
583A LEU* 4.3 5.2 - - + -
584A LYS* 2.9 57.0 + - + +
592A GLY 4.1 10.1 - - - +
593A MET* 4.1 17.5 - - + -
596A HIS* 3.5 52.3 - - + +
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Residues in contact with ASP 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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579A THR* 3.0 8.0 + - - +
580A LEU* 1.3 82.0 - - - +
582A ALA* 1.3 64.0 + - - +
584A LYS* 3.2 9.5 + - - +
585A ALA* 2.9 21.5 + - - +
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Residues in contact with ALA 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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564A THR* 4.3 8.8 - - + +
565A PHE* 4.1 19.7 - - + -
579A THR* 3.1 16.7 + - + +
581A ASP* 1.3 79.2 + - - +
583A LEU* 1.3 57.8 + - - +
585A ALA* 3.2 9.6 + - - +
586A SER* 2.8 29.3 + - - -
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Residues in contact with LEU 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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561A LEU* 3.6 31.6 - - + -
565A PHE* 3.9 15.2 - - + -
574A LEU* 5.4 3.1 - - + -
578A TYR* 3.8 23.3 - - + -
579A THR 2.9 16.6 + - - +
580A LEU* 3.7 4.7 - - - +
582A ALA* 1.3 73.6 - - - +
584A LYS* 1.3 66.0 + - - +
586A SER* 3.1 10.0 + - - -
587A VAL* 3.1 28.7 + - + +
592A GLY* 3.3 28.5 - - - +
595A ILE* 3.7 26.7 - - + -
596A HIS* 3.9 6.1 - - + +
599A LEU* 5.0 0.2 - - + -
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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 LEU* 2.9 53.5 + - + +
581A ASP* 3.6 8.5 - - - +
583A LEU* 1.3 75.5 - - - +
585A ALA* 1.3 59.1 + - - +
588A GLY* 2.8 38.9 + - - +
589A SER* 3.7 42.4 - - - +
592A GLY* 4.3 2.9 - - - -
593A MET* 4.8 9.9 - - - -
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Residues in contact with ALA 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 ASP* 2.9 13.4 + - - +
582A ALA* 3.5 12.6 - - - +
583A LEU 3.2 0.2 - - - -
584A LYS* 1.3 76.9 - - - +
586A SER* 1.3 62.6 + - - +
588A GLY 4.7 0.5 + - - -
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Residues in contact with SER 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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560A ARG* 3.1 38.5 + - - +
561A LEU* 4.0 1.4 + - - -
564A THR* 2.7 36.0 + - - -
565A PHE* 4.7 4.0 - - - -
582A ALA 2.8 15.9 + - - -
583A LEU* 3.1 7.4 + - - -
585A ALA* 1.3 79.6 - - - +
587A VAL* 1.3 69.7 + - - +
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Residues in contact with VAL 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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557A THR* 3.5 30.7 - - + +
560A ARG* 3.9 25.3 + - + +
561A LEU* 3.8 15.7 - - + -
583A LEU* 3.1 21.5 + - + +
586A SER* 1.3 90.3 - - - +
588A GLY* 1.3 58.8 + - - +
591A LEU* 3.8 24.0 - - + +
592A GLY* 3.9 21.8 - - - +
595A ILE* 4.3 4.0 - - + -
12T C 5.7 1.0 - - - +
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Residues in contact with GLY 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 LYS* 2.8 24.7 + - - +
585A ALA 4.6 0.4 + - - -
586A SER 3.7 0.8 - - - -
587A VAL* 1.3 79.8 - - - +
589A SER* 1.3 60.5 + - - -
590A LYS 3.5 2.0 - - - -
591A LEU 4.3 1.3 - - - -
592A GLY 2.9 22.5 + - - -
12T C 4.0 13.9 - - - -
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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