Contacts of the helix formed by residues 572 - 584 (chain A) in PDB entry 6AH0
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 PHE 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A MET* 6.5 1.3 - - - +
570A ASP 2.3 16.0 + - - -
571A ALA* 1.3 72.3 - - - +
573A GLN* 1.3 60.4 + - - +
574A LEU 3.2 0.4 - - - -
575A ALA* 3.4 2.6 + - - +
576A ASP* 3.1 19.4 + - - -
628A GLY* 5.6 0.9 + - - -
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Residues in contact with GLN 573 (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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162A LYS 4.9 12.3 - - - -
163A ARG* 5.9 3.0 - - - +
570A ASP* 2.6 17.1 + - - +
572A PHE* 1.3 73.5 - - - +
574A LEU* 1.3 54.5 + - - +
576A ASP* 3.3 2.4 + - - +
577A GLY* 2.9 26.0 + - - -
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Residues in contact with LEU 574 (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 SER* 5.9 3.4 - - - +
569A VAL* 4.7 4.9 - - - +
570A ASP 2.4 37.3 + - - +
573A GLN* 1.3 67.1 - - - +
575A ALA* 1.3 55.3 + - - +
577A GLY* 3.2 3.4 + - - -
578A LEU* 2.9 25.3 + - - -
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Residues in contact with ALA 575 (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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570A ASP 3.7 3.2 + - - -
571A ALA 4.6 5.4 + - - -
572A PHE* 3.4 6.9 + - - +
573A GLN 3.3 0.6 - - - -
574A LEU* 1.3 75.8 - - - +
576A ASP* 1.3 62.5 + - - +
578A LEU* 3.2 3.5 + - - +
579A GLN 3.0 18.0 + - - -
628A GLY* 3.9 14.7 - - - -
629A PHE 4.4 3.0 + - - +
630A TRP 5.1 1.4 + - - -
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Residues in contact with ASP 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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572A PHE 3.1 14.5 + - - -
573A GLN 3.7 2.7 - - - -
575A ALA* 1.3 77.0 - - - +
577A GLY* 1.3 60.9 + - - +
579A GLN* 3.2 1.7 + - - -
580A TYR* 2.9 20.8 + - - -
626A GLY* 5.7 2.7 - - - -
627A CYS 3.7 25.3 - - - +
628A GLY* 3.9 4.1 - - - -
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Residues in contact with GLY 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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164A MET* 5.7 8.5 - - - -
573A GLN 2.9 13.6 + - - -
574A LEU* 3.2 5.3 + - - -
576A ASP* 1.3 75.9 - - - +
578A LEU* 1.3 56.0 + - - +
580A TYR* 3.2 2.2 + - - -
581A ILE* 2.9 25.8 + - - -
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Residues in contact with LEU 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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574A LEU 2.9 14.4 + - - -
575A ALA* 3.2 4.4 + - - +
577A GLY* 1.3 75.8 - - - +
579A GLN* 1.3 62.5 + - - +
581A ILE* 3.2 2.4 + - - +
582A PHE* 3.1 20.4 + - - -
630A TRP* 5.3 3.7 - - - -
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Residues in contact with GLN 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 3.0 13.1 + - - -
576A ASP 3.2 3.1 + - - -
578A LEU* 1.3 76.2 - - - +
580A TYR* 1.3 62.0 + - - +
582A PHE* 3.4 0.9 + - - +
583A ALA* 3.0 19.8 + - - -
627A CYS 5.1 5.8 - - - -
629A PHE 5.3 2.7 - - - +
630A TRP* 4.4 21.3 - - - +
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Residues in contact with TYR 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 ASP 2.9 14.1 + - - -
577A GLY* 3.6 3.6 - - - -
579A GLN* 1.3 76.3 - - - +
581A ILE* 1.3 55.7 + - - +
583A ALA* 3.2 2.3 + - - +
584A HIS* 2.8 28.1 + - - -
627A CYS 5.4 0.4 + - - -
3000A IHP 5.2 13.0 + - - -
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Residues in contact with ILE 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 GLY 2.9 13.4 + - - -
578A LEU* 3.2 3.8 + - - +
580A TYR* 1.3 75.9 - - - +
582A PHE* 1.3 63.5 + - - +
584A HIS* 3.3 10.2 + - - +
585A VAL* 3.3 14.4 + - - -
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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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578A LEU 3.1 14.0 + - - -
579A GLN* 4.0 2.0 - - - +
581A ILE* 1.3 77.7 - - - +
583A ALA* 1.3 60.5 + - - +
584A HIS 3.6 0.2 + - - -
585A VAL* 4.0 5.5 + - - -
605A CYS* 5.2 5.5 - - - -
633A GLY* 5.1 22.5 - - - +
634A TRP 5.6 0.2 - - - +
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Residues in contact with ALA 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 GLN 3.0 15.0 + - - -
580A TYR 3.6 3.1 - - - -
582A PHE* 1.3 77.0 - - - +
584A HIS* 1.3 57.4 + - - +
585A VAL 3.5 1.4 + - - -
586A GLY 5.4 0.2 + - - -
605A CYS* 4.7 22.2 - - - +
609A LYS* 6.1 3.6 - - - +
633A GLY* 5.7 0.2 - - - -
3000A IHP 5.3 8.8 + - - -
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Residues in contact with HIS 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 TYR 2.8 15.5 + - - -
581A ILE* 3.3 5.1 + - - +
583A ALA* 1.3 78.0 - - - +
585A VAL* 1.3 51.3 + - - +
586A GLY 3.4 2.5 - - - -
587A GLN* 3.1 9.0 + - - +
588A LEU* 2.6 34.0 + - - -
3000A IHP 6.0 2.0 - - - -
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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