Contacts of the helix formed by residues 573 - 583 (chain A) in PDB entry 1O86
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 PRO 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 4.8 5.1 - - - +
225A GLU* 4.3 17.0 - - + +
572A ARG* 1.3 99.4 - - + +
574A TRP* 1.3 65.8 + - - +
575A PRO* 3.0 16.1 - - + -
576A GLU* 3.0 34.7 + - + +
577A ALA* 4.2 0.9 + - - +
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Residues in contact with TRP 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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224A TYR* 3.3 22.2 + + - +
225A GLU* 5.0 3.2 + - + -
226A THR* 3.0 29.6 + - + -
232A ASP* 5.9 0.2 - - - -
405A ALA* 3.6 39.4 + - + +
406A ASN* 3.4 27.4 - - + +
409A PHE* 3.9 9.8 - + + -
572A ARG 3.3 2.8 + - - -
573A PRO* 1.3 70.6 - - - +
575A PRO* 1.3 81.0 - - + +
576A GLU 3.0 0.2 - - - -
577A ALA* 2.9 16.1 + - - +
578A MET* 3.0 31.8 + - + +
585A PRO 3.4 25.4 - - - -
586A ASN* 4.6 1.8 - - - -
587A MET* 3.7 41.1 - - + -
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Residues in contact with PRO 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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573A PRO* 3.1 16.6 - - + -
574A TRP* 1.3 123.9 - - + +
576A GLU* 1.3 57.4 + - + +
578A MET* 3.4 2.9 + - + +
579A GLN* 2.9 26.9 + - - +
585A PRO* 3.8 27.7 - - + +
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Residues in contact with GLU 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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568A LEU* 4.8 6.0 - - + +
572A ARG* 2.6 60.5 + - + +
573A PRO* 3.0 22.2 + - + +
574A TRP 2.9 1.0 + - - -
575A PRO* 1.3 77.1 - - + +
577A ALA* 1.3 60.8 + - - +
579A GLN* 3.2 7.5 + - - +
580A LEU* 2.9 34.1 + - + +
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Residues in contact with ALA 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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405A ALA* 3.8 15.0 - - + -
409A PHE* 3.5 22.4 - - + -
565A ALA* 4.1 14.8 - - + +
568A LEU* 4.2 21.4 - - + +
573A PRO 4.2 0.6 + - - -
574A TRP* 2.9 7.1 + - - +
576A GLU* 1.3 78.2 - - - +
578A MET* 1.3 63.2 + - - +
580A LEU* 3.3 6.6 + - - +
581A ILE* 3.2 28.1 + - - +
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Residues in contact with MET 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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409A PHE* 3.8 12.4 - - + -
529A ILE* 3.8 30.3 - - + -
532A GLN* 3.9 8.1 - - - +
533A PHE* 3.8 14.1 - - + -
574A TRP* 3.0 25.9 + - + +
575A PRO 3.5 9.0 - - - +
577A ALA* 1.3 78.2 - - - +
579A GLN* 1.3 55.9 - - - +
581A ILE* 3.4 2.6 + - - -
582A THR* 2.8 49.6 + - - +
584A GLN* 3.4 29.6 - - - +
585A PRO 3.6 17.3 - - - +
586A ASN 3.7 10.8 - - - +
587A MET* 4.1 5.2 - - - -
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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 PRO 2.9 16.8 + - - +
576A GLU* 3.2 8.0 + - - +
578A MET* 1.3 75.0 - - - +
580A LEU* 1.3 63.7 + - + +
583A GLY* 2.7 36.4 + - - -
584A GLN* 3.0 47.5 + - - +
585A PRO* 3.1 16.1 - - - +
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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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561A ARG* 3.9 18.4 + - - +
564A THR* 4.2 31.2 + - - +
565A ALA* 4.3 7.4 - - + -
568A LEU* 3.5 34.8 - - + -
576A GLU* 2.9 15.1 + - + +
577A ALA* 3.6 7.2 - - - +
579A GLN* 1.3 78.1 - - + +
581A ILE* 1.3 62.1 + - - +
583A GLY 4.9 0.2 + - - -
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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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409A PHE* 4.4 6.7 - - + -
413A ILE* 5.7 1.8 - - + -
533A PHE* 3.7 57.0 - - + -
536A ALA* 3.3 5.1 - - + +
537A LEU* 4.4 18.2 - - + -
561A ARG* 3.2 39.6 + - - +
562A LEU* 4.1 13.7 - - + -
565A ALA* 3.6 27.1 - - + -
577A ALA 3.2 15.0 + - - +
578A MET 4.0 2.0 - - - +
579A GLN 3.2 0.4 - - - -
580A LEU* 1.3 78.8 - - - +
582A THR* 1.3 63.5 + - + +
583A GLY 3.7 0.4 - - - -
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Residues in contact with THR 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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532A GLN* 3.9 27.6 - - + +
533A PHE* 3.9 13.5 - - + -
536A ALA* 3.8 10.6 - - + +
561A ARG* 5.1 3.5 + - - -
578A MET* 2.8 41.3 + - - +
581A ILE* 1.3 77.2 - - + +
583A GLY* 1.3 58.1 + - - +
584A GLN* 2.9 34.7 + - - +
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Residues in contact with GLY 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 ARG* 5.5 0.6 - - - +
579A GLN* 2.7 33.8 + - - -
580A LEU 4.7 0.2 - - - -
581A ILE 3.7 0.8 - - - -
582A THR* 1.3 71.7 - - - +
584A GLN* 1.3 60.6 + - - +
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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