Contacts of the helix formed by residues 578 - 591 (chain W) in PDB entry 5O9G
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 GLU 578 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574W ASN* 4.9 5.8 - - - +
575W GLN* 3.9 25.7 + - + +
576W ASP 3.5 0.2 - - - -
577W GLU* 1.3 79.5 - - + +
579W GLN* 1.3 59.1 + - - +
580W GLU 3.3 1.6 - - - -
581W GLU* 3.3 24.2 + - - +
582W TYR* 2.9 29.0 + - + +
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Residues in contact with GLN 579 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574W ASN* 4.3 8.1 - - - +
575W GLN 3.2 16.2 + - - +
576W ASP* 3.5 29.2 - - - +
577W GLU 3.2 1.4 - - - -
578W GLU* 1.3 79.4 - - - +
580W GLU* 1.3 57.5 + - - +
582W TYR* 4.2 8.3 - - + -
583W ILE* 2.9 36.9 + - + +
839W LEU* 3.4 39.0 - - - +
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Residues in contact with GLU 580 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576W ASP 4.4 2.1 + - - +
577W GLU* 3.4 15.3 + - - +
579W GLN* 1.3 79.1 - - - +
581W GLU* 1.3 77.4 + - - +
583W ILE* 3.7 8.5 - - - +
584W HIS* 2.7 35.5 + - - +
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Residues in contact with GLU 581 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577W GLU 3.2 19.9 - - - +
578W GLU* 3.3 25.3 - - + +
580W GLU* 1.3 99.2 - - - +
582W TYR* 1.3 59.6 + - - +
583W ILE 3.3 0.2 - - - -
584W HIS* 3.5 8.8 - - + +
585W ASP* 2.9 32.1 + - - +
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Residues in contact with TYR 582 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549W ILE* 3.4 34.0 - - + +
553W ALA* 6.0 0.3 - - - +
564W PHE* 5.2 15.2 - + - -
574W ASN* 3.7 30.7 - - - +
578W GLU 2.9 18.3 + - - +
579W GLN* 3.9 7.6 - - + +
581W GLU* 1.3 77.0 - - - +
583W ILE* 1.3 61.0 + - + +
585W ASP* 4.2 2.0 - - - +
586W LEU* 2.9 60.5 + - + +
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Residues in contact with ILE 583 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546W GLN* 4.7 11.4 - - - +
552W LEU* 5.8 4.3 - - + -
579W GLN* 2.9 27.3 + - + +
580W GLU* 3.7 10.8 - - - +
582W TYR* 1.3 78.6 - - + +
584W HIS* 1.3 60.1 + - - +
585W ASP 3.3 0.4 - - - -
586W LEU* 4.7 13.5 - - + -
587W HIS* 2.5 54.1 + - + +
839W LEU* 5.3 4.7 - - + -
841W TYR* 3.7 53.2 - - + -
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Residues in contact with HIS 584 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580W GLU 2.7 24.2 + - - +
581W GLU* 3.1 12.1 + - + +
583W ILE* 1.3 79.6 - - - +
585W ASP* 1.3 60.0 + - - +
587W HIS* 4.7 0.8 - - - +
588W ARG* 4.3 39.0 + - - +
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Residues in contact with ASP 585 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564W PHE* 5.0 10.3 - - - -
581W GLU 2.9 14.0 + - - +
582W TYR* 4.4 2.0 - - - +
584W HIS* 1.3 79.3 - - - +
586W LEU* 1.3 60.1 + - - +
587W HIS 3.3 1.6 - - - -
588W ARG* 3.9 1.5 + - - +
589W ARG* 2.8 39.4 + - - +
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Residues in contact with LEU 586 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549W ILE* 4.2 4.5 - - + -
552W LEU* 3.8 30.3 - - + -
556W VAL* 5.8 3.1 - - + -
564W PHE* 3.7 39.0 - - + +
582W TYR* 2.9 54.7 + - + +
583W ILE* 4.5 9.2 - - + -
585W ASP* 1.3 74.9 - - - +
587W HIS* 1.3 59.9 + - - +
589W ARG* 3.8 6.5 - - + -
590W ILE* 2.9 40.6 + - + +
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Residues in contact with HIS 587 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583W ILE* 2.5 33.7 + - + +
584W HIS* 4.7 1.6 - - - +
586W LEU* 1.3 77.1 - - - +
588W ARG* 1.3 70.1 + - + +
590W ILE* 3.1 11.2 + - + +
591W GLN* 2.9 64.6 + - + +
841W TYR* 3.8 42.4 - + + +
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Residues in contact with ARG 588 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584W HIS* 4.3 34.6 + - - +
585W ASP* 3.9 2.3 + - - +
587W HIS* 1.3 92.1 + - + +
589W ARG* 1.3 60.2 - - - +
591W GLN* 3.9 10.4 - - + +
592W PRO* 3.3 19.8 - - - +
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Residues in contact with ARG 589 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563W ARG* 3.6 40.0 + - - +
564W PHE* 3.8 34.2 - - + -
585W ASP* 2.8 29.0 + - - +
586W LEU* 3.6 12.1 - - + +
587W HIS 3.1 0.2 - - - -
588W ARG* 1.3 79.8 - - - +
590W ILE* 1.3 57.8 + - - +
592W PRO* 3.9 3.5 - - - +
593W PHE* 3.9 12.9 - - - -
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Residues in contact with ILE 590 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552W LEU* 4.7 21.3 - - + -
556W VAL* 4.1 24.5 - - + -
563W ARG* 4.3 18.2 - - - +
586W LEU* 2.9 25.5 + - + +
587W HIS* 3.1 15.9 + - + +
589W ARG* 1.3 77.0 - - - +
591W GLN* 1.3 69.9 + - + +
592W PRO* 3.4 1.6 - - - -
593W PHE* 3.0 29.8 + - + +
594W ILE* 3.2 20.7 - - + +
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Residues in contact with GLN 591 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587W HIS* 2.9 62.2 + - + +
588W ARG* 4.0 7.6 - - + +
590W ILE* 1.3 79.5 - - - +
592W PRO* 1.3 69.1 - - + +
593W PHE 3.0 1.6 + - - -
594W ILE* 3.2 36.0 + - - +
596W ARG* 5.1 14.0 + - - +
841W TYR 5.7 1.6 - - - -
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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