Contacts of the helix formed by residues 658 - 664 (chain C) in PDB entry 5O9Z
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 TYR 658 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C LEU* 5.3 0.7 - - - +
502C CYS* 4.5 12.3 - - + -
652C SER* 3.9 27.4 - - - -
653C ALA 4.9 1.6 - - - +
655C LEU 4.1 12.6 - - - +
656C PRO 3.3 1.6 + - - -
657C ASN* 1.3 74.9 - - - +
659C GLU* 1.3 59.1 + - - +
660C ASP 3.2 2.2 - - - -
661C VAL* 3.2 11.3 + - - +
662C ALA* 2.9 25.7 + - - +
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Residues in contact with GLU 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657C ASN* 3.3 2.6 - - - -
658C TYR* 1.3 76.6 - - - +
660C ASP* 1.3 59.4 + - - +
662C ALA* 3.6 10.8 - - + +
663C THR* 2.9 28.2 + - - -
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Residues in contact with ASP 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ASN* 3.8 19.0 + - + +
658C TYR 3.2 0.8 - - - -
659C GLU* 1.3 78.6 - - - +
661C VAL* 1.3 56.7 + - - +
663C THR* 3.4 6.0 + - - -
664C PHE* 2.9 28.3 + - - +
924C TYR* 5.7 1.4 - - - +
927C ILE* 4.8 24.0 - - + +
928C ARG* 5.4 6.1 - - + +
931C ARG* 6.0 4.3 - - + -
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Residues in contact with VAL 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C LEU* 5.0 3.3 - - + +
617C ILE* 5.4 12.1 - - + -
652C SER* 5.7 5.8 - - - -
657C ASN 4.2 2.1 + - - +
658C TYR* 3.2 14.5 + - + +
660C ASP* 1.3 75.4 - - - +
662C ALA* 1.3 60.8 + - - +
664C PHE* 3.8 7.9 - - - +
665C LEU* 3.0 29.5 + - - +
924C TYR* 6.3 1.1 - - - -
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Residues in contact with ALA 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C LEU* 3.8 28.4 - - + +
658C TYR 2.9 13.9 + - - +
659C GLU* 3.6 13.5 - - + +
660C ASP 3.3 0.2 - - - -
661C VAL* 1.3 77.7 - - - +
663C THR* 1.3 60.5 + - - +
665C LEU* 3.4 4.6 + - - +
667C VAL* 3.3 34.5 + - + +
669C PRO* 5.9 7.2 - - + -
672C GLY 5.7 1.1 - - - +
673C LEU* 5.4 10.5 - - + -
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Residues in contact with THR 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C GLU 2.9 17.2 + - - -
660C ASP* 3.8 6.3 - - - -
662C ALA* 1.3 74.1 - - - +
664C PHE* 1.3 63.9 + - - +
665C LEU 3.2 0.7 - - - -
666C ARG* 3.2 13.0 + - - +
667C VAL 4.9 4.9 - - - +
669C PRO* 6.2 4.9 - - - -
927C ILE* 5.8 5.2 - - - -
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Residues in contact with PHE 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632C VAL* 5.7 4.9 - - - +
636C ILE* 5.8 3.6 - - - +
660C ASP 2.9 17.6 + - - +
661C VAL* 3.9 8.7 - - - +
662C ALA 3.4 0.2 - - - -
663C THR* 1.3 77.2 - - - +
665C LEU* 1.3 57.9 + - - +
666C ARG* 3.2 2.6 + - - +
922C TYR 5.7 1.6 - - - +
923C ALA 5.3 2.9 - - - -
924C TYR* 4.4 27.4 - - + +
927C ILE* 5.6 5.1 - - + +
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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