Contacts of the strand formed by residues 688 - 691 (chain H) in PDB entry 3AOH
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 ILE 688 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682H TYR 4.3 0.4 - - - -
686H ASP 2.6 32.3 - - - +
687H ALA* 1.3 77.3 - - - +
689H VAL* 1.3 69.4 + - - +
690H ILE* 5.4 0.7 - - + -
839H LEU* 4.1 24.0 - - + +
845H ASN* 5.6 2.7 - - - +
846H LYS 4.5 2.0 - - - +
847H GLY* 3.1 29.8 - - - +
848H VAL 2.9 13.1 + - - +
849H VAL* 3.3 8.7 - - + -
850H ALA* 2.7 29.3 + - - -
869H VAL* 3.6 26.0 - - + -
870H ILE 4.3 4.3 - - - -
871H LEU* 3.9 20.0 - - + -
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Residues in contact with VAL 689 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679H PHE* 4.5 2.2 - - + -
682H TYR* 3.5 38.8 - - + +
683H ASN* 3.9 16.8 - - - +
688H ILE* 1.3 75.7 - - - +
690H ILE* 1.3 65.5 + - - +
851H LYS 3.6 5.4 - - - +
853H LEU* 3.3 32.1 - - + -
858H MET* 4.4 0.9 - - + -
869H VAL* 3.1 25.8 - - - +
870H ILE* 3.2 45.8 + - + -
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Residues in contact with ILE 690 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688H ILE* 5.4 1.6 - - + -
689H VAL* 1.3 77.4 - - - +
691H SER* 1.3 60.3 + - - +
694H LEU* 3.4 35.4 - - + -
695H LEU* 5.6 1.1 - - + +
833H LEU* 3.1 41.3 - - + +
839H LEU* 5.6 2.5 - - + -
849H VAL* 3.3 21.3 - - + -
851H LYS 3.1 1.6 + - - -
852H ILE* 3.1 37.3 - - + -
853H LEU* 2.5 34.5 + - - +
858H MET* 3.6 5.0 - - - +
868H ASP 3.7 2.9 - - - +
869H VAL* 5.5 1.8 - - + -
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Residues in contact with SER 691 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690H ILE* 1.3 72.1 - - - +
692H GLU* 1.3 57.2 + - - +
693H GLU* 2.5 41.6 + - - +
694H LEU* 2.5 21.5 + - - +
852H ILE* 4.3 1.3 - - - -
853H LEU 3.4 1.1 + - - -
855H VAL* 4.8 4.1 - - - -
858H MET* 2.9 35.2 - - - -
866H PRO* 6.0 0.9 - - - +
867H VAL 3.8 8.7 + - - -
868H ASP* 2.9 20.3 + - - +
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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
------------------------------------------------------------
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