Contacts of the strand formed by residues 786 - 792 (chain A) in PDB entry 6RUT
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 786 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782A LEU* 3.3 18.9 + - + -
783A SER* 2.8 43.1 + - - +
784A GLU 3.6 1.0 - - - -
785A GLU* 1.4 96.3 - - + +
787A SER* 1.3 62.6 + - - +
801A ILE* 3.7 15.5 - - + -
802A TYR 3.3 16.2 - - - -
803A LYS* 3.8 37.0 - - + -
804A ASN* 4.0 4.8 - - - +
812A ASP* 4.5 7.0 - - + -
815A LEU* 4.0 24.0 - - + -
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Residues in contact with SER 787 (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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769A ILE* 5.0 3.1 - - - -
779A VAL* 4.6 12.0 - - - +
780A LEU 3.4 12.5 + - - -
781A PRO* 3.6 11.1 - - - +
782A LEU* 4.2 4.9 - - - +
783A SER 5.0 0.7 + - - -
786A PHE* 1.3 74.7 + - - +
788A ALA* 1.3 60.1 + - - +
789A VAL* 5.9 0.2 - - - -
800A ASP 3.9 0.2 - - - +
801A ILE* 3.5 5.5 - - - +
802A TYR* 2.9 36.3 + - - +
804A ASN* 5.3 1.4 + - - -
809A PHE* 3.6 33.5 - - - -
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Residues in contact with ALA 788 (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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44A ALA* 4.1 13.2 - - + -
778A GLY 4.1 0.2 - - - +
779A VAL* 3.4 7.3 - - - +
780A LEU* 2.8 40.1 + - + +
782A LEU* 3.7 31.6 - - + +
787A SER* 1.3 74.1 - - - +
789A VAL* 1.3 61.5 + - - +
790A ILE* 5.7 0.7 - - + -
799A ILE* 4.2 6.5 - - + -
800A ASP 3.2 8.1 - - - +
801A ILE* 4.1 4.7 - - + -
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Residues in contact with VAL 789 (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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735A PHE* 3.8 30.3 - - + -
769A ILE* 3.8 18.6 - - + -
774A GLN* 5.2 1.6 - - - +
776A LEU* 3.8 17.5 - - + -
778A GLY 3.9 2.2 - - - -
779A VAL* 4.1 11.9 - - + -
787A SER 5.4 0.7 - - - -
788A ALA* 1.3 76.9 - - - +
790A ILE* 1.3 66.3 + - - +
791A ALA* 4.0 3.4 + - + +
798A LYS 3.3 5.9 - - - +
799A ILE* 3.4 2.5 - - - -
800A ASP* 2.8 40.6 + - + +
802A TYR* 3.5 32.3 - - + -
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Residues in contact with ILE 790 (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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30A VAL* 3.8 24.5 - - + -
40A TYR* 4.0 29.4 - - + +
776A LEU* 3.6 5.2 - - - +
777A THR* 2.8 48.0 + - + +
778A GLY 3.0 22.1 + - - +
780A LEU* 3.8 32.8 - - + -
788A ALA 5.4 0.2 - - - -
789A VAL* 1.3 71.8 - - - +
791A ALA* 1.3 60.8 + - - +
797A ASN* 3.8 20.2 - - + +
798A LYS 3.7 5.6 - - - +
799A ILE* 4.9 14.1 - - + -
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Residues in contact with ALA 791 (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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735A PHE* 4.4 5.6 - - + -
774A GLN* 3.8 33.2 - - + +
775A THR 3.3 17.5 - - - +
776A LEU* 4.1 2.7 - - - -
777A THR* 3.7 3.1 - - - -
789A VAL* 4.0 4.5 + - + +
790A ILE* 1.3 76.8 - - - +
792A LYS* 1.3 64.7 + - - +
793A ASP 4.4 0.4 - - - -
797A ASN* 3.5 5.4 - - - +
798A LYS* 3.0 37.7 + - + +
800A ASP* 6.5 0.2 - - - -
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Residues in contact with LYS 792 (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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32A GLU* 4.4 16.0 + - - -
733A MET* 6.0 0.3 - - - +
773A THR 4.9 0.2 - - - +
774A GLN* 4.5 2.2 - - - -
775A THR* 2.9 45.9 + - + +
776A LEU 5.1 1.6 + - - -
777A THR* 2.9 39.5 + - - +
791A ALA* 1.3 75.0 - - - +
793A ASP* 1.3 61.7 + - - +
795A ASP* 3.5 30.5 - - - +
796A GLN 3.6 10.1 - - - +
797A ASN* 3.5 21.1 - - - +
798A LYS* 5.8 0.2 - - - -
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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