Contacts of the strand formed by residues 811 - 816 (chain A) in PDB entry 2WAC
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 ALA 811 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708A THR* 4.4 4.3 - - - +
717A PHE* 4.2 16.7 - - + -
718A ALA 3.5 8.5 - - - +
719A GLN* 4.4 1.3 - - + -
784A ILE 3.3 14.4 + - - +
785A ASP* 3.6 23.8 - - - +
786A TYR* 3.7 18.2 - - - +
809A PRO* 3.8 12.7 - - - +
810A TYR* 1.3 80.1 - - - +
812A THR* 1.3 64.6 + - - +
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Residues in contact with THR 812 (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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717A PHE* 3.3 4.7 - - - -
718A ALA 3.0 30.9 + - - -
809A PRO 4.8 4.3 + - - -
810A TYR 5.3 0.7 - - - -
811A ALA* 1.3 77.2 + - - +
813A GLU* 1.3 67.2 + - - +
814A TYR* 3.3 40.0 + - + +
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Residues in contact with GLU 813 (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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711A THR* 4.4 2.8 - - - +
715A THR* 2.8 30.9 + - - +
716A PHE 3.3 8.1 - - - +
717A PHE* 3.6 40.3 - - + -
789A LYS* 5.1 6.4 + - - -
812A THR* 1.3 81.0 - - - +
814A TYR* 1.3 69.6 + - - +
856A PRO* 3.6 35.4 - - + +
857A ASN 4.3 1.0 + - - -
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Residues in contact with TYR 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A GLU* 4.1 14.0 + - - -
705A VAL* 5.8 0.6 - - + +
715A THR* 3.1 6.6 - - - -
716A PHE* 2.8 57.9 + + + -
718A ALA* 4.2 8.7 - - + -
812A THR* 3.3 46.2 + - + +
813A GLU* 1.3 75.4 - - - +
815A ALA* 1.3 60.0 + - - +
846A LEU* 3.6 25.1 - - + +
848A VAL* 4.0 21.0 - - + +
856A PRO* 3.8 7.0 - - - -
857A ASN* 3.4 26.0 - - + +
859A ALA* 3.9 16.4 - - + -
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Residues in contact with ALA 815 (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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714A LEU 6.0 0.2 - - - -
715A THR* 4.3 15.7 - - + -
716A PHE* 4.2 1.6 - - - -
814A TYR* 1.3 73.3 - - - +
816A LEU* 1.3 63.9 + - - +
817A ALA 3.1 0.3 + - - -
856A PRO* 3.8 14.9 - - + +
857A ASN 2.9 11.0 + - - +
858A LEU* 3.5 16.3 - - + -
859A ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 816 (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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714A LEU* 3.3 29.6 + - + +
716A PHE* 3.9 14.5 - - + -
815A ALA* 1.3 70.9 - - - +
817A ALA* 1.3 66.5 + - - +
818A LEU 3.3 2.6 + - - -
819A VAL* 3.5 32.0 + - + +
835A PHE* 3.8 41.5 - - + -
858A LEU* 5.5 0.2 - - - +
859A ALA 3.7 11.7 - - - +
860A THR* 5.1 1.1 - - - -
861A LEU* 4.5 13.7 - - + +
871A GLY* 4.0 26.7 - - - +
874A LEU* 4.0 14.4 - - + -
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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