Contacts of the strand formed by residues 778 - 783 (chain B) 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 ASN 778 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774B VAL* 3.6 4.2 - - - +
775B GLN* 2.7 45.2 + - + +
777B SER* 1.3 94.7 + - - +
779B ALA* 1.3 59.0 + - - +
791B THR* 4.1 19.6 - - + +
792B LEU 3.4 11.0 - - - +
793B PRO* 3.6 16.8 - - - +
794B THR* 4.2 1.8 - - - -
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Residues in contact with ALA 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B VAL* 3.9 26.0 - - + -
773B ARG 3.5 8.5 - - - +
774B VAL* 4.2 5.4 - - + -
775B GLN* 4.5 0.4 - - - +
778B ASN* 1.3 76.1 - - - +
780B THR* 1.3 62.6 + - - +
781B VAL* 3.7 4.9 + - + +
790B GLU 3.8 0.3 - - - +
791B THR* 3.6 3.1 - - - -
792B LEU* 2.8 35.2 + - - +
794B THR* 4.1 16.2 - - + -
797B LEU* 4.4 9.2 - - + -
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Residues in contact with THR 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B VAL* 3.8 1.2 - - - +
772B GLU* 2.8 47.2 + - - +
773B ARG* 3.2 32.0 + - - +
779B ALA* 1.3 71.9 - - - +
781B VAL* 1.3 62.9 + - - +
789B LYS* 4.9 9.2 - - + -
790B GLU 3.4 15.7 - - - +
791B THR* 3.3 21.7 + - - +
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Residues in contact with VAL 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B ALA* 4.5 1.3 - - + -
769B ALA* 4.0 16.2 - - + -
770B LYS 3.1 12.8 - - - +
771B VAL* 4.1 9.9 - - + +
772B GLU* 5.4 1.6 - - - -
779B ALA* 4.4 5.8 - - + +
780B THR* 1.3 79.7 - - - +
782B LEU* 1.3 59.9 + - - +
783B TYR* 4.0 30.2 + - + +
789B LYS* 3.3 26.5 - - - +
790B GLU* 3.0 23.3 + - + +
792B LEU* 4.4 10.8 - - + -
797B LEU* 4.3 28.5 - - + -
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Residues in contact with LEU 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717B PHE* 4.3 17.9 - - + -
769B ALA* 3.2 3.8 - - - -
770B LYS* 2.9 41.8 + - + +
772B GLU* 3.9 24.3 + - - +
781B VAL* 1.3 72.6 - - - +
783B TYR* 1.3 67.0 + - - +
784B ILE* 3.1 22.2 + - + +
787B GLY* 3.4 34.8 - - - +
788B ASN 3.8 1.3 - - - -
789B LYS* 3.8 21.5 - - + -
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Residues in contact with TYR 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758B ALA* 3.9 17.7 - - + -
760B PHE* 3.3 31.7 + + + -
767B TYR* 3.4 38.8 - + + -
768B ARG 3.7 6.7 - - - +
769B ALA* 4.4 3.4 - - + -
781B VAL* 4.0 10.8 - - + -
782B LEU* 1.3 70.1 - - - +
784B ILE* 1.3 57.0 + - - +
785B ASP 3.2 2.9 - - - -
786B TYR* 2.9 14.1 + - + -
787B GLY* 2.7 32.2 + - - -
788B ASN* 2.8 55.9 + - - +
790B GLU* 2.6 38.9 + - + -
792B LEU* 3.4 12.3 - - - +
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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
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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