Contacts of the strand formed by residues 780 - 785 (chain A) in PDB entry 3WAJ
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 780 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A GLY* 1.3 70.1 - - - -
781A VAL* 1.3 64.9 + - - +
782A VAL* 3.3 4.4 + - + +
822A VAL 3.4 1.2 - - - +
823A VAL* 3.4 0.8 - - - -
824A LEU* 2.9 33.3 + - + +
853A ILE* 3.7 40.4 - - + -
857A GLN* 3.7 24.0 - - + +
858A VAL* 3.8 4.0 - - - +
862A GLU 3.8 3.1 - - - +
864A ILE* 4.8 5.2 - - + -
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Residues in contact with VAL 781 (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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779A GLY 4.0 7.0 - - - +
780A ALA* 1.3 71.9 - - - +
782A VAL* 1.3 55.4 + - - +
783A THR* 4.7 2.5 - - + -
821A THR* 3.6 30.7 - - + -
822A VAL 3.6 4.0 - - - +
823A VAL* 4.5 14.1 - - + +
861A GLY* 3.9 16.4 - - - +
862A GLU 2.8 13.4 + - - +
863A ILE* 4.1 24.0 - - + -
864A ILE* 2.5 36.5 + - - +
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Residues in contact with VAL 782 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A ALA 4.3 3.6 - - - +
781A VAL* 1.3 74.1 - - - +
783A THR* 1.3 61.3 + - - +
820A TYR* 3.3 26.3 - - + +
821A THR* 3.4 1.0 - - - +
822A VAL* 2.6 56.1 + - + +
824A LEU* 4.0 22.7 - - + -
842A ILE* 5.2 1.3 - - + -
851A ILE* 4.0 20.4 - - + -
853A ILE* 4.2 18.6 - - + -
864A ILE* 3.5 18.8 - - + +
866A LEU* 4.3 8.3 - - + -
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Residues in contact with THR 783 (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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781A VAL* 4.7 1.3 - - + -
782A VAL* 1.3 77.0 - - - +
784A GLY* 1.3 55.6 + - - +
819A THR* 4.3 4.7 + - - +
820A TYR* 2.4 36.1 + - - -
821A THR* 2.8 19.7 + - - -
863A ILE* 4.1 18.2 - - + -
864A ILE 2.9 16.7 + - - +
865A GLN* 3.4 18.3 - - - +
866A LEU* 2.6 32.9 + - - -
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Residues in contact with GLY 784 (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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783A THR* 1.3 83.0 + - - +
785A LYS* 1.3 60.6 + - - -
819A THR* 2.3 27.3 + - - -
820A TYR* 2.9 22.5 + - - -
865A GLN* 4.9 5.2 - - - -
866A LEU 3.3 13.5 - - - -
867A ASP* 4.5 1.8 - - - -
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Residues in contact with LYS 785 (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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784A GLY* 1.3 76.8 - - - -
786A VAL* 1.3 68.5 + - - +
817A ASN 5.8 0.2 - - - +
818A GLY 3.3 13.5 - - - +
819A THR* 4.0 9.2 - - - +
820A TYR* 4.6 0.2 - - - -
866A LEU 3.9 1.2 + - - -
867A ASP* 3.2 30.9 + - - +
868A LEU* 2.7 35.5 + - - +
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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