Contacts of the strand formed by residues 782 - 791 (chain A) in PDB entry 2VJ0
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 GLN 782 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A GLN* 4.3 2.2 + - - -
740A PHE* 3.8 26.4 - - + +
741A TYR 3.2 14.8 - - - +
742A GLY* 4.2 2.0 - - - +
781A ALA* 1.3 76.4 - - - +
783A VAL* 1.3 73.9 + - - +
784A GLN* 5.4 3.0 - - - +
4P GLY 4.7 1.1 - - - +
5P TRP* 3.4 37.8 - - + +
6P VAL* 2.8 53.0 + - - +
8P PHE* 4.2 6.3 - - - -
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Residues in contact with VAL 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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740A PHE* 3.4 2.4 - - - -
741A TYR* 2.8 53.3 + - + +
752A PHE* 4.6 0.7 - - + -
773A VAL* 4.5 16.6 - - + -
774A ASP* 5.6 3.4 - - + +
776A THR 4.9 6.3 - - - +
777A VAL* 3.9 37.7 - - + -
781A ALA* 5.0 5.4 - - + -
782A GLN* 1.3 82.1 - - - +
784A GLN* 1.3 68.2 + - - +
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Residues in contact with GLN 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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738A PHE* 4.2 19.3 - - + -
739A ILE 3.1 13.5 - - - +
740A PHE* 3.3 33.6 - - + -
741A TYR* 4.5 5.4 - - - -
773A VAL* 4.5 10.3 - - - +
782A GLN* 5.4 2.9 - - - +
783A VAL* 1.3 83.4 - - - +
785A GLN* 1.3 67.5 + - - +
786A VAL* 5.3 2.4 - - + +
6P VAL* 5.2 2.4 - - - +
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Residues in contact with GLN 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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737A MET 3.8 0.3 - - - +
738A PHE* 3.5 3.7 - - - +
739A ILE* 3.0 49.2 + - + +
741A TYR* 2.7 33.9 + - + +
754A PRO* 3.7 17.3 + - - +
756A LEU* 5.0 2.6 - - - +
770A THR* 2.9 37.4 + - - +
771A LYS* 4.2 4.2 - - + +
773A VAL* 3.6 23.7 - - + +
784A GLN* 1.3 77.1 - - - +
786A VAL* 1.3 63.1 + - - +
787A ILE* 4.4 6.9 - - + +
801A LEU* 5.1 1.8 - - - +
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Residues in contact with VAL 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ARG* 3.8 31.6 - - + +
737A MET 3.5 3.8 - - - +
738A PHE* 3.4 34.5 - - + -
769A GLN 3.7 1.2 - - - +
770A THR* 2.7 29.5 + - - -
771A LYS* 4.4 1.9 + - - +
784A GLN* 5.3 4.0 - - + +
785A GLN* 1.3 75.3 - - - +
787A ILE* 1.3 57.6 + - - +
788A ASN* 3.9 20.8 + - - +
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Residues in contact with ILE 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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736A ARG* 3.5 3.1 - - - -
737A MET* 2.7 47.0 + - + +
739A ILE* 3.2 36.3 - - + -
756A LEU* 3.2 40.4 - - + -
768A LEU* 4.2 13.9 - - + -
769A GLN 3.4 7.9 - - - +
770A THR* 4.0 8.7 - - - +
785A GLN* 4.4 5.4 - - + +
786A VAL* 1.3 76.1 - - - +
788A ASN* 1.3 70.0 + - - +
789A ILE* 3.8 14.5 - - + +
818A LEU* 4.4 6.7 - - + -
820A ILE* 5.0 1.3 - - + -
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Residues in contact with ASN 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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735A GLY 3.7 3.8 - - - +
736A ARG* 3.1 40.8 + - - +
767A ASN 3.6 1.2 - - - +
768A LEU* 3.6 3.6 - - - -
769A GLN* 2.8 49.5 + - + +
786A VAL* 3.9 15.5 + - - +
787A ILE* 1.3 72.5 - - - +
789A ILE* 1.3 59.8 + - - +
1940A DTD 5.1 1.0 - - - -
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Residues in contact with ILE 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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730A PHE* 3.9 21.5 - - + -
734A LEU* 3.3 8.5 - - - +
735A GLY 2.9 39.8 + - - +
737A MET* 4.0 22.2 - - + -
766A LEU* 3.8 17.5 - - + -
767A ASN 3.5 3.6 - - - -
768A LEU* 4.0 16.4 - - + -
787A ILE* 3.8 9.4 - - + +
788A ASN* 1.3 77.1 - - - +
790A GLU* 1.3 64.3 + - - +
820A ILE* 3.5 24.5 - - + -
825A PHE* 3.8 26.7 - - + -
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Residues in contact with GLU 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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733A ASN* 3.7 11.9 + - - +
734A LEU* 3.9 17.9 - - + +
766A LEU* 3.6 4.4 - - - -
767A ASN* 2.8 64.4 + - + +
789A ILE* 1.3 75.6 - - - +
791A CYS* 1.3 62.8 + - - +
792A ILE* 3.5 23.8 + - + +
896A LYS* 3.6 23.6 + - - +
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Residues in contact with CYS 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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733A ASN* 2.8 32.5 + - + +
765A ASN 3.9 2.5 - - - -
766A LEU* 4.2 4.4 - - + +
789A ILE 4.2 0.4 - - - -
790A GLU* 1.3 72.2 - - - +
792A ILE* 1.3 58.3 + - - +
793A SER 3.3 24.5 - - - -
795A PHE* 3.8 18.4 - - - -
822A LEU* 4.9 1.8 - - - -
825A PHE* 3.8 29.5 - - + -
894A HIS 4.3 0.2 - - - -
895A THR* 3.6 23.3 - - - -
896A LYS* 2.9 20.4 + - - +
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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