Contacts of the helix formed by residues 782 - 792 (chain E) in PDB entry 3ZPV
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 THR 782 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776E ARG* 3.6 1.3 - - - +
780E GLY 4.7 1.3 - - - +
781E LEU* 1.3 76.8 - - - +
783E GLU* 1.3 66.1 + - - +
784E ALA* 3.7 7.5 + - - +
785E ALA* 3.0 18.9 + - - +
786E PHE* 3.0 22.0 + - - +
332F ASN* 2.9 37.6 + - + +
335F ALA* 4.7 1.9 - - - +
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Residues in contact with GLU 783 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762E GLU* 4.9 8.7 - - - +
776E ARG* 3.5 33.9 + - - +
782E THR* 1.3 73.5 - - - +
784E ALA* 1.3 62.1 + - - +
786E PHE* 3.5 5.2 + - + +
787E GLN* 3.1 47.5 + - + +
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Residues in contact with ALA 784 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782E THR* 3.2 7.7 + - - +
783E GLU* 1.3 77.6 - - - +
785E ALA* 1.3 64.7 + - - +
787E GLN* 3.3 13.3 + - - +
788E MET* 3.0 34.7 + - + +
335F ALA* 4.1 9.0 - - + -
339F LEU* 4.0 27.4 - - + -
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Residues in contact with ALA 785 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781E LEU* 4.2 4.5 - - + -
782E THR* 3.0 12.4 + - - +
784E ALA* 1.3 75.3 - - - +
786E PHE* 1.3 57.7 + - - +
788E MET* 3.3 3.0 + - - +
789E LEU* 2.9 36.0 + - - +
331F ALA* 3.5 29.3 - - + +
332F ASN* 3.2 27.8 - - - +
335F ALA* 3.8 10.2 - - + +
346F ILE* 5.3 0.4 - - - +
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Residues in contact with PHE 786 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A LYS* 4.1 17.9 - - + -
762E GLU* 3.8 28.0 - - + -
763E ALA 3.5 39.7 - - - -
764E VAL* 4.0 20.0 - - + -
776E ARG* 3.4 32.5 - - + -
781E LEU* 4.5 9.1 - - + +
782E THR 3.0 10.6 + - - +
783E GLU* 3.6 7.4 - - + +
785E ALA* 1.3 78.3 - - - +
787E GLN* 1.3 68.8 + - + +
789E LEU* 3.5 4.7 + - + +
790E ASN* 3.0 53.6 + - - -
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Residues in contact with GLN 787 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783E GLU* 3.1 38.4 + - + +
784E ALA* 3.3 12.2 + - - +
786E PHE* 1.3 86.9 - - + +
788E MET* 1.3 61.4 + - + +
790E ASN* 3.5 5.4 + - - +
791E LYS* 3.1 38.2 + - - +
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Residues in contact with MET 788 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784E ALA* 3.0 21.9 + - + +
785E ALA* 3.9 3.8 - - - +
787E GLN* 1.3 76.6 - - + +
789E LEU* 1.3 66.4 + - - +
791E LYS* 3.3 21.9 + - + +
792E GLU* 3.2 31.3 + - + +
335F ALA* 3.7 35.2 - - + +
338F VAL* 3.8 35.0 - - + -
339F LEU* 4.2 19.5 - - + -
345F THR* 6.2 0.2 - - - -
346F ILE* 3.9 24.2 - - + +
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Residues in contact with LEU 789 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764E VAL* 5.1 3.6 - - + -
781E LEU* 4.1 15.5 - - + -
785E ALA 2.9 21.3 + - - +
786E PHE* 3.8 4.9 - - + +
788E MET* 1.3 77.2 - - - +
790E ASN* 1.3 66.8 + - - +
791E LYS 3.2 0.3 + - - -
792E GLU 3.4 16.6 + - - +
795E ALA* 4.1 13.5 - - + +
796E GLU 4.5 9.9 - - - +
797E TRP* 4.1 26.5 - - + +
326F PHE* 3.9 37.7 - - + -
331F ALA* 3.9 19.5 - - + -
346F ILE* 3.9 12.1 - - + +
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Residues in contact with ASN 790 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A ASN* 3.2 52.8 + - + +
791A LYS* 3.8 9.2 + - + +
763E ALA 5.1 1.4 - - - +
764E VAL* 5.0 5.0 - - - +
786E PHE* 3.0 59.8 + - - +
787E GLN* 3.8 5.7 - - - +
788E MET 3.2 0.2 - - - -
789E LEU* 1.3 81.6 - - - +
791E LYS* 1.3 59.6 + - - +
792E GLU 3.6 1.6 + - - -
793E VAL* 5.7 0.5 - - - -
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Residues in contact with LYS 791 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761A ASP 5.2 5.0 - - - +
762A GLU* 5.4 7.1 - - + +
763A ALA 4.9 2.6 + - - +
786A PHE* 4.1 24.2 - - + -
790A ASN* 3.9 11.7 + - + +
787E GLN* 3.1 25.5 + - - +
788E MET* 3.9 22.7 - - + +
789E LEU 3.2 0.4 - - - -
790E ASN* 1.3 78.0 - - - +
792E GLU* 1.3 78.4 + - - +
793E VAL 3.5 3.2 + - - -
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Residues in contact with GLU 792 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759A ASP* 2.8 28.4 - - - +
760A ASN* 5.2 0.7 - - - -
761A ASP 4.7 5.1 - - - +
788E MET* 3.2 21.8 + - + +
789E LEU 3.4 9.9 - - - +
790E ASN 3.4 2.1 - - - +
791E LYS* 1.3 91.7 - - + +
793E VAL* 1.3 67.7 + - - +
794E PHE* 3.1 3.6 + - - -
795E ALA* 3.0 27.7 + - + +
345F THR* 3.6 20.3 - - - +
346F ILE* 4.1 16.6 - - + +
347F ILE* 4.4 11.6 - - + +
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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