Contacts of the helix formed by residues 789 - 800 (chain A) in PDB entry 3V53
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 789 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788A ALA* 1.3 81.7 - - + +
790A LEU* 1.3 66.0 + - - +
791A VAL 3.4 0.7 + - - -
792A ASP* 3.5 19.3 + - - +
793A PHE* 3.8 6.9 + - - +
736E LYS 3.2 25.6 + - - +
737E HIS* 3.8 14.0 - - + -
738E ILE 4.4 2.5 + - - -
739E LYS* 4.9 27.4 - - - +
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Residues in contact with LEU 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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779A ILE* 4.7 13.0 - - + -
788A ALA 3.3 4.8 - - - +
789A THR* 1.3 80.4 + - - +
791A VAL* 1.3 65.0 + - - +
793A PHE* 3.0 26.3 + - + +
794A VAL* 3.3 14.6 + - + +
814A VAL* 5.8 11.4 - - + -
738E ILE* 4.6 18.4 - - + +
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Residues in contact with VAL 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A ARG* 4.6 9.9 - - + +
775A ILE* 4.1 15.8 - - + +
776A ASN* 3.7 39.7 - - + +
779A ILE* 3.8 28.0 - - + -
788A ALA* 3.5 26.7 - - - +
789A THR 3.2 0.4 - - - -
790A LEU* 1.3 78.8 - - - +
792A ASP* 1.3 66.3 + - - +
794A VAL* 3.4 7.4 + - - +
795A CYS* 3.2 31.8 + - - -
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Residues in contact with ASP 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A ARG* 2.9 34.4 + - - -
788A ALA 3.8 13.7 - - - +
789A THR* 3.5 11.2 + - - +
790A LEU 3.3 0.4 - - - -
791A VAL* 1.3 73.9 - - - +
793A PHE* 1.3 65.5 + - - +
795A CYS* 3.3 9.0 + - - +
796A SER* 3.0 25.5 + - - -
739E LYS* 6.6 0.2 - - + -
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Residues in contact with PHE 793 (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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789A THR 3.8 3.4 + - - +
790A LEU* 3.0 18.6 + - + +
792A ASP* 1.3 79.8 - - - +
794A VAL* 1.3 73.1 + - + +
796A SER* 2.7 23.7 + - - -
797A LYS* 3.2 38.9 + - + +
807A ILE* 5.1 2.5 - - + -
810A ASP* 3.8 35.9 - - + -
811A VAL* 5.0 7.6 - - + -
738E ILE* 4.7 10.5 - - + -
739E LYS* 4.5 29.3 - - + +
742E ILE* 3.9 33.0 - - + -
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Residues in contact with VAL 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A ILE* 4.5 10.3 - - + -
779A ILE* 5.7 4.5 - - + -
790A LEU* 3.3 18.5 + - + +
791A VAL* 3.4 8.0 + - - +
792A ASP 3.3 0.2 - - - -
793A PHE* 1.3 85.1 - - + +
795A CYS* 1.3 66.1 + - - +
797A LYS* 3.3 6.0 + - - +
798A VAL* 3.1 27.7 + - + +
807A ILE* 4.2 17.7 - - + -
811A VAL* 4.7 14.4 - - + -
822A PHE* 4.6 12.8 - - + -
823A ILE* 5.2 0.9 - - + -
826A MET* 3.8 28.9 - - + -
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Residues in contact with CYS 795 (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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767A MET* 3.4 24.9 - - - +
772A ARG* 3.7 37.5 - - - +
775A ILE* 3.8 21.5 - - - +
791A VAL* 3.2 22.2 + - - -
792A ASP* 3.5 9.6 - - - +
794A VAL* 1.3 75.8 - - - +
796A SER* 1.3 56.8 + - - +
798A VAL* 3.0 3.7 + - - -
799A MET* 2.9 27.0 + - + +
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Residues in contact with SER 796 (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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792A ASP 3.0 13.7 + - - -
793A PHE* 2.7 27.5 + - - -
795A CYS* 1.3 75.8 - - - +
797A LYS* 1.3 55.9 + - - +
799A MET* 3.4 9.2 + - - +
800A ALA* 2.8 33.8 + - - +
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Residues in contact with LYS 797 (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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793A PHE* 3.2 39.9 + - + +
794A VAL 3.7 8.1 - - - +
795A CYS 3.2 0.4 - - - -
796A SER* 1.3 81.7 + - - +
798A VAL* 1.3 62.9 + - - +
800A ALA* 3.4 7.5 + - + +
801A HIS 3.3 3.6 + - - -
802A SER* 3.1 52.6 + - - -
806A SER* 4.2 10.8 + - - -
807A ILE* 4.3 21.6 - - + +
810A ASP* 3.0 27.7 + - - -
742E ILE* 5.4 2.8 - - - +
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Residues in contact with VAL 798 (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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759A TRP* 3.2 28.4 - - + -
762A VAL* 4.2 12.3 - - + +
767A MET* 3.5 25.8 - - + -
771A ILE* 5.2 1.6 - - + -
775A ILE* 5.2 2.9 - - + -
794A VAL* 3.1 17.0 + - + +
795A CYS* 3.0 1.9 + - - +
797A LYS* 1.3 76.3 - - - +
799A MET* 1.3 58.7 + - - +
801A HIS* 3.1 16.7 + - - +
807A ILE* 4.5 14.4 - - + -
826A MET* 4.1 26.9 - - + -
827A TRP* 5.5 0.4 - - + -
830A LEU* 4.2 21.3 - - + -
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Residues in contact with MET 799 (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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762A VAL* 4.0 23.1 - - - +
763A ASP* 3.9 17.9 - - - +
764A SER* 4.4 6.1 - - - +
767A MET* 3.7 39.9 - - + -
795A CYS* 2.9 11.3 + - + +
796A SER* 3.6 11.2 - - - +
798A VAL* 1.3 74.0 - - - +
800A ALA* 1.3 55.4 + - - +
801A HIS* 3.0 30.5 + - + -
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Residues in contact with ALA 800 (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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796A SER 2.8 17.9 + - - +
797A LYS* 3.7 15.3 - - + +
798A VAL 3.2 0.4 - - - -
799A MET* 1.3 73.4 - - - +
801A HIS* 1.3 71.3 + - - +
802A SER* 3.3 9.4 + - - +
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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