Contacts of the helix formed by residues 797 - 807 (chain A) in PDB entry 3BWT
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 PHE 797 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753A THR 3.4 7.1 - - - +
754A LEU 3.3 23.1 - - - +
755A ASP 3.7 13.7 - - - +
756A PRO* 3.6 43.5 - - + -
759A ASN* 3.7 9.5 - - - +
760A TYR* 6.2 0.9 - + - -
795A HIS* 3.1 6.2 + + - +
796A LYS* 1.3 104.9 - - + +
798A GLY* 1.3 68.4 + - - +
799A SER 3.1 2.0 - - - -
800A ASN* 3.0 31.5 + - - +
801A VAL* 3.9 0.9 + - - +
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Residues in contact with GLY 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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753A THR* 3.2 27.8 + - - +
754A LEU* 4.3 3.4 - - - -
792A LEU* 3.2 13.2 - - - -
795A HIS* 3.0 17.7 + - - -
797A PHE* 1.3 76.1 - - - +
799A SER* 1.3 60.8 + - - +
801A VAL* 3.1 16.3 + - - +
802A ILE* 3.2 13.9 + - - +
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Residues in contact with SER 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A LEU 2.9 17.1 + - - -
793A SER 3.6 17.0 - - - -
795A HIS 3.0 19.6 + - - -
796A LYS 3.7 8.5 + - - -
798A GLY* 1.3 73.3 - - - +
800A ASN* 1.3 70.8 + - - +
802A ILE* 3.8 6.5 - - - +
803A GLU* 3.0 28.8 + - - +
836A TYR* 4.1 11.4 + - - +
840A VAL* 3.9 11.5 - - - +
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Residues in contact with ASN 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A ASN* 3.0 27.7 + - - +
760A TYR* 4.3 12.2 + - - -
763A GLN* 3.3 16.9 - - - +
796A LYS 4.0 8.8 + - - +
797A PHE* 3.0 23.5 + - - +
799A SER* 1.3 86.7 + - - +
801A VAL* 1.3 58.4 + - - +
803A GLU* 3.8 6.3 - - - +
804A LYS* 3.0 25.5 + - - +
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Residues in contact with VAL 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A THR* 3.9 20.9 - - + -
759A ASN* 3.8 33.9 - - + +
762A VAL* 4.1 20.6 - - + -
763A GLN* 4.2 3.4 - - + -
766A ILE* 5.3 3.4 - - + -
781A ILE* 4.9 1.1 - - + -
785A LEU* 3.5 29.8 - - + -
798A GLY 3.1 8.0 + - - +
800A ASN* 1.3 74.5 - - - +
802A ILE* 1.3 66.7 + - + +
804A LYS* 3.0 9.0 + - + +
805A ILE* 2.9 32.1 + - + +
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Residues in contact with ILE 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A LEU* 4.8 4.5 - - + +
789A ALA* 3.9 17.9 - - - +
792A LEU* 3.7 31.2 - - + -
793A SER* 3.5 22.9 - - - +
798A GLY 3.2 12.6 + - - +
799A SER* 3.5 7.6 + - - +
801A VAL* 1.3 77.4 - - - +
803A GLU* 1.3 51.7 + - - +
805A ILE* 3.2 10.2 + - + +
806A LEU* 2.8 35.7 + - + +
815A MET* 3.9 38.4 - - + -
819A ILE* 4.7 2.5 - - + -
840A VAL* 4.0 12.3 - - + -
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Residues in contact with GLU 803 (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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799A SER 3.0 19.7 + - - +
800A ASN* 3.8 6.3 - - - +
802A ILE* 1.3 73.9 - - - +
804A LYS* 1.3 65.2 + - - +
806A LEU* 3.2 8.2 + - - +
807A LYS* 2.9 48.3 + - - +
839A TYR* 3.5 23.9 - - - +
840A VAL* 4.1 18.8 - - + -
843A THR* 3.1 27.5 + - - +
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Residues in contact with LYS 804 (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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763A GLN* 3.7 41.9 + - + +
766A ILE* 4.2 17.5 - - + -
767A THR* 2.7 41.7 + - - +
800A ASN 3.0 16.6 + - - +
801A VAL* 3.0 11.7 + - + +
803A GLU* 1.3 76.2 - - - +
805A ILE* 1.3 57.7 + - + +
807A LYS* 3.2 9.5 + - + +
808A THR* 2.8 32.8 + - - -
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Residues in contact with ILE 805 (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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766A ILE* 3.9 21.5 - - + -
781A ILE* 4.7 1.1 - - + -
782A VAL* 4.1 22.4 - - + -
785A LEU* 4.6 10.5 - - + -
801A VAL* 2.9 33.5 + - + +
802A ILE* 3.5 6.7 - - + +
804A LYS* 1.3 72.7 - - - +
806A LEU* 1.3 63.1 + - - +
807A LYS 3.0 4.7 - - - -
808A THR* 2.9 25.5 + - - +
811A VAL* 3.6 31.3 - - + +
812A SER 3.7 3.3 + - - -
815A MET* 3.9 36.3 - - + -
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Residues in contact with LEU 806 (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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802A ILE* 2.8 23.4 + - + +
803A GLU* 3.2 4.5 + - - +
805A ILE* 1.3 72.6 - - - +
807A LYS* 1.3 57.9 + - - +
808A THR 3.4 0.7 - - - -
812A SER* 3.3 16.8 + - - +
815A MET* 3.6 27.1 - - + -
816A ILE* 3.5 33.4 - - + +
819A ILE* 4.6 3.8 - - + -
840A VAL* 3.7 33.9 - - + +
843A THR* 3.6 30.5 - - + -
844A ALA* 4.1 9.0 - - + +
847A ILE* 3.2 22.3 - - + +
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Residues in contact with LYS 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A GLU* 2.9 38.8 + - - +
804A LYS* 3.5 10.5 - - + +
805A ILE 3.0 0.4 - - - -
806A LEU* 1.3 78.1 - - - +
808A THR* 1.3 59.7 + - - +
809A ALA 3.7 4.1 + - - -
812A SER* 4.6 0.2 - - - -
843A THR* 4.2 20.6 - - + -
846A ASP* 6.0 2.5 - - - -
847A ILE* 4.5 13.7 - - + -
851A GLN* 6.0 0.7 - - - -
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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