Contacts of the helix formed by residues 797 - 808 (chain T) in PDB entry 1BGX
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 GLU 797 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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796T ALA* 1.3 77.6 - - - +
798T ALA* 1.3 64.2 + - - +
800T ALA* 3.7 5.9 + - - +
801T ARG* 3.5 57.3 + - - +
823T ILE* 3.6 23.4 - - - +
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Residues in contact with ALA 798 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775T MET* 5.3 12.2 - - - +
796T ALA 3.4 3.0 - - - +
797T GLU* 1.3 80.5 - - - +
799T VAL* 1.3 64.9 + - + +
801T ARG* 3.9 11.9 + - - +
802T LEU* 3.5 20.7 + - - +
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Residues in contact with VAL 799 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607T VAL* 5.2 3.6 - - + -
768T LEU* 6.2 0.4 - - + -
772T LEU* 4.3 13.9 - - + -
775T MET* 4.4 22.9 - - + +
777T ALA* 4.1 23.3 - - + -
789T LEU* 4.5 14.6 - - + -
791T ALA* 3.9 26.2 - - + -
796T ALA 3.9 10.2 + - - +
797T GLU 3.4 0.4 - - - -
798T ALA* 1.3 82.8 - - + +
800T ALA* 1.3 58.1 + - - +
801T ARG 3.3 0.7 - - - -
802T LEU* 4.4 9.9 - - + -
803T ALA* 3.0 31.0 + - + +
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Residues in contact with ALA 800 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607T VAL* 3.9 22.4 - - + +
609T LEU* 4.5 0.6 - - - +
796T ALA 3.3 18.9 + - - +
797T GLU* 3.9 8.1 - - - +
799T VAL* 1.3 77.8 - - - +
801T ARG* 1.3 60.3 + - + +
803T ALA* 4.4 3.7 - - - +
804T LYS* 3.6 22.2 + - - +
821T VAL* 4.0 19.3 - - + +
823T ILE* 3.9 17.0 - - + -
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Residues in contact with ARG 801 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797T GLU* 3.5 49.6 + - - +
798T ALA* 4.2 9.8 - - - +
799T VAL 3.3 0.2 - - - -
800T ALA* 1.3 78.1 - - + +
802T LEU* 1.3 63.2 + - - +
804T LYS* 3.8 7.9 + - - +
805T GLU* 3.6 18.7 + - - +
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Residues in contact with LEU 802 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768T LEU* 5.3 3.4 - - + -
771T ARG* 4.0 45.3 - - + +
772T LEU* 6.4 1.1 - - + -
774T GLU* 6.4 0.2 - - - -
775T MET* 4.0 27.4 - - + -
798T ALA 3.5 15.5 + - - +
799T VAL* 3.3 11.6 + - + +
801T ARG* 1.3 78.0 - - - +
803T ALA* 1.3 64.1 + - - +
804T LYS 3.2 0.2 - - - -
805T GLU* 3.3 21.6 + - + +
806T VAL* 3.2 24.6 + - + +
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Residues in contact with ALA 803 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609T LEU* 3.8 20.2 - - + -
768T LEU* 4.0 23.4 - - + +
789T LEU* 3.9 23.6 - - + -
799T VAL* 3.0 20.1 + - + +
800T ALA 4.4 1.1 - - - +
802T LEU* 1.3 77.5 - - - +
804T LYS* 1.3 60.8 + - - +
805T GLU 3.3 0.2 - - - -
806T VAL* 3.6 1.6 + - - +
807T MET* 3.3 31.2 + - - +
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Residues in contact with LYS 804 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609T LEU* 4.1 4.7 - - - +
800T ALA 3.6 15.2 + - - +
801T ARG* 4.0 9.0 - - - +
802T LEU 3.2 0.6 - - - -
803T ALA* 1.3 77.0 - - - +
805T GLU* 1.3 61.9 + - - +
807T MET* 4.3 2.4 - - - +
808T GLU* 3.0 62.7 + - - +
818T GLU* 3.0 22.8 + - - -
819T VAL* 3.4 24.7 + - + -
821T VAL* 4.0 24.9 - - + -
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Residues in contact with GLU 805 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771T ARG* 5.4 6.0 + - - -
801T ARG 3.6 10.8 + - - +
802T LEU* 3.3 21.1 + - - +
804T LYS* 1.3 79.8 - - - +
806T VAL* 1.3 62.6 + - - +
808T GLU* 4.8 3.4 - - - -
809T GLY* 3.2 26.9 + - - +
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Residues in contact with VAL 806 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764T ALA* 3.9 24.6 - - + +
767T LYS* 4.0 13.3 - - + +
768T LEU* 4.0 23.6 - - + +
771T ARG* 3.6 37.0 - - - +
802T LEU* 3.2 22.4 + - + +
803T ALA 4.1 4.5 - - - +
804T LYS 3.4 0.2 - - - -
805T GLU* 1.3 84.2 - - + +
807T MET* 1.3 63.3 + - + +
809T GLY 3.6 3.5 - - - +
810T VAL* 3.5 24.6 + - - +
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Residues in contact with MET 807 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609T LEU* 3.8 36.1 - - + +
610T ASP 5.3 0.2 - - - +
611T TYR* 3.3 52.7 + - + +
761T MET* 4.0 17.0 - - + -
764T ALA* 4.4 12.3 - - + -
768T LEU* 5.3 4.9 - - + -
787T LEU* 4.1 25.1 - - + -
803T ALA* 3.3 21.1 + - - +
804T LYS 4.3 0.9 - - - +
806T VAL* 1.3 79.4 - - + +
808T GLU* 1.3 59.6 + - - +
810T VAL* 3.6 8.3 - - - +
817T LEU* 3.4 13.3 - - - +
819T VAL* 3.9 19.7 - - + -
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Residues in contact with GLU 808 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804T LYS* 3.0 57.0 + - - +
805T GLU* 4.6 3.0 - - - +
807T MET* 1.3 77.1 - - - +
809T GLY* 1.3 59.1 + - - +
810T VAL* 3.3 7.5 + - - +
811T TYR 4.7 6.1 - - - +
817T LEU* 2.9 45.9 - - - +
818T GLU* 3.5 9.2 - - - +
819T VAL* 3.7 19.5 - - + -
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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