Contacts of the helix formed by residues 793 - 805 (chain A) in PDB entry 1JQO
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 GLY 793 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609A GLY* 5.1 5.4 - - - -
610A ARG 5.3 2.6 - - - +
611A LEU* 5.5 1.1 - - - -
724A ALA* 3.8 36.8 - - - -
727A GLU* 4.0 5.6 - - - +
728A TYR* 4.6 8.0 - - - -
789A PRO 5.5 0.2 + - - -
791A TRP 2.9 4.4 + - - -
792A LEU* 1.3 77.8 - - - +
794A VAL* 1.3 53.2 + - - +
795A GLY 2.6 15.9 + - - -
796A ALA* 3.1 12.6 + - - +
797A ALA 3.6 5.4 + - - -
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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
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610A ARG* 5.6 0.4 - - + -
611A LEU* 4.3 25.4 - - + +
724A ALA* 4.5 2.0 - - - +
790A VAL 4.5 2.5 - - - +
791A TRP* 3.2 17.5 + - - +
793A GLY* 1.3 68.4 - - - +
795A GLY* 1.3 66.6 + - - +
797A ALA* 3.9 10.5 - - - +
798A PHE* 3.3 50.7 + - + +
826A LEU* 5.8 1.6 - - + -
829A LEU* 3.5 32.5 - - + -
867A THR* 3.9 13.6 - - + +
870A LEU* 4.9 0.3 - - - +
871A LEU* 5.9 4.5 - - + -
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Residues in contact with GLY 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A GLU* 5.1 1.6 - - - -
791A TRP 3.8 1.8 + - - -
792A LEU 4.1 3.3 + - - -
793A GLY 2.6 8.5 + - - -
794A VAL* 1.3 79.5 - - - +
796A ALA* 1.3 60.2 + - - -
798A PHE 3.2 5.7 + - - -
799A LYS* 3.3 10.9 + - - +
866A GLU* 5.3 6.1 - - - -
867A THR* 3.2 34.5 + - - +
870A LEU* 3.4 13.5 - - - +
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Residues in contact with ALA 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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723A VAL* 3.8 17.9 - - + -
727A GLU* 3.3 38.0 + - + +
793A GLY 3.1 2.6 + - - -
795A GLY* 1.3 71.3 - - - +
797A ALA* 1.3 66.3 + - - +
799A LYS* 4.0 7.4 - - - +
800A PHE* 2.8 28.6 + - - +
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Residues in contact with ALA 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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611A LEU* 3.6 31.0 - - + -
720A MET* 3.3 39.1 - - + +
723A VAL* 4.0 13.1 - - - +
724A ALA* 4.2 6.9 - - + +
793A GLY 3.6 2.6 + - - -
794A VAL* 3.9 10.8 - - - +
795A GLY 3.3 1.2 - - - -
796A ALA* 1.3 78.4 - - - +
798A PHE* 1.3 63.6 + - + +
800A PHE* 3.8 1.7 - - - +
801A ALA 3.5 9.9 + - - -
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Residues in contact with PHE 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU* 4.5 13.2 - - + -
720A MET* 4.4 12.3 - - - -
794A VAL* 3.3 35.4 - - + +
795A GLY 3.2 7.3 + - - +
796A ALA 3.1 0.4 - - - -
797A ALA* 1.3 79.5 - - + +
799A LYS* 1.3 66.9 + - - +
800A PHE 3.0 2.2 + - - -
801A ALA* 3.1 12.5 + - - +
802A ILE* 3.2 19.5 + - + +
812A LEU* 4.5 9.8 - - + +
822A PHE* 4.2 11.4 - + - -
826A LEU* 4.0 28.7 - - + -
870A LEU* 3.9 28.5 - - + -
871A LEU* 4.7 7.4 - - + -
874A ILE* 3.5 39.0 - - + -
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Residues in contact with LYS 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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795A GLY 3.3 9.1 + - - +
796A ALA* 3.3 9.7 + - - +
798A PHE* 1.3 77.5 - - - +
800A PHE* 1.3 51.5 + - - +
802A ILE* 3.2 15.4 + - - +
803A ASP* 2.7 75.6 + - - +
866A GLU* 4.4 18.4 - - - +
870A LEU* 4.0 19.1 - - + +
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Residues in contact with PHE 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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716A LEU* 5.2 1.8 - - + -
719A GLU* 3.7 36.6 - - + -
720A MET* 4.8 4.0 - - + -
723A VAL* 3.6 34.8 - - + -
796A ALA 2.8 18.1 + - - +
797A ALA 3.8 6.1 - - - +
799A LYS* 1.3 73.3 - - - +
801A ALA* 1.3 74.7 + - + +
802A ILE 3.0 4.5 - - - -
803A ASP* 3.2 5.9 + - + +
804A LYS* 2.8 58.6 + - + +
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Residues in contact with ALA 801 (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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716A LEU* 3.6 35.7 - - + -
720A MET* 4.3 7.9 - - + -
797A ALA 3.5 9.3 + - - +
798A PHE 3.1 9.2 + - - +
800A PHE* 1.3 85.6 - - - +
802A ILE* 1.3 58.1 + - - +
804A LYS* 4.4 2.2 - - - -
805A ASP 3.2 3.3 + - - +
808A ASN* 2.7 38.8 + - + +
812A LEU* 4.6 9.4 - - + -
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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
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798A PHE* 3.2 15.4 + - + +
799A LYS* 3.6 14.1 - - - +
800A PHE 3.0 0.6 - - - -
801A ALA* 1.3 77.6 - - - +
803A ASP* 1.3 69.3 + - - +
804A LYS 2.9 5.3 + - - -
805A ASP 3.1 24.4 + - - +
806A VAL* 3.6 15.0 + - + +
808A ASN* 4.8 0.4 - - - -
809A PHE* 3.3 49.1 - - + -
812A LEU* 4.8 9.6 - - + -
870A LEU* 4.3 19.5 - - + -
873A GLN* 6.0 0.2 - - - +
874A ILE* 5.3 1.3 - - + -
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Residues in contact with ASP 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A LYS* 2.7 64.1 + - - +
800A PHE* 3.9 5.8 - - + +
802A ILE* 1.3 72.8 - - - +
804A LYS* 1.3 60.3 + - - +
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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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715A LYS* 5.6 3.0 - - - +
716A LEU* 4.5 7.9 - - - +
719A GLU* 3.4 37.1 + - - +
800A PHE* 2.8 39.2 + - + +
801A ALA* 3.9 4.3 - - - +
803A ASP* 1.3 81.8 - - - +
805A ASP* 1.3 64.8 + - - +
808A ASN* 3.4 21.9 + - - +
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Residues in contact with ASP 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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801A ALA 3.2 9.7 + - - +
802A ILE* 3.1 11.6 + - - +
804A LYS* 1.3 86.7 - - - +
806A VAL* 1.3 64.3 + - - +
807A ARG* 2.4 71.5 + - - +
808A ASN* 3.1 29.5 + - - +
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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