Contacts of the helix formed by residues 807 - 818 (chain A) in PDB entry 5J3V
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 ASN 807 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804A ILE* 3.5 13.9 - - - +
805A ARG* 2.8 45.1 + - + +
806A ASP* 1.3 76.0 - - - +
808A GLU* 1.3 58.3 + - - +
809A GLU* 2.8 47.1 + - - +
810A LYS* 2.9 15.1 - - - +
811A ASP* 3.0 27.6 + - - +
842A TRP* 4.4 2.1 - - - -
11C THR* 3.6 16.6 + - + +
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Residues in contact with GLU 808 (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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737A ILE* 5.8 2.4 - - - +
777A ARG* 5.0 6.3 + - - +
807A ASN* 1.3 73.9 - - - +
809A GLU* 1.3 81.8 + - - +
811A ASP* 3.1 16.0 + - - +
812A SER* 3.0 35.9 + - - -
846A LYS* 4.6 6.8 + - - -
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Residues in contact with GLU 809 (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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734A GLU* 5.6 0.5 - - - +
773A ILE* 3.7 30.1 - - + +
777A ARG* 3.9 20.1 + - - +
807A ASN* 2.8 24.7 + - - +
808A GLU* 1.3 85.1 + - - +
810A LYS* 1.3 59.3 + - - +
812A SER* 3.3 16.9 + - - -
813A ALA* 3.3 15.2 + - - +
11C THR* 3.9 24.0 - - - +
12C GLY 4.6 3.4 - - - +
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Residues in contact with LYS 810 (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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773A ILE* 5.7 1.3 - - - -
801A LEU* 3.5 21.7 + - + +
802A ARG 4.7 0.2 + - - -
804A ILE* 2.9 28.9 + - + +
805A ARG 3.3 26.7 - - - +
806A ASP* 2.8 25.5 + - - +
807A ASN* 2.9 14.3 - - - +
809A GLU* 1.3 76.1 - - - +
811A ASP* 1.3 63.2 + - - +
813A ALA* 4.0 3.5 - - - +
814A PHE* 3.1 43.5 + - + -
841A SER* 3.4 28.3 + - - -
842A TRP* 3.4 28.2 - - + +
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Residues in contact with ASP 811 (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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807A ASN 3.0 14.6 + - - +
808A GLU* 3.1 18.3 + - - +
810A LYS* 1.3 74.6 - - - +
812A SER* 1.3 56.3 + - - +
814A PHE* 3.2 3.1 + - - +
815A ARG* 2.8 62.9 + - - +
842A TRP* 3.7 14.6 - - + -
846A LYS* 3.0 31.9 + - - +
849A LEU* 3.3 16.5 - - - +
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Residues in contact with SER 812 (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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737A ILE* 5.5 4.0 - - - -
776A GLY 4.2 5.2 - - - +
777A ARG* 3.3 37.3 + - - +
780A TYR* 4.6 5.5 - - - +
808A GLU* 3.0 21.6 + - - -
809A GLU 3.3 10.4 + - - -
811A ASP* 1.3 82.3 + - - +
813A ALA* 1.3 63.1 + - - +
815A ARG* 3.5 11.0 + - - +
816A GLY* 3.3 16.6 + - - -
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Residues in contact with ALA 813 (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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772A ALA 4.6 0.7 - - - +
773A ILE* 3.9 20.9 - - + -
776A GLY* 3.8 13.1 - - - -
797A TRP* 3.6 12.8 - - + -
801A LEU* 3.8 27.6 - - + -
809A GLU 3.3 16.3 + - - +
810A LYS 4.0 2.5 - - - +
811A ASP 3.2 0.6 - - - -
812A SER* 1.3 81.1 + - - +
814A PHE* 1.3 57.8 + - - +
816A GLY* 3.1 3.8 + - - -
817A ILE 3.1 21.0 + - - -
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Residues in contact with PHE 814 (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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797A TRP* 4.1 17.9 - + - -
801A LEU* 3.9 23.6 - - + -
810A LYS* 3.1 44.0 + - + +
811A ASP 3.8 2.7 - - - +
813A ALA* 1.3 73.7 - - - +
815A ARG* 1.3 63.5 + - - +
816A GLY 3.0 4.9 - - - -
817A ILE* 3.2 29.6 - - + +
818A CYS* 3.2 14.9 + - - -
835A PHE* 5.1 2.5 - + - -
838A ALA* 3.6 45.5 - - + -
839A VAL* 4.3 4.7 - - + -
842A TRP* 3.5 27.1 - + + -
849A LEU* 4.1 3.4 - - + -
853A PHE* 3.6 26.0 - + + -
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Residues in contact with ARG 815 (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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780A TYR* 3.4 33.3 - - + -
811A ASP* 2.8 52.5 + - - +
812A SER* 3.7 10.7 - - - +
813A ALA 3.2 0.2 - - - -
814A PHE* 1.3 76.9 - - - +
816A GLY* 1.3 51.0 + - - +
818A CYS* 4.2 4.2 - - - +
819A THR* 2.7 30.0 + - - -
846A LYS* 3.4 18.7 - - - +
848A ASP* 2.3 38.4 + - - +
849A LEU* 4.0 20.3 - - + +
852A MET* 4.6 19.9 - - + +
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Residues in contact with GLY 816 (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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776A GLY 3.4 25.6 - - - -
779A GLY 4.2 2.3 - - - -
780A TYR* 3.6 15.0 - - - -
812A SER 3.3 4.6 + - - -
813A ALA 3.1 4.2 + - - -
814A PHE 3.0 0.6 - - - -
815A ARG* 1.3 77.1 - - - +
817A ILE* 1.3 64.1 + - - +
818A CYS 3.1 1.8 - - - -
819A THR* 3.2 11.7 + - - -
820A MET* 3.2 21.3 + - - +
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Residues in contact with ILE 817 (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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790A LEU* 3.7 22.9 - - + -
793A PHE* 4.1 5.8 - - + -
794A ILE* 4.7 6.3 - - + -
797A TRP* 3.5 52.7 - - + -
813A ALA 3.1 5.1 + - - -
814A PHE* 3.2 25.8 - - + +
816A GLY* 1.3 75.8 - - - +
818A CYS* 1.3 60.5 + - - +
820A MET* 3.6 26.3 - - + +
821A ILE* 3.1 37.0 + - + +
835A PHE* 3.9 23.3 - - + -
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Residues in contact with CYS 818 (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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814A PHE 3.2 17.4 + - - +
815A ARG 4.3 1.6 - - - +
816A GLY 3.1 0.6 - - - -
817A ILE* 1.3 85.5 - - - +
819A THR* 1.3 62.4 + - - +
821A ILE* 3.3 2.8 + - - +
822A SER* 3.1 26.2 + - - -
835A PHE* 4.3 1.8 - - - -
849A LEU* 4.5 2.0 - - - -
852A MET* 4.0 30.5 - - + -
853A PHE* 3.5 34.3 - - - -
856A ILE* 3.7 25.3 - - + +
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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