Contacts of the helix formed by residues 806 - 823 (chain A) in PDB entry 6J8H
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 VAL 806 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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798A MET* 5.2 6.3 - - + -
802A GLU 5.0 4.5 - - - +
803A TYR 4.0 3.8 - - - +
804A PHE 3.8 1.2 - - - +
805A GLN* 1.3 91.0 - - + +
807A GLY* 1.3 63.1 + - - +
808A TRP* 4.4 4.0 - - + +
809A ASN* 2.9 53.8 + - + +
810A ILE* 3.2 10.7 + - - +
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Residues in contact with GLY 807 (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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805A GLN 3.7 3.4 + - - -
806A VAL* 1.3 69.6 - - - +
808A TRP* 1.3 63.5 + - - +
810A ILE* 2.6 35.6 - - - +
811A PHE* 2.9 6.9 + - - +
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Residues in contact with TRP 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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806A VAL* 3.3 4.4 - - + +
807A GLY* 1.3 75.9 - - - +
809A ASN* 1.3 53.2 + - - +
811A PHE* 3.0 45.1 + + - +
812A ASP* 2.6 36.8 + - - +
843A PHE* 4.6 5.4 - - + +
844A LYS* 4.3 39.7 - - + +
846A ALA* 4.2 23.1 - - + -
847A LYS* 4.3 28.0 - - + -
853A ASN* 5.6 4.3 - - - -
856A ILE* 5.4 12.1 - - + -
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Residues in contact with ASN 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A LYS* 4.6 2.8 - - - +
798A MET* 3.9 5.3 - - - +
803A TYR* 2.7 78.7 + - - +
804A PHE* 4.6 3.2 - - - -
806A VAL* 2.9 29.9 + - + +
807A GLY 3.1 0.4 - - - -
808A TRP* 1.3 78.7 - - - +
810A ILE* 1.3 59.0 + - - +
812A ASP* 3.2 7.4 + - - +
813A SER* 2.8 27.5 + - - -
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Residues in contact with ILE 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A PHE* 3.6 34.8 - - + +
806A VAL 3.6 12.3 - - - +
807A GLY* 2.6 29.8 - - - +
809A ASN* 1.3 77.0 - - - +
811A PHE* 1.3 71.2 + - + +
813A SER* 2.5 20.3 + - - +
814A LEU* 2.4 38.8 - - + +
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Residues in contact with PHE 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 GLY 2.9 9.1 + - - +
808A TRP* 3.0 42.4 + + + +
810A ILE* 1.3 88.8 - - + +
812A ASP* 1.3 66.5 + - + +
814A LEU* 3.6 11.5 + - + +
815A ILE* 3.3 35.4 - - + +
840A LEU* 4.7 36.8 - - + -
841A ARG* 4.8 15.9 - - - -
843A PHE* 5.0 10.3 - + + -
844A LYS* 5.3 4.3 - - + -
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Residues in contact with ASP 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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787A PHE* 5.3 1.3 - - - -
790A GLU* 3.8 10.6 - - - +
791A MET* 3.8 12.6 - - - +
803A TYR* 5.4 2.2 - - - +
808A TRP 2.6 19.8 + - - +
809A ASN* 3.6 8.7 - - - +
811A PHE* 1.3 80.8 - - + +
813A SER* 1.3 61.3 + - - +
815A ILE* 3.4 8.2 + - - +
816A VAL* 3.0 37.4 + - - +
841A ARG* 4.1 11.6 + - - +
844A LYS* 2.2 42.8 + - - +
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Residues in contact with SER 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A MET* 4.2 21.3 - - - +
804A PHE* 4.6 17.9 - - - -
809A ASN* 2.8 20.6 + - - -
810A ILE* 2.5 23.7 + - - -
812A ASP* 1.3 78.8 + - - +
814A LEU* 1.3 61.5 + - - +
816A VAL* 3.4 2.3 + - - +
817A THR* 2.7 40.4 + - - +
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Residues in contact with LEU 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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810A ILE* 2.4 49.7 + - + +
811A PHE* 3.7 12.3 - - + +
812A ASP 3.4 0.4 - - - -
813A SER* 1.3 84.5 + - - +
815A ILE* 1.3 67.7 + - + +
817A THR* 2.7 23.5 + - - -
818A LEU* 3.2 15.7 + - + +
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Residues in contact with ILE 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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811A PHE* 3.3 38.4 - - + +
812A ASP* 3.7 7.4 - - - +
813A SER 3.2 0.4 - - - -
814A LEU* 1.3 82.4 - - + +
816A VAL* 1.3 64.4 + - - +
818A LEU* 3.3 13.2 + - + +
819A SER* 3.1 17.5 + - - -
837A PHE 4.7 5.4 - - - +
838A ARG* 3.7 33.2 - - + +
840A LEU* 5.7 4.9 - - + -
841A ARG* 3.6 32.8 - - + +
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Residues in contact with VAL 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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784A THR* 5.0 2.4 - - + +
787A PHE* 4.1 15.3 - - + +
788A ALA* 3.4 42.2 - - + +
791A MET* 4.2 18.4 - - + -
812A ASP* 3.0 36.7 + - - +
813A SER 3.4 4.7 + - - +
815A ILE* 1.3 75.0 - - + +
817A THR* 1.3 63.4 + - + +
819A SER* 3.3 16.2 + - - +
820A LEU* 3.4 14.6 + - + +
841A ARG* 5.0 7.0 - - - +
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Residues in contact with THR 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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791A MET* 5.6 4.3 - - - -
813A SER* 2.7 28.5 - - - +
814A LEU* 2.7 22.0 + - - -
816A VAL* 1.3 77.1 - - + +
818A LEU* 1.3 63.1 + - - +
820A LEU* 3.2 14.6 + - - +
821A VAL* 2.9 26.6 + - - +
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Residues in contact with LEU 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 LEU* 3.2 11.5 + - + +
815A ILE* 3.5 12.6 - - + +
816A VAL 3.2 0.2 - - - -
817A THR* 1.3 83.6 + - - +
819A SER* 1.3 62.7 + - - +
821A VAL* 3.4 12.0 + - + +
822A GLU* 3.3 19.1 + - + +
834A LEU* 3.8 43.5 - - + +
835A ARG* 5.4 2.5 - - - +
837A PHE* 6.1 3.6 - - + -
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Residues in contact with SER 819 (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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784A THR* 3.2 35.1 - - - +
815A ILE 3.1 15.2 + - - -
816A VAL* 3.6 9.0 + - - -
817A THR 3.2 0.4 - - - -
818A LEU* 1.3 79.4 - - - +
820A LEU* 1.3 61.5 + - - +
822A GLU* 3.2 20.7 + - - +
823A LEU* 3.9 3.6 + - - +
838A ARG* 4.0 21.7 + - - +
841A ARG* 5.0 2.3 + - - -
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Residues in contact with LEU 820 (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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784A THR* 4.8 5.8 - - + +
788A ALA* 4.3 24.2 - - + -
816A VAL* 3.4 9.8 + - + +
817A THR* 3.2 12.6 + - - +
819A SER* 1.3 78.9 - - - +
821A VAL* 1.3 64.1 + - + +
822A GLU 3.4 0.5 + - - -
823A LEU* 3.5 16.0 + - - +
824A PHE 4.5 1.7 + - - -
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Residues in contact with VAL 821 (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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817A THR* 2.9 24.9 - - - +
818A LEU* 3.7 12.3 - - + +
819A SER 3.3 0.2 - - - -
820A LEU* 1.3 74.6 - - + +
822A GLU* 1.3 65.3 + - - +
823A LEU 3.3 0.3 + - - -
824A PHE 3.3 0.7 + - - -
825A LEU* 3.1 50.6 + - + +
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Residues in contact with GLU 822 (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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818A LEU* 3.3 10.7 + - + +
819A SER* 3.2 15.4 + - - +
820A LEU 3.2 0.6 - - - -
821A VAL* 1.3 79.6 - - - +
823A LEU* 1.3 65.0 + - - +
824A PHE* 3.4 3.1 + - - -
825A LEU 4.6 4.9 + - - +
832A SER* 3.4 17.7 + - - -
834A LEU* 3.9 8.3 - - - +
835A ARG* 2.2 66.7 + - + +
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Residues in contact with LEU 823 (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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781A LEU* 5.7 13.5 - - + -
819A SER 3.9 2.9 + - - +
820A LEU* 3.5 11.5 + - - +
821A VAL 3.2 1.0 - - - -
822A GLU* 1.3 82.0 - - - +
824A PHE* 1.3 76.3 + - + +
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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