Contacts of the helix formed by residues 809 - 820 (chain A) in PDB entry 2N8Z
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 809 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748A MET* 5.1 4.7 - - + -
751A PHE* 3.7 11.2 - - + -
752A ARG* 3.5 45.1 - - + -
755A PHE* 3.9 39.0 - + + -
764A GLY 3.5 7.7 + - - +
771A PHE* 3.7 13.1 - - - -
808A THR* 1.3 72.5 + - - +
810A GLN* 1.3 70.6 + - + +
812A PHE* 2.9 39.2 - + - -
813A ILE* 3.2 34.8 - - + +
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Residues in contact with GLN 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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808A THR* 2.9 15.1 + - + +
809A PHE* 1.3 91.7 - - + +
811A ALA* 1.3 64.1 + - + +
813A ILE* 3.4 9.0 + - - +
814A ASP* 3.1 31.5 + - - +
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Residues in contact with ALA 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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799A VAL* 3.3 44.0 - - + +
807A VAL* 4.0 0.2 - - + -
808A THR* 2.9 32.9 + - + +
810A GLN* 1.3 79.9 - - + +
812A PHE* 1.3 65.5 + - - +
814A ASP* 3.1 21.5 + - - +
815A PHE 3.8 1.2 + - - -
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Residues in contact with PHE 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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751A PHE* 3.4 50.5 - + + -
754A SER* 5.5 1.3 - - - -
755A PHE* 4.9 2.2 - - + -
771A PHE* 3.4 36.6 - + + -
774A CYS* 6.1 4.0 - - - -
775A LEU* 5.0 9.9 - - + -
778A LEU* 5.1 4.7 - - + -
799A VAL* 3.9 2.3 - - - +
807A VAL* 4.2 1.7 - - + +
808A THR 3.2 4.9 + - - -
809A PHE* 2.9 42.0 - + - -
811A ALA* 1.3 77.6 - - - +
813A ILE* 1.3 79.2 + - + +
815A PHE* 3.2 41.1 + + + -
816A MET* 3.1 19.7 + - + -
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Residues in contact with ILE 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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743A ILE* 3.8 28.0 - - + -
748A MET* 6.1 0.2 - - - -
751A PHE* 4.2 5.2 - - + -
809A PHE* 3.2 40.6 + - + +
810A GLN* 3.5 12.6 - - - +
811A ALA 3.2 0.2 - - - -
812A PHE* 1.3 99.6 - - + +
814A ASP* 1.3 65.7 + - - +
816A MET* 3.6 11.0 - - + -
817A SER* 2.9 26.8 + - - -
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Residues in contact with ASP 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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798A ILE* 4.2 9.3 - - + +
799A VAL* 6.1 0.7 - - - -
810A GLN* 3.1 22.0 + - - +
811A ALA* 3.2 16.2 - - - +
812A PHE 3.1 0.4 - - - -
813A ILE* 1.3 79.1 - - - +
815A PHE* 1.3 59.7 + - - +
817A SER* 3.7 10.4 - - - -
818A ARG* 2.8 46.6 + - - +
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Residues in contact with PHE 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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775A LEU* 4.1 22.0 - - + -
780A TYR* 5.3 12.1 - + - -
795A ILE* 3.4 43.1 - - + -
798A ILE* 4.3 22.2 - - + -
799A VAL* 3.5 20.6 - - + -
807A VAL* 5.9 0.2 - - + -
812A PHE* 3.2 43.2 + + + -
814A ASP* 1.3 75.4 - - - +
816A MET* 1.3 76.0 + - + +
817A SER 3.1 2.5 - - - -
818A ARG* 3.0 24.2 + - - +
819A GLU* 3.3 22.4 + - + +
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Residues in contact with MET 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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743A ILE* 3.7 24.5 - - + -
747A GLN* 4.2 7.4 - - - +
751A PHE* 3.7 29.4 - - + -
780A TYR* 5.5 7.0 - - - +
812A PHE* 3.1 16.2 + - + +
813A ILE* 3.1 34.0 + - + +
815A PHE* 1.3 91.4 - - + +
817A SER* 1.3 65.4 + - - +
819A GLU* 3.1 8.7 + - + +
820A THR* 3.0 45.7 + - - +
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Residues in contact with SER 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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741A SER 5.2 1.4 + - - +
813A ILE* 2.9 19.0 + - - -
814A ASP* 3.7 9.2 - - - -
816A MET* 1.3 82.1 - - - +
818A ARG* 1.3 59.0 + - - +
820A THR* 3.7 21.2 - - - +
821A ALA* 3.9 9.2 + - - +
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Residues in contact with ARG 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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798A ILE* 4.2 22.1 - - - +
814A ASP* 2.8 41.2 + - - +
815A PHE* 3.0 17.8 + - - +
817A SER* 1.3 80.3 - - - +
819A GLU* 1.3 70.6 + - - +
821A ALA* 3.4 18.1 - - - +
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Residues in contact with GLU 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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815A PHE* 3.6 20.4 - - + +
816A MET* 3.1 8.2 + - + +
818A ARG* 1.3 83.9 - - - +
820A THR* 1.3 55.3 + - - +
821A ALA 3.1 8.6 + - - -
822A ASP* 4.2 6.4 + - - +
823A THR* 4.9 3.1 + - - +
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Residues in contact with THR 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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741A SER 3.7 18.1 - - - +
742A SER* 4.3 18.9 + - - -
743A ILE* 5.5 0.5 - - - -
747A GLN* 5.3 2.6 + - - -
816A MET* 3.0 40.1 + - - +
817A SER* 3.7 17.9 - - - +
819A GLU* 1.3 74.6 - - - +
821A ALA* 1.3 65.5 + - - +
822A ASP 3.3 3.0 + - - -
823A THR* 3.3 38.5 + - - +
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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