Contacts of the helix formed by residues 854 - 869 (chain A) in PDB entry 6M0X
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 THR 854 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628A ARG* 4.9 14.1 - - - +
636A SER* 5.6 7.9 - - - -
851A ASP* 3.3 25.9 + - + +
852A ILE 3.7 0.2 - - - +
853A TYR* 1.3 78.7 - - - +
855A GLN* 1.3 60.9 + - - +
856A ASP* 3.8 7.6 + - - +
857A GLY* 2.8 24.5 + - - -
858A TYR 2.9 23.6 + - - -
908A ASN* 3.1 9.3 + - - -
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Residues in contact with GLN 855 (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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853A TYR 4.2 0.4 + - - -
854A THR* 1.3 70.1 - - - +
856A ASP* 1.3 57.9 + - - +
858A TYR* 3.0 8.6 + - - +
859A ASP* 2.6 81.4 + - - +
906A PRO* 3.0 27.7 + - - +
907A CYS* 2.7 39.8 + - - -
908A ASN* 3.5 10.3 - - + +
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Residues in contact with ASP 856 (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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669A ASP* 5.3 4.9 - - - +
854A THR* 3.3 6.8 + - - +
855A GLN* 1.3 78.5 - - - +
857A GLY* 1.3 61.8 + - - +
859A ASP* 4.0 7.6 - - - +
860A ALA* 3.2 24.4 + - - +
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Residues in contact with GLY 857 (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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849A ILE* 3.5 23.3 - - - +
851A ASP 3.2 25.8 - - - -
852A ILE* 4.2 5.5 - - - +
854A THR* 2.8 16.2 + - - -
855A GLN 3.1 0.2 - - - -
856A ASP* 1.3 76.1 - - - +
858A TYR* 1.3 60.2 + - - +
860A ALA* 3.7 0.3 + - - +
861A PHE* 3.2 18.0 + - - +
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Residues in contact with TYR 858 (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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852A ILE 3.9 4.7 + - - +
854A THR 2.9 7.6 + - - +
855A GLN* 3.0 7.6 + - - +
857A GLY* 1.3 74.6 - - - +
859A ASP* 1.3 73.2 + - - +
860A ALA 3.2 0.2 - - - -
861A PHE* 2.8 22.4 + - - +
862A MET* 3.0 44.8 + - + +
890A LEU* 3.6 23.8 - - + +
895A ASN* 3.9 14.4 - - + +
907A CYS 4.3 11.4 - - - -
908A ASN* 3.4 34.8 - - + +
909A PRO* 3.4 31.0 - - + +
910A PHE* 3.7 17.5 - + - -
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Residues in contact with ASP 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A GLN* 2.6 55.3 + - - +
856A ASP* 3.8 9.0 + - - +
858A TYR* 1.3 80.8 - - - +
860A ALA* 1.3 62.6 + - - +
862A MET* 3.4 6.0 + - - +
863A LYS* 3.2 27.4 + - + +
906A PRO* 5.7 2.4 - - - +
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Residues in contact with ALA 860 (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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849A ILE* 4.2 17.0 - - + -
856A ASP 3.2 20.9 + - - +
857A GLY* 3.8 5.6 - - - +
859A ASP* 1.3 76.3 - - - +
861A PHE* 1.3 62.7 + - - +
863A LYS* 3.4 9.5 + - - +
864A ILE* 3.3 29.5 + - + +
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Residues in contact with PHE 861 (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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849A ILE* 3.9 10.3 - - + +
852A ILE* 5.2 1.6 - - + -
857A GLY 3.2 11.1 + - - +
858A TYR* 2.8 16.3 + + - +
860A ALA* 1.3 80.8 - - - +
862A MET* 1.3 69.9 + - + -
864A ILE 3.3 0.5 + - - -
865A TYR* 2.8 51.5 + + - +
872A PHE* 3.4 31.5 - + - -
882A PHE* 4.5 6.7 - + - -
886A ILE* 4.0 17.3 - - + -
890A LEU* 3.7 24.9 - - + -
910A PHE* 3.8 29.2 - + + -
935A LEU* 3.8 27.6 - - + -
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Residues in contact with MET 862 (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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858A TYR* 3.0 55.3 + - + +
859A ASP* 4.0 5.8 - - - +
861A PHE* 1.3 94.9 - - - +
863A LYS* 1.3 60.8 + - - +
865A TYR* 3.6 29.4 - - + -
866A LYS* 2.7 66.1 + - + +
890A LEU* 4.2 8.7 - - + -
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Residues in contact with LYS 863 (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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859A ASP* 3.2 17.4 + - + +
860A ALA* 3.7 12.3 - - - +
861A PHE 3.4 0.4 - - - -
862A MET* 1.3 78.1 - - - +
864A ILE* 1.3 62.8 + - + +
866A LYS* 4.4 6.6 - - - +
867A LYS* 3.3 23.0 + - - +
6C T 3.1 42.0 + - - -
7C T 5.0 3.6 + - - -
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Residues in contact with ILE 864 (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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849A ILE* 4.3 5.2 - - + -
860A ALA* 3.3 18.7 + - + +
861A PHE 3.8 0.2 - - - +
862A MET 3.2 0.2 - - - -
863A LYS* 1.3 77.1 - - + +
865A TYR* 1.3 59.8 + - - +
867A LYS* 4.0 3.5 - - - +
868A ASP 3.0 35.8 + - - +
871A LYS* 3.6 42.2 - - + +
872A PHE* 3.7 28.9 - - + -
937A TYR* 3.6 44.9 - - + +
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Residues in contact with TYR 865 (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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861A PHE* 2.8 39.8 + + + +
862A MET* 3.0 32.5 + - + +
864A ILE* 1.3 76.7 - - - +
866A LYS* 1.3 70.5 + - + +
867A LYS 3.3 0.3 + - - -
868A ASP* 3.6 0.3 + - - -
869A LYS* 3.4 54.8 + - + +
872A PHE* 4.2 6.3 - + + -
882A PHE* 4.0 12.1 - + - -
887A GLU* 2.5 34.5 + - - -
890A LEU* 4.0 15.3 - - + +
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Residues in contact with LYS 866 (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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862A MET* 2.7 57.5 + - + +
863A LYS* 4.6 5.8 - - - +
865A TYR* 1.3 77.8 - - + +
867A LYS* 1.3 59.4 + - - +
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Residues in contact with LYS 867 (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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863A LYS 3.3 19.5 + - - +
864A ILE* 4.0 2.5 - - - +
865A TYR 3.1 0.6 - - - -
866A LYS* 1.3 81.7 - - - +
868A ASP* 1.3 67.8 + - + +
871A LYS* 4.6 26.5 - - + +
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Residues in contact with ASP 868 (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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835A VAL* 3.8 19.9 - - - +
836A GLY* 4.0 11.8 + - - -
864A ILE* 3.0 15.3 + - - +
865A TYR 3.6 0.8 + - - -
867A LYS* 1.3 85.2 - - + +
869A LYS* 1.3 64.7 + - - +
870A SER* 2.4 33.0 + - - -
871A LYS* 2.9 33.9 + - + +
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Residues in contact with LYS 869 (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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864A ILE 4.3 2.7 - - - -
865A TYR* 3.4 51.9 + - + +
868A ASP* 1.3 72.8 + - - +
870A SER* 1.3 61.1 + - - +
871A LYS 3.0 1.6 + - - -
872A PHE* 3.1 22.0 + - - +
875A TYR* 3.3 51.4 + - + +
882A PHE* 4.2 5.6 - - + -
883A GLU* 4.7 5.5 + - - -
887A GLU* 3.3 17.6 + - - +
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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