Contacts of the helix formed by residues 898 - 909 (chain A) in PDB entry 1M8X
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 898 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A SER 3.4 16.7 + - - -
892A LEU* 2.9 23.3 - - - +
895A ASP* 3.0 15.1 + - - -
897A PHE* 1.3 74.0 - - - +
899A ASN* 1.3 66.3 + - - +
900A TYR 3.0 2.7 - - - -
901A VAL* 2.9 19.7 + - - +
902A ILE* 3.4 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LEU 2.7 11.2 + - - -
893A MET* 3.4 22.0 - - - +
895A ASP 3.1 19.8 + - - +
896A VAL 3.3 14.6 + - - -
898A GLY* 1.3 75.1 - - - +
900A TYR* 1.3 67.0 + - - +
902A ILE* 3.5 3.3 + - - +
903A GLN* 2.7 57.3 + - - +
933A TYR* 3.8 18.6 - - + +
936A ARG* 4.4 1.2 - - - +
937A VAL* 3.9 8.9 - - + +
19C U 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A GLN* 3.2 36.8 - - - +
896A VAL 2.9 22.6 + - - -
897A PHE* 3.0 32.9 - + + +
898A GLY 3.0 1.0 + - - -
899A ASN* 1.3 85.1 + - - +
901A VAL* 1.3 64.1 + - - +
903A GLN* 3.3 11.8 + - - +
904A LYS* 3.1 28.2 + - - +
19C U 3.2 59.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A SER* 3.6 31.9 - - - +
863A SER* 3.8 19.5 - - - +
866A ILE* 3.7 33.0 - - + -
867A GLN* 4.6 4.9 - - + -
870A LEU* 3.9 9.9 - - + -
881A VAL* 4.8 2.5 - - + -
885A ILE* 4.6 8.3 - - + -
892A LEU* 5.0 2.9 - - + -
897A PHE 4.6 0.4 - - - +
898A GLY 2.9 9.1 + - - +
900A TYR* 1.3 72.7 - - - +
902A ILE* 1.3 66.4 + - - +
904A LYS* 3.0 18.4 + - - +
905A PHE* 3.2 23.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ILE* 3.9 24.5 - - + -
889A ALA* 4.2 11.9 - - + +
892A LEU* 3.9 32.3 - - + -
893A MET* 4.0 18.2 - - + +
898A GLY 3.4 4.2 + - - +
899A ASN 3.8 6.3 - - - +
900A TYR 3.4 0.4 - - - -
901A VAL* 1.3 76.2 - - - +
903A GLN* 1.3 62.8 + - - +
905A PHE* 3.1 17.7 + - - +
906A PHE* 3.3 22.4 + - + -
917A LEU* 4.1 22.4 - - + -
937A VAL* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A ASN* 2.7 42.8 + - - +
900A TYR* 3.4 15.2 - - - +
902A ILE* 1.3 76.6 - - - +
904A LYS* 1.3 62.6 + - - +
906A PHE* 3.1 9.3 + - - +
907A GLU* 3.0 35.0 + - - +
936A ARG* 3.8 33.3 - - - +
937A VAL* 4.3 9.9 - - + -
940A LYS* 3.6 27.5 - - + +
19C U 3.9 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A GLN* 3.8 49.7 + - + +
868A LEU* 5.5 4.7 - - - +
870A LEU* 4.0 18.6 - - + +
871A GLU* 4.9 7.0 - - + -
900A TYR* 3.1 18.6 + - - +
901A VAL* 3.0 10.1 + - - +
903A GLN* 1.3 76.6 - - - +
905A PHE* 1.3 54.1 + - - +
907A GLU* 4.0 15.3 + - - +
908A PHE* 2.5 70.7 + - + +
909A GLY 3.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A LEU* 3.7 23.8 - - + -
878A ARG* 3.4 37.5 - - + -
881A VAL* 3.8 12.1 - - + -
882A PHE* 3.7 27.8 - + + -
885A ILE* 3.4 28.7 - - + -
901A VAL* 3.2 20.3 + - + -
902A ILE* 3.1 10.1 + - - +
904A LYS* 1.3 80.8 - - - +
906A PHE* 1.3 58.6 + - - +
909A GLY* 2.6 31.6 + - - +
913A GLN* 3.5 27.1 - - + -
914A LYS* 3.6 9.0 + - - +
917A LEU* 3.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A ILE* 3.3 30.6 + - + -
903A GLN* 3.1 10.1 + - - +
905A PHE* 1.3 77.3 - - - +
907A GLU* 1.3 55.3 + - - +
914A LYS* 2.6 63.0 + - + +
917A LEU* 3.7 22.2 - - + -
918A ALA* 4.3 3.6 - - - -
921A ILE* 3.9 12.3 - - + -
937A VAL* 3.7 26.9 - - + -
940A LYS* 3.6 17.0 - - + +
941A ALA* 3.6 37.0 - - + -
944A PHE* 3.2 16.5 - - + +
945A ILE* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903A GLN* 3.0 30.6 + - - +
904A LYS* 3.7 18.4 + - - +
906A PHE* 1.3 80.8 - - - +
908A PHE* 1.3 94.1 + - + +
914A LYS* 3.7 8.4 + - - -
940A LYS* 3.3 41.4 + - + +
944A PHE* 4.0 19.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A LEU* 4.5 7.9 - - + +
871A GLU* 3.4 49.1 - - + -
878A ARG* 3.2 33.4 + - - +
904A LYS* 2.5 57.4 + - + +
907A GLU* 1.3 98.8 - - + +
909A GLY* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A ARG* 4.9 4.7 - - - -
904A LYS 3.5 0.8 + - - -
905A PHE* 2.6 36.2 + - - +
907A GLU 3.8 0.2 - - - -
908A PHE* 1.3 77.2 - - - +
910A SER* 1.3 62.2 + - - -
911A LEU 4.1 0.2 + - - -
913A GLN* 3.2 13.0 - - - -
914A LYS* 3.0 18.7 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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