Contacts of the helix formed by residues 933 - 945 (chain B) 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 TYR 933 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B MET 3.6 6.0 - - - +
894B VAL 4.1 2.7 - - - -
895B ASP 3.8 4.7 - - - +
896B VAL* 3.3 44.7 - - + +
899B ASN* 3.4 27.9 - - + +
931B GLN* 2.6 25.4 + - - +
932B MET* 1.3 101.4 - - + +
934B GLY* 1.3 65.7 + - - +
935B CYS 3.3 0.4 - - - -
936B ARG* 2.8 21.8 + - - +
937B VAL 3.5 2.1 + - - -
19D U 2.7 50.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 934 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B MET 3.2 15.5 + - - -
928B LEU* 3.2 29.7 - - - +
931B GLN* 2.6 18.9 + - - -
933B TYR* 1.3 71.5 - - - +
935B CYS* 1.3 53.5 + - - +
937B VAL* 2.7 28.1 + - - +
938B ILE* 3.1 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 935 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B LEU 2.7 10.4 + - - -
929B ALA* 2.9 31.9 - - - +
931B GLN 3.0 16.6 + - - +
932B MET 3.4 12.1 - - - -
934B GLY* 1.3 74.8 - - - +
936B ARG* 1.3 65.4 + - - +
938B ILE* 3.8 2.9 - - - +
939B GLN* 2.9 31.6 + - - +
969B ASN* 3.7 13.2 - - + -
973B VAL* 3.8 10.4 - - + +
18D A 3.6 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 936 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B GLN* 3.5 30.9 - - - +
932B MET 3.7 14.8 + - - +
933B TYR 2.8 14.4 + - - +
935B CYS* 1.3 79.0 - - - +
937B VAL* 1.3 59.2 + - - +
939B GLN* 3.8 7.7 + - - +
940B LYS* 3.5 15.4 + - - +
18D A 3.5 65.2 + - - +
19D U 3.6 67.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 937 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B MET* 4.1 21.1 - - + +
899B ASN* 3.5 42.6 - - + +
902B ILE* 3.8 25.6 - - + -
903B GLN* 3.5 10.3 - - + -
906B PHE* 3.9 14.5 - - + -
921B ILE* 4.2 10.1 - - + -
928B LEU* 5.9 0.7 - - + -
933B TYR 4.3 0.9 - - - +
934B GLY* 2.7 16.0 + - - +
936B ARG* 1.3 71.5 - - - +
938B ILE* 1.3 66.4 + - + +
939B GLN 3.1 1.8 - - - -
940B LYS* 3.1 2.8 + - - +
941B ALA* 2.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 938 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B ILE* 3.7 35.2 - - + -
925B VAL* 4.4 20.9 - - + +
928B LEU* 3.7 33.4 - - + -
929B ALA* 4.2 7.9 - - + +
934B GLY 3.1 6.0 + - - +
935B CYS* 3.9 8.7 - - - +
937B VAL* 1.3 74.9 - - - +
939B GLN* 1.3 64.5 + - - +
941B ALA* 3.2 6.5 + - - +
942B LEU* 3.0 34.5 + - + +
953B MET* 4.6 7.2 - - + -
957B LEU* 6.1 0.4 - - + -
973B VAL* 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 939 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935B CYS* 2.9 28.2 + - - +
936B ARG* 3.8 10.4 - - - +
938B ILE* 1.3 78.7 - - - +
940B LYS* 1.3 62.4 + - + +
942B LEU* 3.5 1.5 + - - -
943B GLU 3.3 15.4 + - - -
972B HIS* 3.5 28.6 - - - +
973B VAL* 4.2 9.2 - - + -
976B LYS* 3.5 39.5 - - + +
18D A 2.8 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 940 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903B GLN* 3.7 46.4 - - + +
906B PHE* 4.2 6.7 - - + +
907B GLU* 2.4 39.0 + - + +
936B ARG 3.5 9.8 + - - +
937B VAL 3.1 7.6 + - - +
939B GLN* 1.3 76.4 - - + +
941B ALA* 1.3 68.8 + - - +
943B GLU* 3.0 22.0 + - - +
944B PHE* 3.1 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 941 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B PHE* 3.6 38.7 - - + -
921B ILE* 4.4 1.6 - - + -
937B VAL 2.9 12.4 + - - +
938B ILE* 3.4 11.9 - - - +
940B LYS* 1.3 75.8 - - - +
942B LEU* 1.3 63.9 + - - +
944B PHE 3.0 2.8 + - - -
945B ILE* 3.0 30.5 + - + +
953B MET* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 942 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B ILE* 3.0 34.5 + - + +
939B GLN* 3.7 5.8 - - - +
941B ALA* 1.3 77.0 - - - +
943B GLU* 1.3 58.5 + - - +
944B PHE 3.5 0.2 + - - -
945B ILE* 4.1 5.8 - - - +
950B GLN* 2.4 55.1 + - + +
953B MET* 4.2 27.8 - - + -
954B VAL* 4.3 10.1 - - + -
973B VAL* 4.4 2.0 - - + +
976B LYS* 4.2 15.9 - - + -
977B CYS* 3.7 36.3 - - - +
980B CYS* 4.1 8.2 - - + +
981B VAL* 4.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 943 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939B GLN 3.3 3.9 + - - +
940B LYS* 3.0 21.0 + - - +
942B LEU* 1.3 80.1 - - - +
944B PHE* 1.3 90.7 + - + +
945B ILE 3.8 0.6 - - - +
950B GLN* 4.7 2.2 + - - +
976B LYS* 2.6 40.3 + - - +
980B CYS* 4.1 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 944 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B PHE* 3.2 34.1 - - + +
907B GLU* 3.8 27.6 - - + -
914B LYS* 3.1 28.1 + - - +
940B LYS* 3.1 48.0 - - + +
941B ALA 3.0 4.3 + - - +
943B GLU* 1.3 113.2 - - + +
945B ILE* 1.3 61.8 + - - +
946B PRO* 4.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 945 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B PHE* 3.7 30.3 - - + -
914B LYS* 4.3 14.6 - - + +
915B LEU* 6.1 0.7 - - + -
918B ALA* 5.0 3.8 - - + -
941B ALA 3.0 19.0 + - - +
942B LEU* 4.4 0.7 - - - +
943B GLU 3.8 0.5 - - - +
944B PHE* 1.3 81.3 - - - +
946B PRO* 1.3 77.0 - - + +
949B GLN* 3.6 31.4 - - + +
950B GLN* 3.4 28.2 + - + +
953B MET* 3.5 34.3 - - + -
----------------------------------------------------------
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