Contacts of the helix formed by residues 897 - 909 (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 PHE 897 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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857B SER 3.3 5.4 - - - +
858B GLN 4.1 8.7 - - - -
859B ASP 4.1 4.0 - - - +
860B GLN* 3.2 66.0 - - + -
863B SER* 2.7 36.3 + - - -
867B GLN* 5.7 1.3 - - - -
895B ASP* 2.7 12.6 + - - +
896B VAL* 1.3 114.9 - - + +
898B GLY* 1.3 63.1 + - - +
899B ASN* 3.3 3.1 - - - +
900B TYR* 3.4 18.1 + + - +
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Residues in contact with GLY 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857B SER* 3.1 17.6 + - - -
892B LEU* 2.7 24.6 - - - +
895B ASP* 2.6 22.4 + - - -
897B PHE* 1.3 73.1 - - - +
899B ASN* 1.3 64.2 + - - +
901B VAL* 2.9 18.6 + - - +
902B ILE* 3.4 10.0 + - - +
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Residues in contact with ASN 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892B LEU 2.5 12.5 + - - -
893B MET* 3.5 20.0 - - - +
895B ASP 2.7 23.3 + - - +
896B VAL 2.7 22.6 + - - -
898B GLY* 1.3 75.6 - - - +
900B TYR* 1.3 66.2 + - - +
902B ILE* 3.4 1.3 + - - -
903B GLN* 2.8 56.1 + - - +
933B TYR* 3.4 12.1 - - + +
937B VAL* 3.5 16.8 - - + +
19D U 2.9 26.4 + - - -
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Residues in contact with TYR 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867B GLN* 3.1 44.5 - - - +
896B VAL 3.3 18.6 - - - -
897B PHE* 3.6 19.1 - + - +
898B GLY 3.0 1.2 + - - -
899B ASN* 1.3 102.0 + - - +
901B VAL* 1.3 64.6 + - - +
903B GLN* 3.7 8.5 - - - +
904B LYS* 3.1 25.6 + - - +
19D U 2.9 63.7 - + + +
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Residues in contact with VAL 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857B SER* 3.6 34.1 - - - +
863B SER* 3.9 20.4 - - - +
866B ILE* 4.0 32.8 - - + -
867B GLN* 4.7 3.4 - - + -
870B LEU* 4.1 1.5 - - + +
881B VAL* 4.6 5.2 - - + -
885B ILE* 4.9 7.6 - - + -
892B LEU* 5.0 0.9 - - + -
898B GLY 2.9 9.3 + - - +
900B TYR* 1.3 77.7 - - - +
902B ILE* 1.3 68.9 + - + +
904B LYS* 3.3 18.4 + - - +
905B PHE* 3.4 27.3 + - + -
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Residues in contact with ILE 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885B ILE* 3.8 28.7 - - + -
889B ALA* 4.0 23.6 - - + +
892B LEU* 3.8 32.5 - - + -
893B MET* 3.9 12.6 - - + -
898B GLY 3.4 4.9 + - - +
899B ASN 3.7 5.8 - - - +
900B TYR 3.3 0.2 - - - -
901B VAL* 1.3 76.0 - - + +
903B GLN* 1.3 65.3 - - - +
905B PHE* 2.9 20.9 + - - +
906B PHE* 3.5 17.2 + - + -
917B LEU* 4.5 12.3 - - + -
937B VAL* 3.8 26.9 - - + -
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Residues in contact with GLN 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899B ASN* 2.8 47.0 + - - +
900B TYR* 3.7 9.2 - - - +
901B VAL 3.3 0.2 - - - -
902B ILE* 1.3 76.5 - - - +
904B LYS* 1.3 58.6 + - - +
906B PHE* 3.0 28.2 + - - +
907B GLU* 3.1 16.9 + - - +
936B ARG* 3.5 30.8 - - - +
937B VAL* 3.5 15.0 - - + -
940B LYS* 3.7 28.9 - - + +
19D U 3.2 22.1 + - - +
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Residues in contact with LYS 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867B GLN* 3.2 44.1 + - - +
868B LEU* 5.1 3.2 - - - +
870B LEU* 3.5 33.0 - - + +
871B GLU* 3.9 18.3 + - + +
900B TYR 3.1 11.7 + - - +
901B VAL* 3.3 13.7 - - - +
902B ILE 3.2 0.2 - - - -
903B GLN* 1.3 76.3 - - - +
905B PHE* 1.3 57.4 + - - +
906B PHE 3.4 0.2 - - - -
907B GLU* 3.8 17.6 + - - +
908B PHE* 3.0 50.6 + - + +
909B GLY 4.0 0.2 + - - -
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Residues in contact with PHE 905 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870B LEU* 4.0 14.1 - - + -
878B ARG* 3.4 45.1 - - + -
881B VAL* 3.8 21.5 - - + -
882B PHE* 3.7 26.2 - + + -
885B ILE* 4.0 24.0 - - + -
901B VAL* 3.4 22.1 + - + -
902B ILE* 2.9 11.0 + - - +
904B LYS* 1.3 77.4 - - - +
906B PHE* 1.3 61.4 + - - +
907B GLU 3.2 0.2 - - - -
909B GLY* 2.6 31.6 + - - +
913B GLN* 3.5 20.0 - - + -
914B LYS* 3.8 6.9 + - - +
917B LEU* 3.4 21.0 - - + +
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Residues in contact with PHE 906 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902B ILE* 3.5 29.1 + - + -
903B GLN* 3.0 9.9 + - - +
905B PHE* 1.3 77.6 - - - +
907B GLU* 1.3 61.8 + - - +
914B LYS* 3.1 48.7 - - + -
917B LEU* 3.6 23.1 - - + -
918B ALA* 4.2 5.6 - - - -
921B ILE* 3.9 11.9 - - + -
937B VAL* 3.9 25.1 - - + -
940B LYS* 4.2 17.9 - - + +
941B ALA* 3.6 36.8 - - + -
944B PHE* 3.2 15.4 - - + +
945B ILE* 3.7 18.8 - - + -
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Residues in contact with GLU 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903B GLN* 3.1 17.1 + - - +
904B LYS* 3.8 16.8 + - - +
905B PHE 3.2 0.2 - - - -
906B PHE* 1.3 79.9 - - - +
908B PHE* 1.3 94.4 + - + +
909B GLY 3.7 0.2 - - - -
914B LYS* 5.0 2.9 + - - -
940B LYS* 2.4 43.9 + - + +
944B PHE* 3.8 27.0 - - + -
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Residues in contact with PHE 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B LEU* 4.3 4.5 - - + +
871B GLU* 3.4 50.5 - - + +
878B ARG* 3.4 35.5 + - - +
904B LYS* 3.0 36.0 + - + +
907B GLU* 1.3 110.5 - - + +
909B GLY* 1.3 66.9 + - - +
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Residues in contact with GLY 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B ARG* 4.1 4.9 - - - -
905B PHE* 2.6 34.4 + - - +
906B PHE 4.3 0.4 - - - -
907B GLU 3.7 0.6 - - - -
908B PHE* 1.3 79.7 - - - +
910B SER* 1.3 65.9 + - - -
911B LEU 3.9 0.3 + - - -
913B GLN* 3.5 13.7 - - - -
914B LYS* 3.4 15.3 - - - -
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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