Contacts of the helix formed by residues 859 - 871 (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 ASP 859 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829B ARG* 3.4 28.2 + - - -
833B LEU* 3.8 21.7 - - + +
837B ARG* 3.4 25.8 + - - +
855B GLU 3.3 16.6 - - - +
856B PHE* 3.7 7.2 - - - +
857B SER 3.3 1.0 - - - -
858B GLN* 1.3 78.9 - - - +
860B GLN* 1.3 61.5 + - - +
861B HIS* 3.6 3.1 + - - +
862B GLY* 3.2 19.0 + - - +
863B SER* 2.6 34.8 + - - -
897B PHE* 4.0 2.9 - - - -
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Residues in contact with GLN 860 (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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837B ARG* 5.3 2.0 - - - +
859B ASP* 1.3 76.1 + - - +
861B HIS* 1.3 90.4 + - + +
863B SER* 3.9 2.3 - - - -
864B ARG* 3.3 21.1 + - + +
867B GLN* 5.4 0.2 + - - -
897B PHE* 3.2 46.8 - - + -
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Residues in contact with HIS 861 (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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836B PHE* 3.5 20.1 - - + -
837B ARG* 3.5 38.3 + - + +
859B ASP* 3.6 5.3 + - - +
860B GLN* 1.3 101.4 + - + +
862B GLY* 1.3 66.1 + - - +
864B ARG* 3.9 11.8 - - - +
865B PHE* 3.1 22.3 + - - +
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Residues in contact with GLY 862 (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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833B LEU* 4.8 0.4 - - - -
836B PHE* 4.3 4.9 - - - -
856B PHE* 2.8 40.2 - - - -
859B ASP* 3.1 14.1 + - - -
861B HIS* 1.3 76.8 - - - +
863B SER* 1.3 63.6 + - - +
865B PHE* 3.1 13.7 + - - +
866B ILE* 3.1 16.6 + - - +
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Residues in contact with SER 863 (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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856B PHE 2.6 9.6 + - - -
857B SER* 3.8 12.6 + - - +
859B ASP 2.6 19.3 + - - -
860B GLN 3.9 2.9 - - - -
862B GLY* 1.3 72.3 - - - +
864B ARG* 1.3 62.5 + - - +
866B ILE* 3.0 5.1 + - - +
867B GLN* 2.9 39.9 + - - +
897B PHE* 2.7 36.6 + - - -
901B VAL* 3.9 9.4 - - - +
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Residues in contact with ARG 864 (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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860B GLN* 3.3 17.5 + - - +
861B HIS* 3.9 11.4 - - - +
863B SER* 1.3 79.2 - - - +
865B PHE* 1.3 63.4 + - - +
867B GLN* 3.4 15.0 - - - +
868B LEU* 3.1 62.4 + - + +
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Residues in contact with PHE 865 (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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836B PHE* 3.7 25.4 - + + -
844B LEU* 3.1 60.1 - - + -
845B GLN* 3.9 7.4 - - - -
846B LEU* 3.9 20.9 - - + -
849B ILE* 4.1 10.8 - - + -
856B PHE* 4.4 5.6 - + - -
861B HIS 3.1 15.4 + - - +
862B GLY 3.1 10.1 + - - +
864B ARG* 1.3 79.0 - - - +
866B ILE* 1.3 67.3 + - + +
868B LEU* 4.1 3.4 - - - +
869B LYS* 3.1 39.4 + - + +
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Residues in contact with ILE 866 (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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846B LEU* 4.3 7.0 - - + -
849B ILE* 4.0 22.9 - - + -
853B ILE* 4.0 13.0 - - + +
856B PHE* 3.9 22.4 - - + -
857B SER* 3.5 24.5 - - - +
862B GLY 3.1 8.4 + - - +
863B SER 3.0 6.9 + - - +
865B PHE* 1.3 80.4 - - + +
867B GLN* 1.3 66.3 + - - +
869B LYS* 3.0 4.4 + - - -
870B LEU* 2.9 48.7 + - + +
881B VAL* 4.2 8.7 - - + -
901B VAL* 4.0 15.7 - - + -
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Residues in contact with GLN 867 (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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863B SER* 2.9 44.5 + - - +
864B ARG* 3.4 13.9 - - - +
866B ILE* 1.3 77.5 - - - +
868B LEU* 1.3 66.3 + - + +
869B LYS 3.1 5.0 + - - -
870B LEU* 3.4 6.5 + - - -
871B GLU* 3.6 5.9 - - - +
897B PHE* 5.7 1.0 - - - -
900B TYR* 3.1 55.8 - - + +
901B VAL* 4.4 2.7 - - - +
904B LYS* 3.2 41.6 + - - +
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Residues in contact with LEU 868 (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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864B ARG* 3.1 62.5 + - + +
865B PHE* 4.1 3.4 - - - +
867B GLN* 1.3 82.9 - - + +
869B LYS* 1.3 59.7 + - - +
871B GLU* 3.9 19.5 - - - +
872B ARG* 3.1 31.1 + - - +
904B LYS* 5.1 3.1 - - - +
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Residues in contact with LYS 869 (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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843B ASN* 5.2 4.0 + - - -
844B LEU 3.4 24.2 + - - -
845B GLN* 4.1 17.9 - - - +
846B LEU* 3.4 31.0 - - + +
865B PHE* 3.1 28.8 - - + +
866B ILE 3.0 4.4 + - - +
868B LEU* 1.3 81.3 - - - +
870B LEU* 1.3 60.7 + - - +
871B GLU 3.5 0.9 - - - -
872B ARG* 3.5 12.4 - - - +
873B ALA* 2.9 27.3 + - - +
877B GLU* 5.0 3.5 - - - +
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Residues in contact with LEU 870 (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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846B LEU* 4.6 2.9 - - + -
866B ILE* 2.9 37.3 + - + +
867B GLN 3.4 0.2 + - - -
869B LYS* 1.3 78.4 - - - +
871B GLU* 1.3 68.6 + - - +
872B ARG 3.3 0.2 - - - -
873B ALA* 3.1 14.4 + - + +
878B ARG* 3.1 35.2 + - + +
881B VAL* 4.0 29.4 - - + -
901B VAL* 4.1 5.8 - - + +
904B LYS* 3.5 35.7 - - + +
905B PHE* 4.0 29.4 - - + -
908B PHE* 4.3 2.3 - - - +
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Residues in contact with GLU 871 (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 3.6 11.9 + - - +
868B LEU* 3.9 23.2 - - - +
869B LYS 3.5 0.2 - - - -
870B LEU* 1.3 80.4 - - - +
872B ARG* 1.3 80.1 + - + +
878B ARG* 3.5 8.5 + - - -
904B LYS* 3.9 12.1 + - + +
908B PHE* 3.4 57.4 - - + -
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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