Contacts of the helix formed by residues 859 - 871 (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 ASP 859 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A ARG* 4.4 1.6 + - - -
833A LEU* 3.7 24.4 - - + +
837A ARG* 2.8 34.3 + - - -
855A GLU 3.5 10.8 - - - +
856A PHE 3.1 10.9 + - - +
857A SER 3.2 1.2 - - - -
858A GLN* 1.3 79.2 - - - +
860A GLN* 1.3 63.3 - - - +
861A HIS* 2.9 18.5 + - - +
862A GLY* 2.7 26.0 + - - +
863A SER* 2.6 33.4 + - - -
897A PHE* 4.1 3.4 - - - -
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Residues in contact with GLN 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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837A ARG* 5.1 2.8 - - - +
859A ASP* 1.3 74.2 + - - +
861A HIS* 1.3 87.2 + - + +
863A SER* 4.1 1.7 - - - -
864A ARG* 3.0 37.9 + - + +
897A PHE* 3.2 55.7 - - + -
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Residues in contact with HIS 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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836A PHE* 3.7 21.5 - - + -
837A ARG* 3.4 42.1 + - + +
859A ASP* 2.9 10.6 + - - +
860A GLN* 1.3 99.0 + - + +
862A GLY* 1.3 61.5 + - - +
864A ARG* 3.4 7.6 + - - +
865A PHE* 2.9 29.8 + - - +
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Residues in contact with GLY 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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833A LEU* 4.8 0.4 - - - -
836A PHE* 4.1 3.7 - - - -
856A PHE* 2.9 40.4 - - - -
859A ASP* 2.7 18.7 + - - -
861A HIS* 1.3 72.3 - - - +
863A SER* 1.3 61.2 + - - -
865A PHE* 3.0 7.1 + - - +
866A ILE* 2.8 24.4 + - - +
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Residues in contact with SER 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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856A PHE 2.7 5.9 + - - -
857A SER* 3.5 21.5 - - - +
859A ASP 2.6 18.8 + - - -
860A GLN 4.1 2.0 - - - -
862A GLY* 1.3 69.2 - - - -
864A ARG* 1.3 64.6 + - - +
866A ILE* 3.1 3.5 + - - +
867A GLN* 2.6 52.6 + - - +
897A PHE* 2.7 27.4 + - - -
901A VAL* 3.8 11.3 - - - +
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Residues in contact with ARG 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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860A GLN* 3.0 31.7 + - + +
861A HIS* 3.4 8.7 - - + +
863A SER* 1.3 78.8 + - - +
865A PHE* 1.3 64.8 + - - +
867A GLN* 3.3 22.1 + - - +
868A LEU* 3.2 33.1 + - + +
897A PHE* 6.2 1.5 - - + -
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Residues in contact with PHE 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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836A PHE* 3.8 24.9 - + + -
844A LEU* 3.1 41.1 - - + -
845A GLN 3.9 12.1 - - - -
846A LEU* 4.5 8.1 - - + -
849A ILE* 3.9 28.9 - - + -
856A PHE* 4.3 5.8 - + - -
861A HIS 2.9 14.5 + - - +
862A GLY* 3.0 11.2 + - - +
864A ARG* 1.3 78.7 - - - +
866A ILE* 1.3 68.3 + - - +
868A LEU* 3.4 8.8 + - - +
869A LYS* 3.0 49.6 + - - +
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Residues in contact with ILE 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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846A LEU* 4.8 7.9 - - + -
849A ILE* 4.1 20.2 - - + -
853A ILE* 3.8 17.0 - - + +
856A PHE* 3.8 10.8 - - + -
857A SER* 3.3 40.2 - - - +
862A GLY 2.8 14.4 + - - +
863A SER 3.6 5.8 - - - +
865A PHE* 1.3 75.5 - - + +
867A GLN* 1.3 66.6 + - - +
869A LYS* 3.0 18.0 + - - +
870A LEU* 3.2 24.8 + - + +
881A VAL* 4.5 7.4 - - + -
901A VAL* 3.7 26.2 - - + -
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Residues in contact with GLN 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 SER* 2.6 50.0 + - - +
864A ARG* 3.5 22.5 + - - +
866A ILE* 1.3 74.4 - - - +
868A LEU* 1.3 66.3 + - + +
869A LYS 3.1 4.7 + - - -
870A LEU* 3.8 6.3 + - - +
871A GLU* 4.2 7.3 + - - +
897A PHE* 5.9 0.8 - - - -
900A TYR* 3.2 48.3 - - + +
901A VAL* 4.5 3.8 - - + +
904A LYS* 3.8 41.2 + - + +
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Residues in contact with LEU 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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864A ARG* 3.2 24.9 + - + +
865A PHE* 3.8 2.7 - - - +
866A ILE 3.2 0.6 + - - -
867A GLN* 1.3 83.1 - - + +
869A LYS* 1.3 71.1 + - - +
871A GLU* 5.1 12.1 - - - +
872A ARG* 5.7 6.7 + - - +
904A LYS* 5.5 4.9 - - - -
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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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844A LEU 3.1 11.3 + - - -
845A GLN* 3.5 21.3 - - - +
846A LEU* 3.8 29.6 - - + -
865A PHE* 3.0 52.8 - - + +
866A ILE 3.0 7.4 + - - +
867A GLN 3.1 0.6 + - - -
868A LEU* 1.3 82.8 - - - +
870A LEU* 1.3 58.2 + - - +
871A GLU 3.2 1.7 + - - -
872A ARG* 3.3 4.0 + - - +
873A ALA* 2.5 42.7 + - + +
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Residues in contact with LEU 870 (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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846A LEU* 4.8 4.3 - - + -
866A ILE* 3.2 31.8 + - + +
867A GLN 3.8 4.0 + - - +
869A LYS* 1.3 78.4 - - - +
871A GLU* 1.3 61.3 + - - +
872A ARG 3.5 0.2 + - - -
873A ALA* 3.7 4.2 + - - -
878A ARG* 3.2 60.8 + - + -
881A VAL* 4.1 15.0 - - + -
901A VAL* 3.9 8.3 - - + -
904A LYS* 4.0 25.4 - - + +
905A PHE* 3.7 34.5 - - + -
908A PHE* 4.5 4.3 - - + +
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Residues in contact with GLU 871 (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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867A GLN 4.2 10.2 + - - +
868A LEU* 5.3 9.5 - - - +
869A LYS 3.2 1.9 - - - +
870A LEU* 1.3 82.0 - - - +
872A ARG* 1.3 80.6 + - + +
873A ALA 4.5 0.3 - - - +
878A ARG* 4.0 10.2 + - - -
904A LYS* 4.9 5.9 - - + -
908A PHE* 3.4 54.5 - - + +
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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