Contacts of the helix formed by residues 830 - 838 (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 SER 830 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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828B GLY 4.2 1.0 - - - +
829B ARG* 1.3 83.3 - - - +
831B ARG* 1.3 62.2 - - - +
832B LEU 3.5 2.2 + - - -
833B LEU* 3.2 13.3 + - - +
834B GLU* 3.2 15.6 + - - +
852B HIS* 3.5 23.9 + - - -
855B GLU* 2.5 33.5 + - - -
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Residues in contact with ARG 831 (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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829B ARG 4.4 0.2 - - - -
830B SER* 1.3 71.3 - - - +
832B LEU* 1.3 61.2 + - - +
834B GLU* 4.3 8.2 - - - +
835B ASP* 2.8 57.1 + - - +
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Residues in contact with LEU 832 (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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830B SER* 3.2 7.9 + - - +
831B ARG* 1.3 79.6 - - - +
833B LEU* 1.3 62.3 + - - +
835B ASP* 3.8 1.2 - - - +
836B PHE* 3.0 23.8 + - + +
841B TYR* 3.6 40.6 - - + +
844B LEU* 4.7 11.9 - - + -
848B GLU* 3.4 25.6 - - + +
849B ILE* 4.0 10.8 - - + -
852B HIS* 3.5 33.7 - - + +
856B PHE* 4.2 10.1 - - + -
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Residues in contact with LEU 833 (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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829B ARG* 3.6 32.5 - - + +
830B SER* 3.2 17.8 + - - +
832B LEU* 1.3 79.4 - - - +
834B GLU* 1.3 64.2 + - - +
836B PHE* 2.8 18.5 + - + +
837B ARG* 2.9 22.8 + - + +
855B GLU* 3.8 35.2 - - + +
856B PHE* 3.7 34.5 - - + -
859B ASP* 3.8 27.6 - - + +
862B GLY* 4.8 0.4 - - - -
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Residues in contact with GLU 834 (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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829B ARG* 3.1 44.1 + - + +
830B SER 3.2 13.7 + - - +
831B ARG* 3.8 9.4 - - + +
833B LEU* 1.3 78.5 - - - +
835B ASP* 1.3 67.6 + - - +
837B ARG* 3.3 16.9 + - - +
838B ASN* 3.1 32.2 + - - +
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Residues in contact with ASP 835 (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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963A LYS* 5.5 4.2 + - - -
831B ARG* 2.8 56.4 + - - +
834B GLU* 1.3 75.8 - - - +
836B PHE* 1.3 63.1 + - - +
838B ASN* 2.9 13.3 + - - +
840B ARG* 3.1 45.4 + - + +
841B TYR* 3.2 31.6 + - + -
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Residues in contact with PHE 836 (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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832B LEU* 3.0 13.9 + - + +
833B LEU* 2.8 17.1 + - + +
835B ASP* 1.3 76.5 - - - +
837B ARG* 1.3 62.3 + - - +
838B ASN 3.0 5.2 + - - -
839B ASN* 3.2 13.0 + - - +
841B TYR* 3.7 24.0 - - + +
844B LEU* 4.3 24.9 - - + -
856B PHE* 3.9 20.4 - + + -
861B HIS* 3.5 35.0 - - + -
862B GLY* 4.3 1.6 - - - -
865B PHE* 3.7 37.2 - + + -
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Residues in contact with ARG 837 (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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829B ARG* 2.6 46.3 - - - +
833B LEU* 2.9 22.9 + - + +
834B GLU* 3.7 13.6 + - - +
836B PHE* 1.3 80.3 - - + +
838B ASN* 1.3 67.1 + - - +
839B ASN* 3.6 2.2 + - - -
859B ASP* 3.4 31.3 + - - +
860B GLN* 5.3 2.0 - - - +
861B HIS* 3.5 32.9 + - + -
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Residues in contact with ASN 838 (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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834B GLU* 3.1 28.2 + - - +
835B ASP* 2.9 9.1 + - - +
837B ARG* 1.3 85.8 - - - +
839B ASN* 1.3 60.1 + - - +
840B ARG* 2.6 33.7 + - + +
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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