Contacts of the helix formed by residues 888 - 894 (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 ALA 888 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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854A MET* 3.4 31.4 - - + -
884A GLU 5.2 1.7 + - - +
885A ILE 3.5 5.7 + - - -
886A LEU 3.3 0.4 - - - -
887A GLN* 1.3 78.2 - - + +
889A ALA* 1.3 63.0 + - - +
890A TYR 3.3 2.7 - - - -
891A GLN* 3.1 34.5 + - - +
892A LEU* 3.3 8.3 + - - +
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Residues in contact with ALA 889 (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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885A ILE 2.9 14.4 + - - +
886A LEU 3.1 18.1 + - - +
887A GLN 3.2 1.6 + - - -
888A ALA* 1.3 75.9 - - - +
890A TYR* 1.3 64.3 + - - +
892A LEU* 3.0 6.3 + - - +
893A MET* 2.9 29.6 + - - +
902A ILE* 4.2 7.9 - - + +
917A LEU* 3.8 26.7 - - + -
920A ARG* 4.1 13.5 - - + -
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Residues in contact with TYR 890 (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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887A GLN 4.9 1.4 + - - -
888A ALA 3.3 0.8 - - - -
889A ALA* 1.3 77.4 - - - +
891A GLN* 1.3 61.4 + - - +
893A MET* 2.9 29.0 + - - +
894A VAL* 3.1 43.3 + - + +
920A ARG* 4.8 11.2 - - - +
924A HIS* 3.5 42.0 - + + +
927A SER* 3.3 22.7 + - - -
928A LEU* 3.5 31.0 - - + +
931A GLN* 5.4 1.0 - - - +
843B ASN* 4.2 30.2 - - + +
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Residues in contact with GLN 891 (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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854A MET* 3.8 11.6 - - + +
858A GLN* 2.8 36.6 + - - +
888A ALA* 3.1 23.3 + - + +
890A TYR* 1.3 84.8 - - - +
892A LEU* 1.3 59.2 + - - +
894A VAL* 3.8 9.4 - - - +
895A ASP* 3.4 19.1 + - - +
843B ASN* 6.2 0.4 - - - +
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Residues in contact with LEU 892 (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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854A MET* 3.3 44.4 - - + -
857A SER* 3.9 23.6 - - - +
858A GLN* 3.5 26.5 - - + -
885A ILE* 3.8 22.7 - - + +
888A ALA 3.3 4.4 + - - +
889A ALA 3.0 7.6 + - - +
891A GLN* 1.3 75.4 - - - +
893A MET* 1.3 61.0 + - - +
894A VAL 3.2 0.4 - - - -
895A ASP* 3.2 8.3 + - - -
898A GLY* 2.9 10.9 - - - +
899A ASN 2.7 30.6 + - - -
901A VAL* 5.0 3.4 - - + -
902A ILE* 3.9 19.3 - - + -
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Residues in contact with MET 893 (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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889A ALA* 2.9 25.6 + - - +
890A TYR* 2.9 19.4 + - - +
892A LEU* 1.3 76.6 - - - +
894A VAL* 1.3 58.3 + - - +
895A ASP 3.2 0.6 + - - -
899A ASN* 3.4 17.3 - - - +
902A ILE* 4.0 15.3 - - + -
917A LEU* 5.4 1.8 - - - +
920A ARG 5.4 1.3 - - - +
921A ILE* 3.2 30.5 - - + -
928A LEU* 3.2 39.9 - - + -
933A TYR 3.4 0.7 - - - -
934A GLY* 3.3 19.2 + - - -
937A VAL* 3.3 41.6 - - + +
938A ILE* 4.8 1.3 - - + -
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Residues in contact with VAL 894 (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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890A TYR* 3.1 37.1 + - + +
891A GLN* 3.8 10.1 - - - +
893A MET* 1.3 75.8 - - - +
895A ASP* 1.3 55.9 + - - +
928A LEU* 3.5 29.6 - - + -
931A GLN* 3.7 30.7 - - + -
933A TYR* 3.6 6.3 - - - -
934A GLY* 4.6 0.2 - - - -
843B ASN* 4.7 11.0 - - - +
845B GLN* 3.1 30.2 + - - +
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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