Contacts of the helix formed by residues 882 - 889 (chain A) in PDB entry 3POZ
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 882 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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880A TRP 3.9 0.6 + - - -
881A MET* 1.3 75.3 - - - +
883A LEU* 1.3 66.8 + - - +
884A GLU* 3.5 28.3 - - - +
885A SER* 2.9 16.7 + - - +
886A ILE* 3.1 9.9 + - - +
895A SER* 3.7 18.5 + - - -
898A TRP* 3.4 34.4 - - + +
899A SER* 4.8 0.2 + - - -
958A ARG* 3.7 3.6 - - - +
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Residues in contact with LEU 883 (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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881A MET 3.7 1.0 + - - -
882A ALA* 1.3 73.1 - - - +
884A GLU* 1.3 61.3 + - - +
886A ILE* 3.3 9.1 + - + -
887A LEU* 2.9 59.4 + - + +
898A TRP* 4.0 15.4 - - + -
924A SER* 4.0 33.0 - - - +
927A LEU* 4.3 10.1 - - + -
928A GLU* 3.9 24.7 - - + +
953A ILE* 3.5 40.8 - - + -
958A ARG* 5.6 0.4 - - - +
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Residues in contact with GLU 884 (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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882A ALA* 3.5 13.7 - - - +
883A LEU* 1.3 77.9 + - - +
885A SER* 1.3 60.6 + - - +
887A LEU* 4.5 4.3 - - - +
888A HIS* 3.0 30.0 + - + +
890A ILE* 3.3 45.7 + - + +
892A THR* 4.6 2.4 + - - -
895A SER* 3.6 9.7 + - - -
953A ILE 4.5 3.6 - - - +
955A ALA* 3.8 12.8 - - + +
958A ARG* 2.8 44.8 + - - -
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Residues in contact with SER 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A MET* 3.7 16.7 - - - +
882A ALA* 2.9 16.5 + - - +
884A GLU* 1.3 76.1 - - - +
886A ILE* 1.3 62.6 + - - +
889A ARG* 3.0 26.4 + - - +
890A ILE 2.7 27.0 + - - +
891A TYR* 3.7 25.7 + - - -
895A SER* 3.5 20.3 - - - -
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Residues in contact with ILE 886 (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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878A ILE* 4.0 33.2 - - + +
881A MET* 3.9 37.5 - - + +
882A ALA 3.1 9.6 + - - +
883A LEU* 3.6 10.8 - - + +
885A SER* 1.3 80.0 - - - +
887A LEU* 1.3 64.6 + - + +
889A ARG* 4.5 3.1 + - - +
923A ILE* 4.2 10.8 - - + -
924A SER* 4.1 23.1 - - - +
927A LEU* 4.1 20.6 - - + -
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Residues in contact with LEU 887 (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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883A LEU* 2.9 39.0 + - + +
884A GLU* 4.8 1.1 - - - -
886A ILE* 1.3 77.4 - - + +
888A HIS* 1.3 89.9 + - + +
889A ARG* 3.8 0.9 - - - -
924A SER* 4.0 21.1 - - - +
928A GLU* 3.6 26.9 - - + +
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Residues in contact with HIS 888 (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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884A GLU* 3.0 14.3 + - + +
887A LEU* 1.3 102.1 + - + +
889A ARG* 1.3 74.9 + - - +
890A ILE* 3.1 27.8 + - + +
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Residues in contact with ARG 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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864A ALA 3.9 16.3 + - - +
865A GLU* 4.1 25.6 + - - +
866A GLU 3.9 11.4 + - - -
867A LYS 3.3 38.0 + - - +
885A SER 3.0 19.7 + - - +
886A ILE 5.2 3.4 - - - +
887A LEU 3.8 0.6 - - - -
888A HIS* 1.3 80.8 - - - +
890A ILE* 1.3 60.2 + - - +
891A TYR* 3.5 24.1 + - + +
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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