Contacts of the helix formed by residues 88 - 92 (chain 3) in PDB entry 1AR9
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 88 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863 SER* 2.7 17.6 + - - -
873 LEU* 1.3 75.9 + - - +
893 PRO* 1.3 68.1 - - - +
903 ALA 3.1 2.0 - - - -
913 SER* 2.9 22.1 + - - -
923 ASP* 2.8 34.1 + - - +
953 LEU* 4.3 1.7 - - - +
1803 ILE 5.4 2.0 - - - -
1813 ASP* 3.9 11.5 + - - -
1863 GLU* 5.7 1.7 - - - -
1873 GLY 5.2 2.9 + - - -
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Residues in contact with PRO 89 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873 LEU* 3.7 3.6 - - + -
883 SER* 1.3 86.8 - - - +
903 ALA* 1.3 57.4 + - - +
953 LEU* 3.4 43.2 - - + +
1003 LEU* 4.5 17.5 - - + -
1013 GLY* 3.5 10.4 - - - -
1043 LEU* 3.7 18.8 - - + -
1103 TRP* 3.5 51.4 - - + +
1143 LEU* 4.4 11.9 - - + -
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Residues in contact with ALA 90 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883 SER 3.1 0.8 - - - -
893 PRO* 1.3 83.4 - - - +
913 SER* 1.3 56.5 + - - +
963 SER* 3.1 11.5 - - - +
1013 GLY 4.5 1.8 - - - -
1043 LEU* 3.8 15.9 - - + -
1053 ASN* 2.9 39.6 + - - +
1793 THR* 3.3 42.7 - - + +
2303 HIS* 4.7 1.2 + - - -
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Residues in contact with SER 91 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883 SER* 2.9 15.9 + - - -
903 ALA* 1.3 79.9 - - - +
923 ASP* 1.3 63.4 + - - -
933 PRO* 3.2 7.1 - - - +
963 SER* 4.2 3.6 + - - -
1793 THR 4.3 1.0 - - - -
1803 ILE* 3.5 12.0 + - - -
1813 ASP* 2.8 49.5 + - - +
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Residues in contact with ASP 92 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3021 TYR* 3.5 2.3 - - - +
853 LEU* 3.3 13.2 - - + +
863 SER* 3.1 31.9 + - - +
883 SER* 2.8 25.3 + - - +
913 SER* 1.3 70.5 + - - +
933 PRO* 1.3 66.2 - - - +
943 ARG* 2.9 52.4 + - - +
953 LEU* 2.8 24.2 + - + -
963 SER 2.9 13.5 + - - -
1813 ASP* 4.4 2.2 + - - -
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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
------------------------------------------------------------
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