Contacts of the helix formed by residues 144 - 149 (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 LYS 144 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793 ASP* 3.3 23.3 + - + +
803 ASP* 2.9 28.1 + - - +
1423 PRO 3.6 0.4 - - - -
1433 LYS* 1.3 88.6 + - + +
1453 ARG* 1.3 65.9 + - - +
1463 LYS* 4.2 7.4 - - + +
1473 GLU* 2.9 32.9 + - - +
1483 ALA* 3.3 9.0 + - - +
1933 PHE* 3.5 5.4 - - - -
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Residues in contact with ARG 145 (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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773 HIS* 3.3 15.0 + - - -
793 ASP* 3.1 42.9 + - + +
1313 LEU* 4.3 17.3 - - + -
1443 LYS* 1.3 69.4 - - - +
1463 LYS* 1.3 57.6 + - - +
1483 ALA* 3.0 2.6 + - - -
1493 MET* 2.8 35.1 + - + +
1933 PHE* 3.2 28.0 - - + -
1943 TYR 4.0 9.9 - - - -
1953 GLN* 2.9 52.7 + - - +
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Residues in contact with LYS 146 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793 ASP* 5.1 10.4 + - - +
1443 LYS* 4.6 5.4 - - + -
1453 ARG* 1.3 79.7 - - - +
1473 GLU* 1.3 75.6 + - - +
1493 MET* 3.4 36.9 - - + +
1503 LEU* 3.6 7.5 - - + +
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Residues in contact with GLU 147 (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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1403 ASP* 5.2 9.2 - - + +
1423 PRO* 3.9 20.8 - - + +
1433 LYS 5.2 0.8 + - - +
1443 LYS* 2.9 31.4 + - - +
1463 LYS* 1.3 87.1 - - - +
1483 ALA* 1.3 67.9 + - - +
1503 LEU* 3.0 31.1 + - + +
1513 GLY 3.9 2.3 + - - -
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Residues in contact with ALA 148 (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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1313 LEU* 4.5 3.6 - - + -
1333 SER* 3.0 35.2 + - - +
1423 PRO* 3.7 16.0 - - + +
1443 LYS 3.3 2.5 + - - +
1453 ARG* 3.0 6.6 + - - +
1473 GLU* 1.3 79.8 - - - +
1493 MET* 1.3 61.5 + - - +
1503 LEU 3.2 1.0 + - - -
1513 GLY* 3.2 12.9 + - - +
1533 HIS* 4.4 1.7 + - - -
1933 PHE* 3.4 35.7 - - + -
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Residues in contact with MET 149 (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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1313 LEU* 4.5 14.9 - - + +
1453 ARG* 2.8 22.3 + - + +
1463 LYS* 3.4 30.3 - - + +
1483 ALA* 1.3 71.8 - - - +
1503 LEU* 1.3 84.3 + - + +
1513 GLY 3.4 0.2 - - - +
1533 HIS* 2.9 41.8 + - + +
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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