Contacts of the helix formed by residues 179 - 183 (chain O) in PDB entry 3L73
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 PRO 179 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B GLN 5.9 0.2 - - - +
63O LEU* 4.0 25.8 - - + -
64O GLY 4.1 13.2 - - - +
148O LYS* 3.6 7.0 - - - +
175O PRO* 4.4 17.0 - - + -
177O TYR 3.2 4.7 - - - +
178O CYS* 1.3 101.3 - - - +
180O ASP* 1.3 69.0 + - - +
181O TYR* 3.5 15.9 - - + -
182O ARG* 3.2 21.2 + - + -
183O ILE* 3.7 1.4 + - - +
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Residues in contact with ASP 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148O LYS* 3.1 28.4 + - - +
179O PRO* 1.3 70.2 - - - +
181O TYR* 1.3 65.4 + - - +
182O ARG 2.8 2.1 + - - -
183O ILE* 2.9 30.0 + - - +
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Residues in contact with TYR 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLN* 3.3 42.2 + - + -
248B ASN* 3.4 33.2 - - + +
249B GLY* 3.6 19.4 + - - -
60O THR 3.8 8.0 + - - -
63O LEU* 3.6 17.8 - - + +
179O PRO* 4.5 17.5 - - + -
180O ASP* 1.3 77.4 - - - +
182O ARG* 1.3 85.6 + - + +
183O ILE 3.6 2.4 + - - +
185O LYS* 3.4 32.8 + - + +
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Residues in contact with ARG 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O THR 4.8 2.0 + - - -
61O ALA 3.5 18.1 + - - -
62O ASN* 3.8 2.0 + - - +
63O LEU* 2.6 49.6 + - - +
178O CYS* 4.1 10.8 - - - -
179O PRO* 3.2 13.0 + - + +
180O ASP 2.8 4.4 + - - -
181O TYR* 1.3 111.1 - - + +
183O ILE* 1.3 63.9 + - - +
184O GLY 3.2 0.7 + - - -
185O LYS* 3.0 36.4 + - + +
186O ILE* 3.6 27.6 - - - +
190O GLN* 2.9 37.0 + - - +
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Residues in contact with ILE 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141O GLN 3.7 20.4 - - - +
142O PRO* 4.7 4.7 - - + -
144O LEU* 3.2 42.4 - - + +
145O LYS* 4.6 20.0 - - + +
148O LYS* 5.5 2.7 - - + -
178O CYS* 3.7 20.2 - - + +
179O PRO 3.7 5.3 + - - +
180O ASP* 2.9 24.6 + - - +
181O TYR 3.4 4.9 - - - +
182O ARG* 1.3 75.3 - - - +
184O GLY* 1.3 63.5 + - - +
185O LYS* 3.4 6.6 + - - +
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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