Contacts of the helix formed by residues 144 - 149 (chain G) in PDB entry 1GZ0
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 GLY 144 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B VAL* 6.1 0.5 - - - +
139G LYS 4.1 6.3 + - - -
142G ALA 2.9 1.2 + - - -
143G CYS* 1.3 74.4 - - - +
145G ALA* 1.3 62.2 - - - +
146G ALA 3.6 1.3 - - - -
147G GLU* 3.7 30.7 + - - +
148G SER* 3.8 11.4 + - - -
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Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G LEU* 3.7 12.3 - - + +
114G ARG* 3.6 28.0 - - - +
117G ASP* 4.3 10.5 - - + -
142G ALA* 2.7 21.2 + - + +
143G CYS 3.9 0.2 + - - -
144G GLY* 1.3 75.1 - - - +
146G ALA* 1.3 59.1 + - - +
147G GLU 2.8 12.4 + - - -
148G SER* 3.1 6.9 + - - -
149G VAL* 3.0 27.6 + - + +
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Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G GLN* 5.3 6.8 + - - -
113G LEU* 4.2 10.5 - - + -
134G LEU* 4.0 36.2 - - + +
139G LYS* 4.1 16.2 - - + -
142G ALA* 3.6 14.0 - - + +
145G ALA* 1.3 76.7 - - - +
147G GLU* 1.3 68.2 + - - +
149G VAL 3.9 9.8 - - - +
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Residues in contact with GLU 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G LYS* 5.1 9.3 - - - +
144G GLY* 3.7 26.6 + - - +
145G ALA 2.8 2.0 + - - -
146G ALA* 1.3 99.6 + - - +
148G SER* 1.3 63.4 + - - +
149G VAL 4.8 0.6 - - - +
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Residues in contact with SER 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B VAL* 5.8 5.3 - - - +
117G ASP* 2.6 30.6 + - - -
144G GLY 3.8 10.0 + - - -
145G ALA 3.4 6.5 + - - -
147G GLU* 1.3 81.5 - - - +
149G VAL* 1.3 67.5 + - - +
150G PRO* 3.4 8.7 - - - +
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Residues in contact with VAL 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G LEU* 4.1 16.0 - - + +
116G ALA* 4.3 4.9 - - + -
117G ASP* 3.3 48.2 - - + +
121G VAL 4.1 18.8 - - - +
123G ALA* 4.5 1.8 - - - -
124G VAL* 3.9 30.1 - - + +
145G ALA 3.0 14.4 + - - +
146G ALA* 3.9 10.6 - - - +
147G GLU 5.1 0.7 - - - -
148G SER* 1.3 80.6 + - - +
150G PRO* 1.3 72.8 - - + +
151G LEU* 3.6 2.6 + - - +
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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