Contacts of the helix formed by residues 135 - 142 (chain C) 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 ASN 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106C PRO* 3.6 24.9 - - - +
133C GLN* 2.6 22.2 + - + +
134C LEU* 1.3 75.6 - - - +
136C ALA* 1.3 59.5 + - - +
137C THR* 2.8 22.3 + - - -
138C ALA* 2.8 13.7 + - - +
139C LYS* 3.0 30.0 + - - +
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C TYR* 5.5 6.7 - - - +
135C ASN* 1.3 78.1 - - - +
137C THR* 1.3 57.1 + - - +
139C LYS* 4.0 11.9 - - - +
140C LYS* 3.1 27.0 + - - +
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Residues in contact with THR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C PRO* 4.6 4.9 - - + -
107C HIS* 4.9 19.5 - - + +
135C ASN* 2.8 18.9 + - - -
136C ALA* 1.3 73.1 - - - +
138C ALA* 1.3 65.9 + - - +
140C LYS* 3.4 5.8 + - + +
141C VAL* 3.1 33.6 + - + +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C PRO* 3.5 24.4 + - + +
109C LEU* 4.5 4.0 - - + -
110C GLY* 3.4 13.3 - - - +
133C GLN 3.7 15.3 - - - +
134C LEU* 3.8 15.5 - - + -
135C ASN* 2.8 16.7 + - - +
137C THR* 1.3 75.0 - - - +
139C LYS* 1.3 66.8 + - - +
140C LYS 3.1 0.2 + - - -
141C VAL 3.3 1.4 + - - -
142C ALA* 2.9 25.8 + - - +
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Residues in contact with LYS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LEU* 3.7 40.3 + - + +
135C ASN* 3.0 21.5 + - - +
136C ALA* 4.0 8.1 - - - +
138C ALA* 1.3 76.8 - - - +
140C LYS* 1.3 63.7 + - - +
142C ALA* 3.5 8.2 + - - +
143C CYS* 3.5 7.6 + - - -
144C GLY 4.0 6.6 + - - -
146C ALA* 4.1 24.5 + - + +
147C GLU* 5.2 11.8 + - - +
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Residues in contact with LYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C TYR* 6.6 0.2 - - + -
66C VAL* 6.5 0.9 - - - -
136C ALA 3.1 17.7 + - - +
137C THR* 3.4 10.3 - - + +
138C ALA 3.0 0.8 - - - -
139C LYS* 1.3 80.0 - - - +
141C VAL* 1.3 67.5 + - + +
143C CYS* 3.1 21.0 + - - -
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C HIS* 3.7 54.7 - - + +
110C GLY* 4.3 1.4 - - - +
111C ALA* 3.7 27.6 - - + +
114C ARG* 3.5 23.8 + - - +
137C THR* 3.1 20.7 + - + +
138C ALA 4.0 2.7 - - - +
140C LYS* 1.3 80.0 - - + +
142C ALA* 1.3 61.2 + - - +
143C CYS* 3.0 2.9 + - - +
226H ASN* 5.4 7.4 - - + +
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLY* 3.3 23.5 + - - +
113C LEU* 4.3 6.1 - - + -
114C ARG* 3.8 10.4 - - - +
138C ALA 2.9 17.9 + - - +
139C LYS* 3.6 9.9 - - - +
140C LYS 3.1 0.2 - - - -
141C VAL* 1.3 76.1 - - - +
143C CYS* 1.3 68.3 + - - +
144C GLY 3.2 0.2 - - - -
145C ALA* 2.9 24.2 + - + +
146C ALA* 3.9 20.9 - - + +
222H VAL* 4.5 0.5 - - - +
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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