Contacts of the helix formed by residues 117 - 129 (chain A) in PDB entry 1GGZ
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ARG* 3.8 7.0 - - - +
115A LYS 4.4 0.4 + - - -
116A LEU* 1.3 74.5 - - - +
118A ASP* 1.3 65.1 + - - +
119A GLU* 3.4 8.8 + - - +
120A GLU* 2.9 39.9 + - - +
121A VAL* 2.9 22.9 + - - +
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Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 3.1 39.9 + - - +
117A SER* 1.3 72.5 - - - +
119A GLU* 1.3 57.6 + - - +
121A VAL* 3.3 1.9 + - - +
122A ASP* 2.9 41.1 + - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A SER* 3.2 8.1 + - - +
118A ASP* 1.3 80.9 - - - +
120A GLU* 1.3 59.0 + - + +
122A ASP* 3.3 7.6 + - - +
123A GLU* 2.9 47.1 + - + +
126A ARG* 5.2 4.2 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LYS 4.5 1.6 - - - +
116A LEU* 3.5 25.3 - - + +
117A SER* 2.9 39.9 + - - +
119A GLU* 1.3 76.3 - - + +
121A VAL* 1.3 65.9 + - - +
123A GLU* 3.3 19.5 + - - +
124A MET* 3.0 27.4 + - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA* 3.3 35.2 - - + +
105A LEU* 3.9 18.4 - - + -
106A ARG* 3.8 28.0 - - + +
116A LEU* 3.7 26.2 - - + -
117A SER 2.9 17.0 + - - +
118A ASP* 3.8 5.2 - - - +
120A GLU* 1.3 76.4 - - - +
122A ASP* 1.3 60.9 + - - +
124A MET* 3.0 11.3 + - - +
125A ILE* 2.9 26.2 + - - +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA* 3.4 24.8 - - - +
118A ASP* 2.9 28.3 + - - +
119A GLU* 3.7 6.5 - - - +
120A GLU 3.3 0.2 - - - -
121A VAL* 1.3 77.3 - - - +
123A GLU* 1.3 55.8 + - - +
125A ILE* 3.3 7.7 + - - +
126A ARG* 2.8 50.9 + - + +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 2.9 39.9 + - + +
120A GLU* 3.5 19.3 - - - +
122A ASP* 1.3 75.7 - - - +
124A MET* 1.4 63.1 + - + +
126A ARG* 3.3 26.4 + - - +
127A ALA* 2.9 25.0 + - - +
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Residues in contact with MET 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 3.9 28.9 - - + -
109A MET* 4.7 11.2 - - + -
116A LEU* 3.7 30.1 - - + -
120A GLU* 3.0 16.4 + - + +
121A VAL* 3.0 12.6 + - - +
123A GLU* 1.4 76.6 - - + +
125A ILE* 1.3 62.4 + - - +
127A ALA* 3.4 6.8 + - - +
128A ALA* 3.1 25.3 + - - +
136A VAL* 5.1 0.2 - - - +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.0 9.6 - - + +
101A SER 4.1 2.0 - - - +
102A ALA* 3.9 37.7 - - + +
105A LEU* 3.8 19.5 - - + -
121A VAL 2.9 18.2 + - - +
122A ASP* 3.5 8.7 - - - +
124A MET* 1.3 76.1 - - - +
126A ARG* 1.3 62.2 + - + +
128A ALA* 3.1 1.9 + - - +
129A ASP* 2.8 38.8 + - + +
134A GLY* 3.5 31.9 - - - +
136A VAL* 3.6 25.2 - - + +
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 5.2 4.9 + - - +
122A ASP* 2.8 44.7 + - + +
123A GLU* 3.7 27.5 + - - +
125A ILE* 1.3 77.9 - - + +
127A ALA* 1.3 62.9 + - - +
128A ALA 3.4 0.3 + - - -
129A ASP* 3.5 16.9 + - - +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLU 2.9 17.2 + - - +
124A MET* 3.7 7.6 - - - +
125A ILE 3.2 0.2 - - - -
126A ARG* 1.3 78.6 - - - +
128A ALA* 1.4 58.5 + - - +
130A THR* 4.7 8.1 - - - +
144A VAL* 5.7 0.4 - - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A MET 3.1 16.6 + - - +
127A ALA* 1.4 77.7 - - + +
129A ASP* 1.3 60.2 + - - +
130A THR* 3.0 14.1 + - - +
136A VAL* 4.0 24.9 - - + -
140A GLU* 3.5 22.4 - - - +
144A VAL* 3.9 28.3 - - + -
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 2.8 24.7 + - + +
126A ARG* 3.5 11.4 + - - +
127A ALA 3.5 1.8 - - - -
128A ALA* 1.3 72.0 - - - +
130A THR* 1.3 60.5 + - - +
131A ASP* 3.0 8.1 + - - +
132A GLY* 3.2 13.9 + - - -
133A ASP* 3.2 4.9 + - - +
134A GLY* 2.8 31.2 + - - -
135A GLN 3.6 7.6 - - - +
136A VAL* 5.0 0.9 - - - -
140A GLU* 3.9 6.1 - - - -
152A CA 2.4 30.1 - - - -
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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