Contacts of the helix formed by residues 124 - 138 (chain A) in PDB entry 1ZU4
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 ASP 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LYS* 6.0 0.3 - - - +
122A GLN* 2.9 34.0 + - + +
123A ALA* 1.3 75.1 - - - +
125A ASP* 1.3 66.3 + - - +
126A GLU* 3.4 12.0 + - - +
127A PHE* 2.8 41.3 + - - +
128A PHE* 3.0 17.2 + - - -
158A ARG* 5.1 5.4 - - + -
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Residues in contact with ASP 125 (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 ASP* 1.3 73.7 - - - +
126A GLU* 1.3 63.1 + - - +
128A PHE* 3.0 13.0 + - - +
129A GLU* 3.0 22.0 + - + +
153A ARG* 2.6 38.2 + - - +
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Residues in contact with GLU 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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124A ASP* 3.3 12.5 + - - +
125A ASP* 1.3 76.8 - - - +
127A PHE* 1.3 62.8 + - - +
129A GLU* 3.2 25.3 + - - +
130A GLU* 3.2 33.7 + - + +
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.7 32.8 - - + -
120A TYR* 3.6 27.8 - + + -
122A GLN 3.4 21.3 - - - +
123A ALA* 3.7 14.6 - - + -
124A ASP* 2.8 14.3 + - - +
126A GLU* 1.3 76.2 - - - +
128A PHE* 1.3 89.5 + + - +
130A GLU* 3.1 7.8 + - + +
131A LEU* 2.8 40.3 + - + -
162A PHE* 4.1 3.1 - + - -
165A ILE* 3.7 35.9 - - + -
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Residues in contact with PHE 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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123A ALA* 3.6 22.7 - - + -
124A ASP 3.0 24.2 + - - -
125A ASP 3.0 4.6 + - - +
127A PHE* 1.3 93.5 - + - +
129A GLU* 1.3 57.7 + - - +
131A LEU* 3.8 11.3 - - + +
132A GLU* 2.9 37.4 + - - +
149A SER* 3.7 21.3 + - - +
152A VAL* 3.6 24.5 - - + -
153A ARG* 3.4 71.1 - - + +
156A THR* 3.7 13.2 - - - -
165A ILE* 6.1 0.2 - - + -
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Residues in contact with GLU 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 ASP* 3.0 17.7 + - + +
126A GLU* 3.4 29.7 + - + +
127A PHE 3.2 0.2 - - - -
128A PHE* 1.3 76.5 - - - +
130A GLU* 1.3 63.5 + - + +
132A GLU* 3.4 13.3 + - - +
133A ASP* 3.1 22.0 + - - +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.4 23.4 - - + +
126A GLU* 3.2 24.7 + - + +
127A PHE* 3.1 10.2 + - + +
129A GLU* 1.3 79.3 - - - +
131A LEU* 1.3 65.4 + - - +
133A ASP* 3.2 10.3 + - - +
134A VAL* 3.2 22.9 + - - +
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Residues in contact with LEU 131 (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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113A ILE* 4.6 4.7 - - + -
116A LEU* 4.0 25.7 - - + +
127A PHE* 2.8 26.3 + - + +
128A PHE* 3.8 31.9 - - + +
129A GLU 3.3 0.2 - - - -
130A GLU* 1.3 75.9 - - - +
132A GLU* 1.3 58.2 + - - +
134A VAL* 3.0 7.5 + - + +
135A LEU* 2.9 48.6 + - + +
149A SER* 4.6 5.8 - - - +
152A VAL* 4.2 23.3 - - + -
165A ILE* 5.6 3.1 - - + -
169A LEU* 4.3 22.7 - - + -
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Residues in contact with GLU 132 (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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128A PHE* 2.9 22.7 + - - +
129A GLU* 3.7 13.9 - - - +
131A LEU* 1.3 74.7 - - - +
133A ASP* 1.3 57.8 + - - +
135A LEU* 3.2 4.9 + - - +
136A ILE* 2.9 39.0 + - + +
145A VAL* 3.7 17.8 - - + +
146A LEU* 5.8 5.2 - - - +
149A SER* 2.7 36.7 + - - +
150A ASN* 5.5 1.7 + - - -
153A ARG* 4.3 12.6 + - - -
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Residues in contact with ASP 133 (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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129A GLU 3.1 14.2 + - - +
130A GLU* 3.6 13.5 - - - +
131A LEU 3.2 0.4 - - - -
132A GLU* 1.3 76.4 - - - +
134A VAL* 1.3 61.6 + - + +
136A ILE* 3.3 26.0 + - - +
137A GLN* 3.3 30.3 + - - +
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Residues in contact with VAL 134 (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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109A PHE* 4.0 24.0 - - + -
112A ASP* 3.7 40.8 - - + +
113A ILE* 4.0 13.0 - - + -
116A LEU* 4.4 17.0 - - + -
130A GLU 3.2 12.6 + - - +
131A LEU* 3.0 10.8 + - + +
133A ASP* 1.3 76.7 - - + +
135A LEU* 1.3 64.2 + - + +
137A GLN* 3.1 22.8 + - - +
138A THR* 3.6 9.5 + - - +
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Residues in contact with LEU 135 (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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109A PHE* 4.3 19.3 - - + -
131A LEU* 2.9 39.6 + - + +
132A GLU* 3.2 6.9 + - - +
134A VAL* 1.3 71.2 - - - +
136A ILE* 1.3 61.2 + - - +
138A THR* 2.8 26.6 + - - -
140A MET* 3.6 26.3 - - + +
145A VAL* 3.8 33.0 - - + +
148A VAL* 3.7 24.0 - - + -
149A SER* 4.1 8.3 - - - +
169A LEU* 4.0 21.3 - - + -
173A LEU* 4.6 0.4 - - + -
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Residues in contact with ILE 136 (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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132A GLU* 2.9 28.1 + - + +
133A ASP* 3.6 19.7 - - - +
134A VAL 3.1 0.4 - - - -
135A LEU* 1.3 76.9 - - - +
137A GLN* 1.3 59.8 + - + +
139A ASP* 3.0 27.9 + - - +
140A MET* 4.4 0.6 + - - +
141A GLY 5.4 1.2 + - - +
142A MET* 6.1 3.4 - - + -
145A VAL* 3.8 24.5 - - + -
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Residues in contact with GLN 137 (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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108A ASN* 4.6 4.8 + - - +
112A ASP* 3.7 28.8 + - - +
133A ASP* 3.3 33.0 + - - +
134A VAL* 3.1 12.9 + - - +
136A ILE* 1.3 76.6 - - + +
138A THR* 1.3 58.4 + - - +
139A ASP* 3.0 10.6 + - - +
360A LYS* 3.6 29.3 + - - +
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Residues in contact with THR 138 (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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108A ASN* 5.7 2.2 - - - +
109A PHE* 3.9 35.4 - - + -
134A VAL 3.6 11.0 - - - +
135A LEU* 2.8 22.4 + - - +
137A GLN* 1.3 75.0 - - - +
139A ASP* 1.3 60.6 + - - +
140A MET* 3.3 27.0 + - + +
360A LYS* 3.4 15.6 - - - +
361A GLY* 4.6 5.4 - - - +
362A GLY* 2.8 37.3 + - - -
399A LEU* 6.2 1.3 - - + -
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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