Contacts of the helix formed by residues 132 - 145 (chain A) in PDB entry 1ZD4
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 GLU 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A LYS* 2.8 20.0 + - - -
93A ASP* 2.7 30.2 - - + +
130A ARG* 2.9 24.7 + - - +
131A ALA* 1.3 101.9 - - - +
133A ARG* 1.3 63.6 + - - +
134A ASP* 3.1 4.3 - - - -
135A GLY* 2.9 16.6 + - - -
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Residues in contact with ARG 133 (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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128A ASP* 3.3 47.5 + - + +
129A ASP* 4.0 12.4 + - - +
130A ARG* 2.8 40.4 + - - +
131A ALA* 3.5 11.1 + - - +
132A GLU* 1.3 77.2 - - - +
134A ASP* 1.3 67.4 + - + +
136A LEU* 3.0 16.6 + - - +
137A ALA* 3.0 11.3 + - - +
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Residues in contact with ASP 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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131A ALA 6.1 0.2 - - - +
132A GLU* 3.0 3.0 + - - +
133A ARG* 1.3 83.3 - - + +
135A GLY* 1.3 64.2 + - - +
137A ALA* 2.9 14.5 + - - +
138A GLN* 2.9 49.4 + - - +
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Residues in contact with GLY 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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96A ILE* 5.8 0.7 - - - -
97A SER* 6.6 0.7 - - - -
130A ARG* 5.7 0.2 - - - -
132A GLU 2.9 11.8 + - - -
134A ASP* 1.3 80.3 - - - +
136A LEU* 1.3 62.2 + - - +
138A GLN* 3.3 14.0 + - - +
139A LEU* 3.3 17.3 + - - +
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Residues in contact with LEU 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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10A LEU* 5.4 2.7 - - + -
96A ILE* 4.3 14.8 - - + +
99A ARG* 3.7 24.7 - - - +
125A THR* 5.1 9.9 - - - +
126A TRP* 3.9 28.0 - - + +
128A ASP* 3.2 33.4 - - + +
130A ARG* 4.5 2.5 - - - +
132A GLU 4.2 1.6 + - - -
133A ARG 3.0 10.0 + - - +
135A GLY* 1.3 75.1 - - - +
137A ALA* 1.3 63.3 + - - +
139A LEU* 3.2 10.1 + - + +
140A MET* 3.1 39.0 + - + +
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Residues in contact with ALA 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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133A ARG 3.0 7.4 + - - +
134A ASP* 2.9 30.6 + - - +
136A LEU* 1.3 77.6 - - - +
138A GLN* 1.3 59.6 + - - +
140A MET* 3.3 5.1 + - - +
141A CYS* 2.9 23.6 + - - +
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Residues in contact with GLN 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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134A ASP* 2.9 42.4 + - - +
135A GLY* 3.3 10.7 + - - +
137A ALA* 1.3 72.7 - - - +
139A LEU* 1.3 63.7 + - - +
141A CYS* 3.0 10.1 + - - +
142A GLU* 3.0 24.1 + - - +
281A GLN* 4.7 9.8 + - - +
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Residues in contact with LEU 139 (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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10A LEU* 5.1 1.6 - - + -
15A ALA* 4.7 9.6 - - + -
96A ILE* 5.7 1.6 - - + +
99A ARG* 3.8 47.1 - - - +
100A LYS* 4.8 0.9 - - - -
101A ILE* 3.3 41.7 - - + +
135A GLY 3.3 8.7 + - - +
136A LEU* 3.2 16.5 + - + +
138A GLN* 1.3 79.0 - - - +
140A MET* 1.3 66.7 + - - +
142A GLU* 3.1 16.3 + - - +
143A LEU* 3.1 27.0 + - + +
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Residues in contact with MET 140 (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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10A LEU* 3.6 42.4 - - + -
121A ILE* 4.7 6.1 - - + -
123A THR* 5.0 4.0 - - + -
125A THR* 6.3 1.1 - - + -
136A LEU* 3.1 30.0 + - + +
137A ALA* 3.9 4.5 - - - +
139A LEU* 1.3 82.3 - - - +
141A CYS* 1.3 56.8 + - - +
143A LEU* 3.7 8.9 - - + +
144A LYS* 2.9 42.0 + - + +
150A LEU* 3.5 42.8 - - + -
152A GLU* 5.2 10.5 - - - +
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Residues in contact with CYS 141 (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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137A ALA 2.9 14.4 + - - +
138A GLN* 3.0 15.7 + - - +
140A MET* 1.3 79.4 - - - +
142A GLU* 1.3 60.5 + - - +
144A LYS* 3.9 17.5 + - - +
145A MET* 4.2 11.6 + - - +
281A GLN* 5.4 3.1 - - - +
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Residues in contact with GLU 142 (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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101A ILE* 3.5 16.0 - - + +
103A ARG* 2.7 42.0 + - - -
106A LEU* 4.7 2.1 - - - +
138A GLN 3.0 12.0 + - - +
139A LEU* 3.1 8.2 + - - +
141A CYS* 1.3 76.7 - - - +
143A LEU* 1.3 62.2 + - - +
145A MET* 3.5 9.5 - - - +
146A HIS* 3.0 34.0 + - - +
281A GLN* 3.1 45.0 + - + +
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Residues in contact with LEU 143 (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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10A LEU* 3.5 32.1 - - + -
14A LEU* 4.7 13.2 - - + +
15A ALA* 5.3 0.7 - - + -
101A ILE* 3.7 36.6 - - + -
106A LEU* 3.9 16.2 - - + -
121A ILE* 4.3 14.4 - - + -
139A LEU* 3.1 30.0 + - + +
140A MET* 4.0 12.8 - - - +
142A GLU* 1.3 78.1 - - - +
144A LYS* 1.3 66.9 + - - +
146A HIS* 3.0 13.7 + - - +
147A PHE* 3.1 24.7 - - + -
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Residues in contact with LYS 144 (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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121A ILE* 5.1 2.4 - - - +
140A MET* 2.9 28.8 + - - +
141A CYS* 4.0 10.3 - - - +
142A GLU 3.6 0.2 - - - -
143A LEU* 1.3 74.5 - - - +
145A MET* 1.3 53.2 + - - +
146A HIS 2.7 12.6 + - - -
147A PHE* 2.8 27.2 + - - +
150A LEU* 3.3 36.6 - - + -
152A GLU* 5.2 5.2 - - - -
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Residues in contact with MET 145 (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 ARG* 3.5 11.1 + - - -
141A CYS 4.2 9.8 + - - +
142A GLU* 3.5 26.7 - - - +
144A LYS* 1.3 76.1 - - - +
146A HIS* 1.3 71.3 + - + +
147A PHE 3.5 0.7 - - - -
228A THR* 3.8 29.8 - - + -
230A CYS* 6.4 1.1 - - - -
253A LEU* 6.4 2.2 - - + -
277A PRO* 5.2 7.6 - - + -
281A GLN* 5.0 7.2 - - - +
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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