Contacts of the helix formed by residues 153 - 168 (chain A) in PDB entry 1ZO0
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 LYS 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLY 4.3 6.5 + - - +
152A SER* 1.3 87.4 + - - +
154A ASP* 1.3 67.4 + - - +
155A SER 3.1 2.0 - - - -
156A PHE* 3.1 18.9 + - - +
157A ALA* 3.2 12.6 + - - +
185A ALA* 4.9 19.5 - - + +
186A LEU* 5.0 16.2 - - + -
189A THR* 3.9 37.5 - - + +
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Residues in contact with ASP 154 (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 GLU* 3.8 20.1 - - - +
152A SER* 4.2 5.8 - - - -
153A LYS* 1.3 79.8 - - - +
155A SER* 1.3 60.4 + - - +
157A ALA* 3.4 9.6 + - - +
158A ALA* 3.1 22.8 + - - +
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Residues in contact with SER 155 (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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120A CYS* 5.6 5.8 - - - -
124A GLU* 5.4 12.4 + - - -
126A LYS* 5.5 10.3 - - - +
130A TRP* 6.1 0.2 - - - -
152A SER* 3.1 28.3 + - - -
153A LYS 4.3 0.2 - - - +
154A ASP* 1.3 80.1 - - - +
156A PHE* 1.3 64.3 + - - +
158A ALA* 3.2 6.9 + - - +
159A LEU* 3.1 35.1 + - - +
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Residues in contact with PHE 156 (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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130A TRP* 3.1 50.0 - + - -
141A ILE* 4.1 16.4 - - + -
143A LEU* 5.2 5.4 - - + -
152A SER 4.8 3.8 - - - +
153A LYS* 3.1 14.2 + - - +
155A SER* 1.3 82.6 + - - +
157A ALA* 1.3 61.9 + - - +
158A ALA 3.3 0.2 + - - -
159A LEU* 3.3 5.9 + - + +
160A LEU* 3.1 23.0 + - + +
174A ILE* 3.8 33.2 - - + -
176A PHE* 6.3 2.9 - + - -
186A LEU* 4.8 21.8 - - + -
190A PHE* 4.3 22.0 - + + -
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Residues in contact with ALA 157 (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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153A LYS 3.2 8.6 + - - +
154A ASP* 3.7 14.6 - - - +
156A PHE* 1.3 78.8 - - - +
158A ALA* 1.3 60.2 + - - +
160A LEU* 3.3 13.3 + - + +
161A GLU* 2.6 39.5 + - - +
190A PHE* 5.5 4.9 - - + -
192A PHE* 5.1 15.9 - - + -
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Residues in contact with ALA 158 (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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154A ASP* 3.1 15.0 + - - +
155A SER* 3.4 12.1 - - - +
156A PHE 3.2 0.2 - - - -
157A ALA* 1.3 76.5 - - - +
159A LEU* 1.3 66.1 + - + +
161A GLU* 3.0 23.4 + - - +
162A PHE* 3.2 21.8 + - + +
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Residues in contact with LEU 159 (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 LEU* 3.4 30.1 - - + -
118A ILE* 4.0 16.6 - - + -
119A GLN 5.7 0.4 - - - -
120A CYS* 3.7 32.1 - - + -
130A TRP* 3.9 33.4 - - + -
155A SER* 3.1 29.2 + - - +
156A PHE* 3.8 7.2 - - + +
158A ALA* 1.3 82.2 - - + +
160A LEU* 1.3 61.5 + - - +
162A PHE* 3.6 6.7 + - - +
163A ALA* 3.2 26.0 + - - +
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Residues in contact with LEU 160 (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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139A LEU* 6.0 1.8 - - + -
141A ILE* 5.4 4.3 - - + -
156A PHE* 3.1 14.7 + - + +
157A ALA* 3.4 15.0 - - + +
158A ALA 3.1 0.8 - - - -
159A LEU* 1.3 76.2 - - - +
161A GLU* 1.3 65.8 + - + +
163A ALA* 4.2 3.8 - - + +
164A GLU* 3.2 26.6 + - + +
172A VAL* 3.2 48.4 - - + +
174A ILE* 6.0 0.2 - - + -
190A PHE* 4.1 20.2 - - + -
192A PHE* 6.1 2.2 - - + -
193A LEU* 4.1 25.8 - - + -
216A TYR* 4.3 4.7 - - + +
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Residues in contact with GLU 161 (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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157A ALA* 2.6 37.4 + - - +
158A ALA* 3.0 11.7 + - - +
160A LEU* 1.3 77.5 - - + +
162A PHE* 1.3 66.4 + - + +
164A GLU* 3.5 14.1 + - - +
165A GLU* 3.1 22.9 + - - +
192A PHE* 6.0 0.7 - - - -
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Residues in contact with PHE 162 (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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98A ASP* 5.2 18.2 - - + -
99A GLU* 4.4 26.0 - - + -
101A LEU* 5.8 15.0 - - + -
158A ALA* 3.2 16.5 + - + +
159A LEU* 4.0 8.7 - - - +
161A GLU* 1.3 79.1 - - + +
163A ALA* 1.3 66.8 + - - +
165A GLU* 2.9 33.3 + - - +
166A GLN* 3.2 28.3 + - - +
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Residues in contact with ALA 163 (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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118A ILE* 6.4 2.0 - - + -
139A LEU* 3.9 28.3 - - + -
159A LEU 3.2 17.1 + - - +
160A LEU* 4.2 5.4 - - + +
162A PHE* 1.3 79.0 - - - +
164A GLU* 1.3 62.8 + - - +
166A GLN* 3.6 5.8 + - - +
167A LEU* 3.0 32.8 + - + +
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Residues in contact with GLU 164 (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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160A LEU* 3.2 20.8 + - + +
161A GLU* 3.8 12.8 - - - +
163A ALA* 1.3 79.5 - - - +
165A GLU* 1.3 57.1 + - - +
167A LEU* 4.9 0.7 - - - -
168A ARG* 2.6 35.1 + - - +
169A ALA* 2.9 32.4 - - - +
170A ASP* 4.4 17.1 - - - +
172A VAL* 5.5 6.7 - - + -
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Residues in contact with GLU 165 (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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161A GLU 3.1 12.7 + - - +
162A PHE* 2.9 26.8 + - + +
164A GLU* 1.3 80.4 - - - +
166A GLN* 1.3 71.8 + - + +
168A ARG* 3.2 27.4 + - - +
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Residues in contact with GLN 166 (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 TYR* 3.7 33.8 + - + +
98A ASP* 4.8 8.9 + - - +
103A VAL* 5.4 0.2 - - - +
162A PHE* 3.2 27.3 + - - +
163A ALA* 4.2 6.2 - - - +
165A GLU* 1.3 90.0 + - - +
167A LEU* 1.3 66.0 + - + +
168A ARG* 3.1 21.2 + - - +
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Residues in contact with LEU 167 (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 GLU* 5.4 7.4 - - - +
134A TRP* 3.0 56.9 - - + +
139A LEU* 3.4 23.3 - - + -
163A ALA* 3.0 16.7 + - + +
164A GLU* 4.9 0.2 - - - -
166A GLN* 1.3 80.5 - - + +
168A ARG* 1.3 66.5 + - - +
169A ALA* 3.0 12.2 + - + +
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Residues in contact with ARG 168 (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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164A GLU* 2.6 23.4 + - - +
165A GLU* 3.2 24.5 + - - +
166A GLN* 3.0 17.1 + - - +
167A LEU* 1.3 75.4 - - - +
169A ALA* 1.3 62.2 + - - +
170A ASP* 5.2 1.4 - - - +
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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