Contacts of the helix formed by residues 157 - 166 (chain A) in PDB entry 4ZBW
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 LEU 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A TYR* 4.4 2.7 - - + -
104A MET* 4.3 10.8 - - + -
152A LEU* 4.2 11.4 - - + -
153A GLY 3.3 24.5 - - - +
154A GLU 4.3 7.6 - - - +
155A GLY* 4.2 1.3 - - - -
156A LYS* 1.3 78.6 - - - +
158A ASP* 1.3 59.8 + - - +
159A ILE 3.4 2.0 - - - -
160A LEU* 3.2 18.5 + - + +
161A LYS* 2.7 51.3 + - + +
175A ILE* 4.0 16.4 - - + -
178A TYR* 3.8 18.6 - - + -
179A GLU* 3.8 31.2 - - + +
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Residues in contact with ASP 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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156A LYS* 3.6 6.7 - - + +
157A LEU* 1.3 80.2 + - - +
159A ILE* 1.3 61.0 + - + +
161A LYS* 3.3 12.6 + - - +
162A ARG* 2.9 55.4 + - - +
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Residues in contact with ILE 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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124A LEU* 3.9 27.6 - - + -
127A GLU* 4.0 20.9 - - + +
128A ASP* 4.7 9.0 - - + +
146A MET* 4.2 6.5 - - + -
151A ILE* 3.7 47.5 + - + +
157A LEU 3.4 0.2 - - - -
158A ASP* 1.3 75.0 - - + +
160A LEU* 1.3 65.9 + - - +
162A ARG* 3.3 26.3 + - - +
163A VAL* 2.9 25.9 + - + +
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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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104A MET* 4.3 2.9 - - + -
105A LEU* 3.9 21.8 - - + -
108A ILE* 4.2 3.4 - - + -
120A PHE* 4.1 7.4 - - + -
143A PHE* 3.7 32.5 - - + -
146A MET* 4.5 9.9 - - + +
151A ILE 5.3 1.0 + - - -
152A LEU* 4.1 20.2 - - + -
157A LEU* 3.2 23.9 + - + +
159A ILE* 1.3 80.3 - - - +
161A LYS* 1.3 57.6 + - - +
163A VAL* 3.5 3.2 + - - +
164A CYS* 2.9 48.3 + - - +
175A ILE* 3.6 26.0 - - + -
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Residues in contact with LYS 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 LEU* 2.7 33.6 + - - +
158A ASP* 3.7 12.9 + - - +
160A LEU* 1.3 72.1 - - - +
162A ARG* 1.3 60.3 + - + +
164A CYS 4.4 0.2 - - - +
165A ALA* 2.9 34.0 + - - +
172A LEU* 3.9 12.8 - - + +
175A ILE* 3.5 31.2 - - + -
176A ASN* 3.8 20.5 + - - +
179A GLU* 2.7 35.5 + - - -
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Residues in contact with ARG 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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127A GLU* 3.1 37.7 + - - +
158A ASP* 2.9 44.7 + - - +
159A ILE* 3.6 26.2 - - - +
161A LYS* 1.3 77.2 - - + +
163A VAL* 1.3 61.3 + - - +
165A ALA* 3.9 5.2 + - - +
166A GLN* 2.8 30.6 + - - +
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Residues in contact with VAL 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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120A PHE* 3.5 43.3 - - + +
123A LEU* 3.7 15.5 - - + +
124A LEU* 4.1 21.3 - - + +
127A GLU* 4.0 21.3 - - + -
146A MET* 6.0 0.4 - - + -
159A ILE* 2.9 26.6 + - + +
160A LEU 3.8 2.9 - - - +
162A ARG* 1.3 75.9 - - - +
164A CYS* 1.3 63.5 + - - +
166A GLN* 3.1 20.8 + - - +
167A ILE* 3.5 16.6 - - + +
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Residues in contact with CYS 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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108A ILE* 4.4 7.4 - - - -
120A PHE* 3.9 21.3 - - - -
160A LEU* 2.9 30.5 + - - +
161A LYS* 3.4 1.8 + - - +
163A VAL* 1.3 78.7 - - - +
165A ALA* 1.3 63.1 + - - +
167A ILE* 3.1 16.8 + - - -
168A ASN 3.2 19.9 + - - +
171A LEU* 4.0 27.8 - - + +
172A LEU* 4.4 5.4 - - - +
175A ILE* 3.8 24.0 - - + -
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Residues in contact with ALA 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 LYS 2.9 18.7 + - - +
162A ARG* 4.1 7.4 - - - +
163A VAL 3.2 0.2 - - - -
164A CYS* 1.3 76.4 - - - +
166A GLN* 1.3 62.1 + - + +
167A ILE 3.3 1.0 + - - -
168A ASN 4.6 5.4 + - - -
169A LYS* 5.3 1.5 + - - +
172A LEU* 3.9 28.0 - - + +
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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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123A LEU* 3.7 34.8 - - + +
126A GLU* 5.0 4.0 + - - +
127A GLU* 4.0 15.0 + - - +
162A ARG* 2.8 25.7 + - - +
163A VAL* 3.1 11.0 + - - +
165A ALA* 1.3 79.4 - - + +
167A ILE* 1.3 62.2 + - - +
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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