Contacts of the helix formed by residues 155 - 168 (chain A) in PDB entry 4O6M
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 ILE 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A TRP* 4.5 16.8 - - + -
151A ILE* 2.9 39.3 + - + +
154A GLU* 1.3 88.3 - - + +
156A ASN* 1.3 75.9 + - - +
157A ARG 3.3 1.3 - - - -
158A LYS* 3.3 19.8 + - - +
159A VAL* 4.1 5.4 + - - +
208A GLN* 5.6 1.6 - - - +
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Residues in contact with ASN 156 (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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151A ILE* 3.0 22.5 + - - +
152A ALA* 3.5 23.1 - - + +
155A ILE* 1.3 85.9 - - - +
157A ARG* 1.3 62.6 + - - +
159A VAL* 3.0 9.7 + - - +
160A SER* 3.0 22.2 + - - +
208A GLN* 3.0 24.4 + - - +
211A SER* 3.3 30.7 + - - +
212A ILE* 3.8 25.0 - - + +
302A ASP* 4.4 3.4 + - - +
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Residues in contact with ARG 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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134A LEU 5.4 6.1 + - - -
135A ILE* 5.1 19.8 - - - +
148A ASP 4.7 14.1 - - - +
152A ALA* 2.9 33.5 + - - +
153A ARG* 3.1 29.5 - - - +
155A ILE 3.3 0.4 - - - -
156A ASN* 1.3 76.4 - - - +
158A LYS* 1.3 62.8 + - - +
160A SER* 3.2 5.6 - - - -
161A LEU* 3.0 42.4 + - + +
215A GLY* 3.5 26.4 + - - -
218A GLY* 5.9 1.2 - - - -
219A GLU* 3.3 28.7 + - - +
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Residues in contact with LYS 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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153A ARG 5.2 0.2 + - - -
154A GLU 5.1 6.0 + - - +
155A ILE 3.3 14.4 + - - +
156A ASN 3.1 0.6 - - - -
157A ARG* 1.3 79.3 - - - +
159A VAL* 1.3 63.9 + - + +
161A LEU* 4.7 3.6 - - - +
162A ARG* 4.0 13.9 + - - +
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Residues in contact with VAL 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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155A ILE 4.6 7.0 - - - +
156A ASN* 3.0 7.7 + - - +
158A LYS* 1.3 81.8 - - + +
160A SER* 1.3 65.1 + - - +
161A LEU 3.3 0.4 - - - -
162A ARG* 3.1 16.9 + - + +
163A ILE* 3.1 24.0 + - + +
209A LEU* 6.4 1.1 - - + -
212A ILE* 3.8 30.7 - - + -
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Residues in contact with SER 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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156A ASN* 3.0 8.4 + - - -
157A ARG* 3.2 18.5 + - - -
159A VAL* 1.3 75.9 - - - +
161A LEU* 1.3 51.8 + - - +
163A ILE* 3.1 4.4 + - - +
164A SER* 2.7 38.5 + - - -
212A ILE* 3.5 29.2 - - - -
215A GLY* 4.7 1.0 - - - -
216A CYS* 3.6 13.2 - - - -
219A GLU* 2.6 30.9 + - - -
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Residues in contact with LEU 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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131A LEU* 3.6 46.5 - - + +
132A SER* 5.0 5.2 - - - -
134A LEU* 4.1 16.2 - - + +
157A ARG* 3.0 32.8 + - + +
158A LYS* 4.7 3.8 - - - +
160A SER* 1.3 77.8 + - - +
162A ARG* 1.3 57.3 + - - +
164A SER* 3.7 2.4 - - - -
165A ARG* 2.8 29.6 + - - +
219A GLU* 3.6 30.7 - - + +
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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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131A LEU* 6.2 0.2 - - - -
158A LYS 4.0 11.1 + - - +
159A VAL* 3.1 13.8 + - + +
161A LEU* 1.3 78.7 - - - +
163A ILE* 1.3 62.4 + - + +
165A ARG* 3.6 14.9 + - - +
166A LEU* 3.6 20.6 - - - +
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Residues in contact with ILE 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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159A VAL* 3.1 30.4 + - + +
160A SER* 3.1 8.0 + - - +
162A ARG* 1.3 76.1 - - + +
164A SER* 1.3 64.9 + - - +
166A LEU* 3.1 13.2 + - + +
167A LEU* 3.0 39.8 + - + +
209A LEU* 5.4 4.7 - - + -
212A ILE* 4.3 9.2 - - + -
213A ILE* 4.1 22.9 - - + -
216A CYS* 4.0 9.2 - - - -
403A MPG 4.5 12.1 - - + -
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Residues in contact with SER 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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131A LEU* 5.3 1.1 - - - -
134A LEU* 5.6 0.2 - - - -
160A SER 2.7 15.8 + - - -
161A LEU* 3.7 6.5 - - - -
163A ILE* 1.3 69.1 - - - +
165A ARG* 1.3 66.9 + - - +
167A LEU* 4.3 5.2 - - - +
168A ALA* 2.9 26.3 + - - +
216A CYS* 3.4 15.9 + - - +
219A GLU* 2.5 40.9 + - - +
220A ILE* 3.5 16.3 - - - +
223A LEU* 4.4 6.5 - - - +
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Residues in contact with ARG 165 (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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17A LEU* 3.9 22.6 - - + +
127A GLU* 2.8 27.9 + - - -
131A LEU* 4.1 20.8 - - + +
161A LEU 2.8 17.7 + - - +
162A ARG* 3.6 12.5 + - - +
164A SER* 1.3 77.9 - - - +
166A LEU* 1.3 81.5 + - + +
168A ALA* 3.7 7.8 + - - +
169A ASP* 3.3 17.8 - - - +
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Residues in contact with LEU 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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162A ARG 3.6 15.0 + - - +
163A ILE* 3.1 11.7 + - + +
165A ARG* 1.3 102.2 - - + +
167A LEU* 1.3 64.6 + - + +
168A ALA 3.2 1.4 + - - -
169A ASP* 3.6 13.5 + - - +
170A THR* 3.7 12.5 - - - +
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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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163A ILE* 3.0 39.4 + - + +
164A SER* 3.2 6.9 + - - +
166A LEU* 1.3 73.8 - - + +
168A ALA* 1.3 65.6 + - - +
169A ASP 3.1 3.4 - - - -
170A THR* 2.7 32.0 + - + +
172A VAL* 4.3 27.3 + - + +
177A ILE* 4.1 17.7 - - + -
216A CYS* 4.6 7.0 - - + -
220A ILE* 3.9 11.6 - - + +
224A LYS* 4.6 1.0 + - - +
403A MPG 3.9 32.1 - - + -
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Residues in contact with ALA 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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17A LEU* 3.7 21.5 - - + +
18A GLY* 3.3 11.1 - - - -
164A SER 2.9 17.0 + - - +
165A ARG 3.7 8.7 - - - +
166A LEU 3.2 0.6 - - - -
167A LEU* 1.3 77.2 - - - +
169A ASP* 1.3 57.5 + - - +
170A THR 3.2 0.2 - - - -
220A ILE* 3.8 8.3 - - + -
223A LEU* 3.7 24.9 - - + -
224A LYS* 2.8 30.6 + - + -
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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