Contacts of the helix formed by residues 159 - 172 (chain A) in PDB entry 5LZK
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LYS* 2.8 35.5 + - - +
157A PHE* 3.5 9.7 - - + -
158A THR* 1.3 75.6 + - - +
160A VAL* 1.3 62.8 + - - +
161A ASP* 3.0 7.2 + - - -
162A ILE* 3.0 37.8 + - + +
163A PHE* 3.2 18.7 + - - +
191A MET* 4.5 0.7 - - - -
244A TYR* 4.9 3.3 + - - -
246A TYR* 3.1 23.4 + - + +
247A MET* 4.4 8.2 + - - +
248A TRP* 5.4 4.2 - - - +
251A GLU* 4.9 5.2 - - - +
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Residues in contact with VAL 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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158A THR 3.3 3.8 + - - +
159A ASP* 1.3 73.4 + - - +
161A ASP* 1.3 74.8 + - - +
163A PHE* 3.4 8.6 + - - +
164A LYS* 2.9 29.5 + - - +
191A MET* 3.8 22.2 - - + -
195A GLN* 3.7 39.3 + - + +
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 2.9 30.5 + - - +
140A ARG* 5.2 9.8 + - - +
159A ASP* 3.0 6.1 + - - +
160A VAL* 1.3 87.9 - - - +
162A ILE* 1.3 64.5 + - - +
164A LYS* 3.4 6.7 + - - +
165A GLU* 3.2 26.1 + - - +
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Residues in contact with ILE 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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136A LYS* 4.4 19.7 - - + -
139A ILE* 4.0 31.6 - - + -
140A ARG* 4.9 5.6 - - + -
143A ILE* 4.1 9.2 - - + -
157A PHE* 4.0 7.9 - - + -
159A ASP* 3.0 34.7 + - + +
161A ASP* 1.3 72.9 - - - +
163A PHE* 1.3 66.4 + - - +
165A GLU* 3.2 9.5 + - - +
166A ILE* 3.1 22.5 + - + +
244A TYR* 4.8 4.0 - - + -
246A TYR* 3.8 49.6 - - + -
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Residues in contact with PHE 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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157A PHE* 3.8 13.4 - + + -
159A ASP 3.2 14.1 + - - +
160A VAL 3.6 8.7 - - - +
162A ILE* 1.3 77.5 - - - +
164A LYS* 1.3 62.6 + - - +
166A ILE* 3.1 9.8 + - + +
167A VAL* 3.0 47.1 + - + +
178A ILE* 5.7 3.8 - - + -
188A PHE* 4.0 24.9 - + - -
191A MET* 3.8 22.9 - - + -
192A THR* 3.6 28.9 - - + -
195A GLN* 5.2 5.2 - - + -
197A CYS* 3.9 24.7 - - + -
199A VAL* 4.3 11.9 - - + -
205A ILE* 5.4 3.6 - - + -
303A IOD 4.0 14.8 - - + -
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Residues in contact with LYS 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 VAL 2.9 17.3 + - - +
161A ASP* 3.7 7.6 - - - +
162A ILE 3.2 0.4 - - - -
163A PHE* 1.3 78.4 - - + +
165A GLU* 1.3 59.6 + - + +
167A VAL* 3.4 8.3 + - + +
168A GLU* 3.0 29.6 + - + +
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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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140A ARG* 2.8 55.4 + - + +
143A ILE* 3.5 26.8 - - + +
144A LYS* 3.0 39.5 + - - +
161A ASP 3.2 15.2 + - - +
162A ILE* 3.2 9.0 + - - +
164A LYS* 1.3 78.8 - - + +
166A ILE* 1.3 61.6 + - - +
168A GLU* 3.5 11.4 + - - +
169A ALA* 3.1 17.5 + - - +
172A ARG* 5.1 2.4 + - - -
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Residues in contact with ILE 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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143A ILE* 3.9 28.3 - - + -
150A ILE* 5.1 12.1 - - + -
152A LEU* 4.2 14.4 - - + -
157A PHE* 4.1 30.1 - - + -
162A ILE* 3.1 12.9 + - + +
163A PHE* 3.6 11.4 - - + +
165A GLU* 1.3 73.9 - - - +
167A VAL* 1.3 66.2 + - + +
169A ALA* 3.2 5.5 + - - +
170A SER* 3.1 19.9 + - - -
176A VAL* 3.6 31.3 - - + +
178A ILE* 4.5 9.9 - - + -
205A ILE* 4.3 9.9 - - + -
232A LEU* 5.9 1.3 - - + -
246A TYR* 5.4 0.4 - - + -
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Residues in contact with VAL 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 PHE* 3.0 51.8 + - + +
164A LYS* 3.8 8.5 - - - +
166A ILE* 1.3 76.2 - - - +
168A GLU* 1.3 61.0 + - - +
170A SER* 2.8 24.9 + - - +
171A THR* 3.1 17.9 + - + +
197A CYS* 4.8 2.5 - - - -
202A LEU* 4.4 25.1 - - + -
205A ILE* 4.4 5.4 - - + -
303A IOD 4.4 4.3 - - + -
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Residues in contact with GLU 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 LYS* 3.0 19.7 + - + +
165A GLU* 3.7 11.0 - - - +
166A ILE 3.3 0.2 - - - -
167A VAL* 1.3 76.4 - - - +
169A ALA* 1.3 62.2 + - - +
171A THR* 2.7 38.3 + - - +
172A ARG* 3.4 23.5 + - - +
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Residues in contact with ALA 169 (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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143A ILE* 4.1 2.7 - - + -
150A ILE* 3.9 27.1 - - + -
165A GLU 3.1 14.6 + - - +
166A ILE 3.2 9.4 + - - +
168A GLU* 1.3 75.9 - - - +
170A SER* 1.3 62.8 + - - +
172A ARG* 3.2 46.1 + - - +
174A VAL* 3.2 20.3 + - + +
176A VAL* 5.0 0.7 - - + -
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Residues in contact with SER 170 (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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166A ILE 3.1 10.1 + - - -
167A VAL* 2.8 24.1 + - - +
169A ALA* 1.3 78.9 - - - +
171A THR* 1.3 61.4 + - - +
173A GLY* 3.2 5.7 + - - -
174A VAL 3.5 16.4 - - - -
176A VAL* 4.1 3.1 - - - +
202A LEU* 5.2 5.4 - - - +
204A ASN* 2.9 35.3 + - - +
205A ILE* 3.7 30.1 - - - +
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Residues in contact with THR 171 (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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167A VAL* 3.1 25.7 + - + +
168A GLU* 2.7 35.5 + - - +
170A SER* 1.3 79.7 - - - +
172A ARG* 1.3 58.5 + - - +
173A GLY 3.3 1.8 + - - -
202A LEU* 6.5 1.3 - - + -
204A ASN* 5.2 0.4 - - - +
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Residues in contact with ARG 172 (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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143A ILE 3.0 22.2 + - - -
144A LYS* 3.2 27.2 + - - +
146A ALA* 3.0 28.7 + - - +
165A GLU* 5.1 3.0 + - - -
168A GLU* 3.6 21.0 - - - +
169A ALA* 3.2 40.0 - - - +
171A THR* 1.3 78.9 + - - +
173A GLY* 1.3 57.5 + - - +
174A VAL* 3.6 6.9 + - + +
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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