Contacts of the helix formed by residues 158 - 171 (chain A) in PDB entry 2LCK
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 SER 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PHE* 5.2 8.5 - - - -
156A TYR* 4.6 8.3 + - - -
157A GLN* 1.3 79.0 - - - +
159A THR* 1.3 56.1 + - - +
160A VAL* 3.5 21.5 - - - +
161A GLU* 3.5 13.3 - - - +
162A ALA* 2.5 42.1 + - - +
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Residues in contact with THR 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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140A VAL* 4.9 16.3 - - - +
144A PHE* 5.4 7.2 - - - -
158A SER* 1.3 74.1 - - - +
160A VAL* 1.3 84.2 + - + +
162A ALA* 3.6 5.6 - - - +
163A TYR* 3.2 24.3 + - - +
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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 SER* 3.5 15.0 - - - +
159A THR* 1.3 88.8 - - + +
161A GLU* 1.3 79.7 + - + +
163A TYR* 3.7 9.4 + - - +
164A LYS* 3.8 14.6 + - - +
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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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155A ARG* 6.2 4.7 - - - -
157A GLN* 4.7 11.2 - - + -
158A SER* 3.4 26.6 + - - +
160A VAL* 1.3 90.8 - - + +
162A ALA* 1.3 64.7 + - - +
163A TYR 3.5 0.2 + - - -
164A LYS* 3.6 21.9 + - - +
165A THR* 3.5 38.6 + - - +
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Residues in contact with ALA 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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144A PHE* 4.8 16.6 - - + -
147A GLN* 6.2 2.5 - - + -
157A GLN* 4.9 11.4 + - + +
158A SER 2.5 26.9 + - - +
159A THR* 3.6 7.6 - - - +
161A GLU* 1.3 75.3 - - - +
163A TYR* 1.3 50.5 + - - +
165A THR* 3.7 5.5 + - - -
166A ILE* 2.6 34.0 - - - +
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Residues in contact with TYR 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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136A PRO* 6.2 4.9 - - + -
139A VAL* 5.9 0.9 - - + -
140A VAL* 4.5 21.5 - - + -
159A THR 3.2 13.3 + - - +
160A VAL* 4.1 4.9 - - - +
161A GLU 3.4 0.4 - - - -
162A ALA* 1.3 78.6 - - - +
164A LYS* 1.3 68.5 + - + +
166A ILE* 2.8 19.3 - - - +
167A ALA* 3.3 20.8 - - + +
172A ILE* 5.9 2.9 - - - +
175A LEU* 3.4 50.8 - - + +
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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* 3.8 12.7 + - - +
161A GLU* 3.6 23.1 + - - +
162A ALA 3.4 0.6 - - - -
163A TYR* 1.3 90.4 - - + +
165A THR* 1.3 71.1 + - - +
167A ALA* 3.2 5.6 - - + +
168A ARG* 3.1 23.6 + - + +
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Residues in contact with THR 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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157A GLN* 4.6 11.7 + - - +
161A GLU* 3.5 29.2 + - - +
162A ALA* 3.7 6.1 + - - -
164A LYS* 1.3 78.7 - - + +
166A ILE* 1.3 70.3 + - - +
168A ARG* 3.0 25.8 + - - +
169A GLU* 3.6 9.4 + - - +
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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 ARG* 5.7 7.9 - - - +
162A ALA 2.6 33.2 - - - +
163A TYR* 2.8 23.1 - - - +
165A THR* 1.3 74.3 + - - +
167A ALA* 1.3 57.1 + - + +
168A ARG 3.2 0.2 + - - -
169A GLU* 3.3 7.6 + - - +
170A GLU* 2.5 54.0 + - + +
175A LEU* 6.1 4.5 - - + -
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Residues in contact with ALA 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 TYR* 3.3 27.4 - - + +
164A LYS* 3.2 16.2 - - + +
166A ILE* 1.3 85.5 - - + +
168A ARG* 1.3 58.1 + - - +
171A GLY* 2.7 42.6 + - - +
175A LEU* 6.1 3.1 - - + -
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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 LYS* 3.1 15.0 + - + +
165A THR* 3.0 15.8 + - - +
167A ALA* 1.3 78.6 - - - +
169A GLU* 1.3 64.3 + - + +
171A GLY* 4.4 1.4 + - - -
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Residues in contact with GLU 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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165A THR 3.6 7.9 + - - +
166A ILE* 3.3 7.5 + - - +
168A ARG* 1.3 80.7 - - + +
170A GLU* 1.3 65.4 + - + +
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Residues in contact with GLU 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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143A ARG* 4.3 10.4 + - - -
166A ILE* 2.5 37.0 + - + +
167A ALA* 4.7 0.2 - - - -
169A GLU* 1.3 75.5 - - + +
171A GLY* 1.3 60.2 + - - +
173A ARG* 4.8 2.9 + - - +
174A GLY* 3.2 37.1 + - - +
177A LYS* 3.8 12.1 + - - +
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Residues in contact with GLY 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 ALA* 2.7 37.9 + - - +
168A ARG 5.0 1.1 - - - -
169A GLU 3.6 1.0 - - - -
170A GLU* 1.3 76.8 - - - +
172A ILE* 1.3 65.4 + - - +
173A ARG* 3.4 1.8 - - - -
174A GLY* 3.6 4.9 + - - -
175A LEU* 3.9 8.7 + - - +
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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