Contacts of the helix formed by residues 168 - 179 (chain A) in PDB entry 3ELP
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 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ILE* 4.0 25.0 - - + +
166A VAL 4.0 0.6 + - - -
167A ILE* 1.3 71.0 - - - +
169A ILE* 1.3 62.6 + - - +
170A GLU* 3.2 10.4 + - - +
171A GLY* 2.4 33.9 + - - +
172A CYS* 2.9 24.8 + - - -
302A LEU* 3.7 21.9 - - + +
305A ARG* 2.9 34.9 + - - -
306A GLN* 3.9 2.7 - - - -
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Residues in contact with ILE 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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156A ILE* 5.5 1.1 - - + -
158A THR* 3.9 12.3 - - + -
167A ILE* 2.9 13.3 + - + +
168A ASP* 1.3 70.9 - - - +
170A GLU* 1.3 58.0 + - - +
172A CYS* 3.3 7.8 + - - +
173A ALA* 2.9 27.9 + - - +
184A LEU* 4.1 7.2 - - + +
186A VAL* 3.5 32.1 - - + -
196A GLN* 3.3 33.7 - - + +
198A PRO* 4.6 4.3 - - + +
201A LEU* 3.9 27.8 - - + +
203A ALA* 4.6 5.6 - - + -
306A GLN* 3.2 25.9 + - - +
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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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168A ASP* 3.2 7.0 + - - +
169A ILE* 1.3 78.4 - - - +
171A GLY* 1.3 63.7 + - - +
173A ALA* 3.2 5.9 + - - +
174A HIS* 3.2 52.7 + - + +
200A ALA 4.5 2.3 - - - +
201A LEU* 3.3 48.8 + - + +
202A GLY* 4.5 2.4 - - - -
305A ARG* 4.5 13.9 - - - +
306A GLN* 4.5 1.8 + - - +
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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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140A ILE* 4.5 11.4 - - - -
168A ASP* 2.4 33.1 + - - -
170A GLU* 1.3 71.4 - - - +
172A CYS* 1.3 59.8 + - - +
174A HIS* 3.5 5.5 + - - +
175A ILE* 3.0 31.5 + - - +
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Residues in contact with CYS 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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137A CYS* 4.4 8.7 - - - -
140A ILE* 4.8 9.6 - - - -
143A LEU* 3.7 25.4 - - + -
156A ILE* 3.6 16.8 - - + -
167A ILE* 3.6 24.0 - - - -
168A ASP 2.9 19.3 + - - +
169A ILE* 3.7 6.1 - - - +
171A GLY* 1.3 73.8 - - - +
173A ALA* 1.3 59.6 + - - +
175A ILE* 3.8 2.9 - - - +
176A VAL* 2.8 36.6 + - - +
184A LEU* 4.4 10.5 - - + -
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Residues in contact with ALA 173 (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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169A ILE 2.9 13.9 + - - +
170A GLU* 3.2 13.7 + - - +
172A CYS* 1.3 77.7 - - - +
174A HIS* 1.3 56.5 + - + +
177A HIS* 2.8 44.5 + - + +
184A LEU* 3.7 19.3 - - + +
201A LEU 3.7 16.2 - - - +
202A GLY* 3.9 16.4 - - - +
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Residues in contact with HIS 174 (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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170A GLU* 3.2 38.0 + - + +
171A GLY* 3.9 5.5 - - - +
173A ALA* 1.3 77.5 - - + +
175A ILE* 1.3 64.3 + - + +
177A HIS* 4.8 4.3 - - + -
178A LYS* 3.0 33.1 + - - +
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Residues in contact with ILE 175 (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 ILE* 3.6 24.2 - - + +
143A LEU* 4.6 10.5 - - + +
144A GLU* 3.5 60.8 - - + +
147A ILE* 5.0 7.3 - - + +
171A GLY 3.0 19.2 + - - +
172A CYS* 3.8 6.7 - - - +
174A HIS* 1.3 81.8 - - + +
176A VAL* 1.3 62.2 + - - +
178A LYS* 3.5 26.5 - - - +
179A HIS* 4.4 1.9 + - - +
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Residues in contact with VAL 176 (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 LEU* 4.1 17.0 - - + -
147A ILE* 4.9 7.0 - - + -
154A VAL* 3.6 27.1 - - + -
172A CYS 2.8 27.6 + - - +
173A ALA* 3.8 3.1 - - - +
175A ILE* 1.3 77.0 - - - +
177A HIS* 1.3 71.3 + - + +
178A LYS 3.5 0.2 + - - -
179A HIS 3.5 7.4 - - - +
182A ILE* 2.8 60.2 - - + +
183A ILE 4.6 0.2 - - - -
184A LEU* 4.2 14.8 - - + -
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Residues in contact with HIS 177 (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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173A ALA* 2.8 34.5 + - + +
174A HIS* 4.5 4.0 - - + +
176A VAL* 1.3 79.2 - - + +
178A LYS* 1.3 66.6 + - - +
179A HIS* 3.2 5.7 + - - -
180A GLY 4.3 5.5 - - - +
182A ILE* 4.6 7.8 + - - -
184A LEU* 4.0 13.5 - - + -
202A GLY 3.6 18.5 + - - -
204A ASP* 2.8 43.0 + - - -
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Residues in contact with LYS 178 (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 GLU* 3.8 27.0 + - - +
174A HIS 3.0 20.9 + - - +
175A ILE* 3.5 20.1 - - + +
176A VAL 3.3 0.6 - - - -
177A HIS* 1.3 76.4 - - - +
179A HIS* 1.3 82.8 + - + +
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Residues in contact with HIS 179 (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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147A ILE* 6.0 5.8 - - + +
175A ILE 4.4 1.8 + - - +
176A VAL 3.5 14.1 + - - +
177A HIS 4.3 0.4 - - - -
178A LYS* 1.3 109.5 + - + +
180A GLY* 1.3 71.4 + - - +
182A ILE* 3.8 5.0 - - - +
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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