Contacts of the helix formed by residues 169 - 180 (chain A) in PDB entry 3IE7
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A SER* 4.0 16.8 + - - -
168A ASN* 1.3 77.0 - - - +
170A GLY* 1.3 71.1 + - - +
171A GLU 3.5 0.2 + - - -
172A TYR* 3.2 15.3 + - - +
173A LEU* 3.1 17.4 + - - -
190A GLU* 3.8 30.1 - - - -
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Residues in contact with GLY 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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169A SER* 1.3 77.2 - - - +
171A GLU* 1.3 55.9 + - - -
172A TYR* 5.8 0.2 - - - -
173A LEU* 3.2 3.7 + - - +
174A ASN* 2.8 38.6 + - - +
190A GLU* 5.3 1.0 + - - +
193A ALA* 4.2 17.1 - - - +
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Residues in contact with GLU 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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147A LEU* 3.6 34.5 - - + +
169A SER 3.5 0.6 + - - -
170A GLY* 1.3 69.7 - - - -
172A TYR* 1.3 64.2 + - + +
174A ASN* 3.3 24.5 + - - +
175A LEU* 2.9 29.5 + - - +
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Residues in contact with TYR 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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140A SER* 5.0 8.7 - - - -
141A PRO* 3.6 36.7 - - + +
145A TYR 3.2 17.0 + - - -
146A THR* 4.2 7.1 - - - -
147A LEU* 3.5 29.1 + - + +
150A PHE* 3.6 46.1 - + + -
168A ASN* 4.1 13.5 - - + +
169A SER 3.2 11.4 + - - +
170A GLY 3.2 0.8 - - - -
171A GLU* 1.3 77.2 - - + +
173A LEU* 1.3 65.8 + - - +
175A LEU* 3.4 2.5 + - - +
176A ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 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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166A CYS* 4.9 1.1 - - + +
168A ASN* 3.5 37.8 - - + +
169A SER* 3.1 14.1 + - - -
170A GLY 3.5 7.0 - - - +
172A TYR* 1.3 75.2 - - - +
174A ASN* 1.3 65.7 + - - +
176A ALA* 3.2 6.1 + - + +
177A VAL* 3.0 28.4 + - + +
184A ILE* 4.2 38.4 - - + -
185A LYS 5.7 0.2 - - - +
186A PRO* 3.9 19.7 - - + -
190A GLU* 3.9 22.0 - - + +
193A ALA* 4.8 2.0 - - + -
194A ILE* 4.0 20.4 - - + -
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Residues in contact with ASN 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 GLY 2.8 27.4 + - - -
171A GLU* 3.3 28.0 + - - +
173A LEU* 1.3 76.4 - - - +
175A LEU* 1.3 56.1 + - - +
177A VAL* 3.3 3.9 + - - +
178A GLU* 2.9 42.2 + - + +
193A ALA* 2.8 33.1 + - - +
194A ILE* 3.1 19.1 - - - +
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Residues in contact with LEU 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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147A LEU* 3.5 35.2 - - + +
150A PHE* 4.1 13.0 - - + -
151A LYS* 3.8 45.5 - - + +
154A LEU* 4.2 2.5 - - + -
171A GLU 2.9 17.9 + - - +
172A TYR 3.7 4.7 - - - +
174A ASN* 1.3 75.1 - - - +
176A ALA* 1.3 60.3 + - - +
178A GLU* 3.2 18.9 + - + +
179A MSE 2.8 44.2 + - + +
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Residues in contact with ALA 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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150A PHE* 4.9 1.1 - - + -
154A LEU* 3.6 16.4 - - + +
166A CYS* 3.9 34.1 - - + -
168A ASN* 5.6 0.4 - - - +
172A TYR 3.1 14.4 + - - +
173A LEU* 3.2 11.0 + - - +
175A LEU* 1.3 75.5 - - - +
177A VAL* 1.3 58.3 + - + +
179A MSE 3.6 0.5 - - - +
180A GLY 2.9 23.9 + - - -
181A VAL* 3.4 21.1 + - + +
184A ILE* 5.1 2.0 - - + -
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Residues in contact with VAL 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 LEU* 3.0 17.7 + - + +
174A ASN* 3.6 8.1 - - - +
176A ALA* 1.3 77.9 - - - +
178A GLU* 1.3 62.5 + - + +
180A GLY* 3.3 11.8 + - - -
181A VAL* 4.7 4.9 - - - +
184A ILE* 4.0 16.8 - - + -
194A ILE* 4.2 17.5 - - + -
209A LEU* 4.7 13.9 - - + -
212A LYS* 3.8 31.0 + - + +
213A ILE* 3.9 32.3 - - + -
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Residues in contact with GLU 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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174A ASN* 2.9 26.7 + - - +
175A LEU* 3.5 30.9 + - + +
177A VAL* 1.3 78.6 - - + +
179A MSE 1.3 63.2 + - - +
180A GLY* 4.5 0.2 - - - -
212A LYS* 4.6 14.8 + - - +
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Residues in contact with MSE 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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151A LYS* 3.5 31.4 - - + +
154A LEU* 3.9 21.5 - - + -
155A ARG* 4.3 34.3 - - + +
158A LYS* 2.5 66.0 + - + +
175A LEU* 2.8 33.7 + - + +
176A ALA 3.6 5.2 - - - +
178A GLU* 1.3 79.1 - - - +
180A GLY* 1.3 57.0 + - - +
181A VAL* 5.2 0.9 - - + -
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Residues in contact with GLY 180 (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 LYS* 3.7 20.9 - - - +
164A LEU* 4.6 0.7 - - - +
176A ALA 2.9 7.2 + - - -
177A VAL 3.3 7.8 + - - -
178A GLU 3.3 3.4 - - - -
179A MSE 1.3 81.5 - - - +
181A VAL* 1.3 65.9 + - - +
212A LYS 5.0 6.7 - - - -
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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