Contacts of the helix formed by residues 181 - 190 (chain E) in PDB entry 1QO0
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 PRO 181 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E ALA* 4.0 0.9 - - - +
179E ARG 4.6 1.3 - - - +
180E GLU* 1.3 95.3 - - + +
182E ILE* 1.3 60.5 + - + +
183E LEU* 3.1 11.2 - - + +
184E LYS* 2.9 32.4 + - + +
185E ILE 3.5 3.8 + - - -
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Residues in contact with ILE 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ILE* 4.3 23.5 - - + +
168E HIS* 4.4 14.8 - - + +
171E LEU* 3.9 23.3 - - + +
172E SER* 3.6 32.8 - - - +
175E ALA* 3.3 20.9 - - + +
180E GLU 3.6 0.4 + - - -
181E PRO* 1.3 73.2 - - + +
183E LEU* 1.3 62.8 + - + +
185E ILE* 3.5 4.9 + - - +
186E ALA* 3.3 20.3 + - - +
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Residues in contact with LEU 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ASP 5.8 0.9 - - - +
145E GLY* 3.9 26.9 - - - +
148E ARG* 3.8 27.4 - - + -
149E ILE* 3.9 17.5 - - + -
181E PRO* 3.1 6.9 - - + +
182E ILE* 1.3 80.4 - - + +
184E LYS* 1.3 62.1 + - - +
186E ALA* 3.5 1.7 + - + +
187E GLN* 3.1 46.4 + - + +
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Residues in contact with LYS 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E GLU* 4.0 19.7 - - + -
181E PRO* 2.9 25.2 + - + +
183E LEU* 1.3 78.6 - - - +
185E ILE* 1.3 54.9 + - - +
187E GLN* 3.2 10.2 + - - +
188E GLU* 2.9 36.5 + - - +
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Residues in contact with ILE 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E LEU* 4.1 23.8 - - + +
174E GLU* 5.0 12.3 - - + -
175E ALA* 4.8 9.9 - - + +
180E GLU* 5.6 1.0 - - - +
181E PRO 3.5 3.6 + - - +
182E ILE 3.5 10.9 + - - +
183E LEU 3.4 0.2 - - - -
184E LYS* 1.3 72.9 - - - +
186E ALA* 1.3 56.4 + - - +
188E GLU* 3.2 10.9 + - - +
189E LEU* 2.7 42.8 + - + +
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Residues in contact with ALA 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ARG* 3.6 14.6 - - + +
149E ILE* 4.1 13.9 - - + -
152E ALA* 3.5 26.9 - - + -
171E LEU* 4.2 6.6 - - + +
182E ILE 3.3 10.8 + - - +
183E LEU* 3.7 9.6 - - + +
184E LYS 3.3 0.2 - - - -
185E ILE* 1.3 80.5 - - - +
187E GLN* 1.3 51.0 + - - +
189E LEU* 3.4 2.0 - - - +
190E LEU* 2.5 42.4 + - - +
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Residues in contact with GLN 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ARG* 5.0 7.8 - - + +
183E LEU* 3.1 54.2 + - + +
184E LYS* 3.2 7.6 + - - +
186E ALA* 1.3 72.4 - - - +
188E GLU* 1.3 59.2 + - - +
190E LEU* 3.1 26.4 - - + +
191E GLY* 4.9 0.5 - - - -
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Residues in contact with GLU 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E LYS* 2.9 19.0 + - - +
185E ILE* 3.6 10.0 - - - +
187E GLN* 1.3 76.4 - - - +
189E LEU* 1.3 62.3 + - - +
190E LEU 3.7 3.1 - - - +
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Residues in contact with LEU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ALA* 4.4 9.9 - - + +
155E LEU* 4.1 15.4 - - + +
156E LEU* 3.7 29.6 - - + -
159E ARG* 3.5 34.9 + - - +
170E HIS* 5.3 4.9 - - + +
171E LEU* 3.7 30.1 - - + -
185E ILE* 2.7 20.2 + - + +
186E ALA 3.4 3.6 - - - +
188E GLU* 1.3 70.7 - - - +
190E LEU* 1.3 73.0 + - - +
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Residues in contact with LEU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ARG* 3.3 26.7 - - + +
151E GLN* 3.3 48.5 - - + +
152E ALA* 3.9 9.2 - - + +
155E LEU* 4.4 17.0 - - + -
186E ALA 2.5 25.2 + - - +
187E GLN* 3.1 18.1 - - - +
188E GLU 3.7 4.2 - - - +
189E LEU* 1.3 83.9 - - - +
191E GLY* 1.3 63.4 + - - +
192E ASN* 4.0 21.1 - - - +
194E PRO* 5.0 4.9 - - + -
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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