Contacts of the helix formed by residues 182 - 190 (chain X) in PDB entry 1SHU
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 GLU 182 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148X ASP 2.9 7.3 + - - -
149X GLY 3.4 29.8 - - - +
150X LYS* 4.1 16.8 - - + +
180X ASP 4.5 5.2 - - - +
181X PHE* 1.3 73.2 - - - +
183X GLN* 1.3 65.7 + - - +
184X ALA* 3.4 2.0 - - - +
185X GLN* 3.3 10.2 + - + +
186X LEU* 3.0 24.1 + - - +
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Residues in contact with GLN 183 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181X PHE* 3.2 40.8 + - + +
182X GLU* 1.3 70.3 - - - +
184X ALA* 1.3 66.3 + - - +
186X LEU* 3.2 4.8 + - - +
187X GLU* 2.8 59.5 + - - +
193X LYS* 5.0 4.4 + - - +
196X VAL* 3.9 17.2 + - - +
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Residues in contact with ALA 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X GLU* 3.4 1.4 + - - +
183X GLN* 1.3 79.5 - - - +
185X GLN* 1.3 63.1 + - - +
187X GLU* 3.2 16.7 + - - +
188X ARG* 3.0 44.8 + - - +
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Residues in contact with GLN 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149X GLY* 3.7 24.2 - - - +
151X LEU* 3.7 20.0 - - + +
156X PRO* 3.4 25.3 - - - +
159X ALA* 5.3 0.2 - - - +
160X GLU* 2.9 25.2 + - - +
182X GLU* 3.3 16.5 + - + +
184X ALA* 1.3 78.8 - - - +
186X LEU* 1.3 64.2 + - - +
188X ARG* 3.1 25.3 + - - +
189X ILE* 3.2 34.8 + - + +
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Residues in contact with LEU 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X THR* 3.6 31.9 - - + +
149X GLY* 3.7 16.6 - - - -
175X CYS* 3.6 29.3 - - + -
176X VAL 4.5 0.7 - - - -
177X GLY* 3.8 21.5 - - - +
181X PHE* 3.7 27.8 - - + -
182X GLU 3.0 15.1 + - - +
183X GLN 3.7 6.3 - - - +
185X GLN* 1.3 81.0 - - - +
187X GLU* 1.3 57.7 + - - +
189X ILE* 3.3 8.9 + - + -
190X ALA* 2.9 32.2 + - - +
196X VAL* 3.8 11.4 - - + -
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Residues in contact with GLU 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183X GLN* 2.8 53.5 + - - +
184X ALA* 3.5 15.6 - - - +
186X LEU* 1.3 76.3 - - - +
188X ARG* 1.3 61.7 + - + +
190X ALA 3.2 16.1 + - - +
191X ASP 4.8 0.2 - - - -
192X SER* 4.2 10.3 - - - -
193X LYS* 3.7 50.0 + - + +
196X VAL* 3.8 9.4 - - + -
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Residues in contact with ARG 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X PRO* 5.4 0.6 - - - +
160X GLU* 2.8 42.2 + - + +
163X ALA* 5.2 0.2 - - - +
167X ARG* 3.6 14.2 + - - -
184X ALA* 3.0 37.1 + - - +
185X GLN* 3.1 39.1 + - - +
186X LEU 3.2 0.4 - - - -
187X GLU* 1.3 79.1 - - + +
189X ILE* 1.3 60.2 - - - +
190X ALA 3.6 2.6 - - - +
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Residues in contact with ILE 189 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120X ILE* 4.5 17.5 - - + -
124X LEU* 4.4 12.1 - - + -
145X ALA* 5.3 1.8 - - + -
151X LEU* 4.5 5.6 - - + -
159X ALA* 4.1 26.2 - - + +
160X GLU* 4.6 6.1 - - + -
163X ALA* 3.4 20.6 - - + +
167X ARG* 2.9 23.4 + - - -
173X VAL* 3.5 12.0 - - + +
175X CYS* 3.7 15.7 - - - -
185X GLN* 3.2 41.3 + - + +
186X LEU* 3.9 10.8 - - + +
188X ARG* 1.3 75.4 - - - +
190X ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X ARG* 3.4 4.7 + - - -
173X VAL* 3.3 19.5 - - - +
175X CYS* 4.0 9.0 - - - +
186X LEU 2.9 17.3 + - - +
187X GLU 3.2 10.0 - - - +
188X ARG 3.6 4.0 - - - +
189X ILE* 1.3 84.5 - - - +
191X ASP* 1.3 66.9 + - - +
192X SER 3.2 17.8 + - - +
195X GLN* 4.0 8.1 - - + +
196X VAL* 3.9 10.3 - - + -
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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