Contacts of the helix formed by residues 168 - 175 (chain C) in PDB entry 1SHZ
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 TRP 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A PHE* 6.5 0.9 - - + -
235A GLU* 5.9 2.9 - - - -
60C MET 4.6 6.1 - - - -
61C ALA* 4.6 6.1 - - + -
64C GLN* 2.7 37.2 - - - +
167C PRO* 1.3 74.8 - - + +
169C GLU* 1.3 64.1 + - - +
170C GLN* 3.1 4.4 + - - +
171C GLU* 3.2 25.6 + - + +
172C LEU* 2.9 30.6 + - + +
197C LEU* 3.4 48.5 + - + +
200C HIS* 3.5 52.3 - + + -
201C LEU* 5.6 2.1 - - - +
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Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LYS* 3.7 34.0 + - + +
161C ARG* 3.1 37.1 + - - +
164C GLY* 3.4 27.6 - - - +
166C THR* 3.2 32.6 + - - +
167C PRO 3.1 4.4 + - - +
168C TRP* 1.3 77.2 - - - +
170C GLN* 1.3 54.6 + - - +
172C LEU* 3.4 8.8 - - + +
173C ALA* 2.7 37.5 + - - +
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Residues in contact with GLN 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LYS* 5.1 21.0 - - + +
168C TRP* 4.8 0.9 - - - -
169C GLU* 1.3 80.1 - - - +
171C GLU* 1.3 71.4 + - + +
173C ALA* 3.6 4.9 - - - +
174C GLN* 2.8 48.6 + - - +
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Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TRP* 3.2 43.1 + - + +
170C GLN* 1.3 99.0 - - + +
172C LEU* 1.3 63.8 + - + +
174C GLN* 3.8 11.0 - - - +
175C LEU* 3.0 25.8 + - - +
193C VAL* 4.5 22.0 - - + +
196C ARG* 5.5 13.7 - - - +
197C LEU* 4.2 11.2 - - + +
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PHE* 4.8 5.2 - - + -
57C ALA* 4.2 17.7 - - + +
58C HIS* 3.8 30.3 - - + +
61C ALA* 3.9 32.1 - - + -
157C PHE* 5.1 1.8 - - + -
161C ARG* 4.1 27.8 - - - +
166C THR* 5.7 0.4 - - - +
167C PRO 4.8 2.0 - - - +
168C TRP* 2.9 24.7 + - + +
169C GLU* 3.4 11.7 - - + +
171C GLU* 1.3 77.9 - - + +
173C ALA* 1.3 62.5 + - - +
175C LEU* 3.2 14.9 + - + +
176C GLU* 3.4 22.2 + - - +
193C VAL* 6.3 0.9 - - + -
197C LEU* 5.3 5.2 - - + -
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Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLU 2.7 22.0 + - - +
170C GLN* 3.6 5.4 - - - +
172C LEU* 1.3 68.5 - - - +
174C GLN* 1.3 54.4 + - - +
175C LEU 3.0 5.2 - - - -
176C GLU* 2.7 41.2 + - - +
177C ALA* 3.2 8.5 + - - +
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Residues in contact with GLN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLN* 2.8 33.9 + - - +
171C GLU* 3.8 10.5 - - - +
173C ALA* 1.3 73.7 - - - +
175C LEU* 1.3 58.1 + - - +
176C GLU 3.1 1.6 + - - -
177C ALA* 4.0 16.4 + - - +
178C TRP* 4.8 1.7 - - - +
189C ARG* 3.9 12.9 + - - +
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA* 3.6 31.0 - - + -
58C HIS* 5.2 8.7 - - + +
171C GLU 3.0 16.3 + - - +
172C LEU* 3.5 9.2 - - + +
173C ALA 3.0 1.0 - - - -
174C GLN* 1.3 76.8 - - - +
176C GLU* 1.3 59.7 + - - +
178C TRP* 4.4 3.7 - - - +
186C TYR* 3.2 39.0 + - + +
189C ARG* 3.1 34.1 - - - +
190C GLU* 4.0 22.7 - - + +
193C VAL* 4.1 23.8 - - + -
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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