Contacts of the helix formed by residues 164 - 174 (chain C) in PDB entry 1YPO
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 ASN 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C PHE* 1.3 75.6 - - - +
165C TRP* 1.3 53.6 + - - +
166C GLU* 3.3 7.9 + - - +
167C LYS* 2.8 58.6 + - - +
168C SER* 2.7 34.5 + - - -
203C TRP* 3.6 0.9 - - - -
256C CYS 3.3 15.9 - - - +
257C ILE* 3.6 24.5 + - - +
258C LEU 3.4 8.5 - - - -
259C ALA* 4.2 1.8 - - - +
174E SER 4.8 10.3 + - - -
176E ASP* 5.2 3.6 + - - -
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Residues in contact with TRP 165 (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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164C ASN* 1.3 73.3 - - - +
166C GLU* 1.3 64.0 + - + +
168C SER* 3.5 2.6 - - - -
169C GLN* 2.9 58.7 + - - +
179C LEU* 3.5 13.4 - - + +
203C TRP* 3.2 43.6 - + + +
204C MET 2.5 26.1 + - - -
205C GLY* 3.3 29.4 - - - -
206C LEU 3.8 3.2 + - - -
207C SER* 3.7 18.2 - - - -
218C GLU* 3.8 7.4 - - + -
243C CYS* 3.2 37.0 - - + -
256C CYS* 3.4 12.2 + - + +
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Residues in contact with GLU 166 (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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164C ASN* 3.2 8.3 + - - +
165C TRP* 1.3 81.9 - - + +
167C LYS* 1.3 78.7 + - - +
169C GLN* 2.9 32.6 + - - +
170C GLU* 3.0 26.9 + - + +
256C CYS* 4.5 2.9 + - + +
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Residues in contact with LYS 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PHE* 3.9 19.7 - - + -
164C ASN* 2.8 50.9 + - - +
166C GLU* 1.3 98.8 + - - +
168C SER* 1.3 56.8 + - - +
170C GLU* 3.3 21.6 + - - +
171C LYS* 3.0 45.1 + - + +
176E ASP* 4.6 18.3 + - - +
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Residues in contact with SER 168 (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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163C PHE* 3.5 22.3 + - - +
164C ASN 2.7 17.7 + - - -
165C TRP* 3.5 9.9 - - - -
167C LYS* 1.3 73.9 - - - +
169C GLN* 1.3 66.7 + - - +
171C LYS* 3.3 8.2 + - - +
172C CYS* 3.2 27.0 + - - -
179C LEU* 4.2 7.4 - - - -
203C TRP* 3.6 8.1 - - - -
260C ALA 4.1 1.7 + - - -
262C SER* 3.5 29.0 + - - -
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Residues in contact with GLN 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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165C TRP* 2.9 34.9 + - + +
166C GLU* 2.9 22.8 + - - +
168C SER* 1.3 76.3 - - - +
170C GLU* 1.3 61.7 + - + +
172C CYS* 3.3 11.8 + - - +
173C LEU* 3.3 25.2 + - + +
179C LEU* 4.1 7.9 - - + -
218C GLU* 3.0 46.0 + - - +
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Residues in contact with GLU 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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166C GLU* 3.0 23.0 + - + +
167C LYS* 3.5 36.0 + - - +
169C GLN* 1.3 77.9 - - + +
171C LYS* 1.3 66.2 + - + +
172C CYS 3.2 0.3 + - - -
173C LEU* 3.2 12.2 + - + +
174C SER* 3.1 22.8 + - - -
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Residues in contact with LYS 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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159C SER* 6.4 2.5 - - - -
163C PHE* 3.6 44.7 - - + -
167C LYS* 3.0 36.8 + - + +
168C SER* 3.3 12.3 + - - +
170C GLU* 1.3 79.3 - - + +
172C CYS* 1.3 58.4 + - - +
174C SER* 2.5 24.9 + - - +
175C LEU* 3.4 13.7 - - - +
264C CYS* 4.6 4.3 - - - -
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Residues in contact with CYS 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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168C SER 3.2 9.8 + - - -
169C GLN 3.6 7.9 - - - +
170C GLU 3.1 1.2 - - - -
171C LYS* 1.3 75.0 - - - +
173C LEU* 1.3 66.0 + - - +
175C LEU* 2.9 14.2 + - - +
176C ASP 3.4 0.2 + - - -
177C ALA* 3.0 19.1 + - - +
178C LYS* 3.7 18.8 - - - -
179C LEU* 3.5 34.5 - - - +
262C SER* 5.1 1.1 - - - -
264C CYS* 2.0 52.3 - - + -
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Residues in contact with LEU 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 GLN* 3.5 24.5 - - + +
170C GLU* 3.2 11.4 + - + +
172C CYS* 1.3 76.2 - - - +
174C SER* 1.3 56.2 + - - +
176C ASP* 2.5 31.4 + - - +
177C ALA 3.2 16.1 + - - +
178C LYS* 4.9 8.1 - - + -
218C GLU* 5.5 2.2 - - - +
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Residues in contact with SER 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 GLU 3.1 10.3 + - - -
171C LYS* 2.5 28.1 + - - +
173C LEU* 1.3 78.9 - - - +
175C LEU* 1.3 67.8 + - - +
176C ASP* 3.2 5.6 + - - +
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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