Contacts of the helix formed by residues 164 - 175 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163H PHE* 1.3 77.7 - - - +
165H TRP* 1.3 59.9 + - - +
166H GLU* 2.9 18.8 + - - +
167H LYS* 2.7 53.9 + - - +
168H SER* 2.7 29.3 + - - -
203H TRP* 3.6 2.2 - - - -
256H CYS 3.2 12.8 - - - +
257H ILE* 4.0 17.9 - - - +
258H LEU 3.4 10.3 - - - -
259H ALA* 4.2 0.6 - - - +
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Residues in contact with TRP 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H ASN* 1.3 75.0 - - - +
166H GLU* 1.3 60.7 + - + +
168H SER* 3.2 2.9 + - - -
169H GLN* 2.8 67.6 + - - +
179H LEU* 3.7 10.6 - - + +
203H TRP* 3.5 33.0 - + + +
204H MET 2.7 29.0 + - - -
205H GLY* 3.8 18.8 - - - -
206H LEU 4.4 1.4 + - - -
207H SER* 3.8 20.4 - - - -
217H TRP 6.0 0.2 - - - -
218H GLU* 3.9 10.5 - - + -
243H CYS* 3.3 44.6 - - + +
244H ALA 4.5 0.4 + - - -
256H CYS* 3.0 16.2 + - + +
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Residues in contact with GLU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164H ASN* 2.9 14.2 + - - +
165H TRP* 1.3 80.2 - - + +
167H LYS* 1.3 67.9 + - + +
169H GLN* 3.0 23.8 + - - +
170H GLU* 3.0 30.3 + - + +
256H CYS* 4.7 1.4 + - - +
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Residues in contact with LYS 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H PHE* 3.5 32.1 - - + -
164H ASN* 2.7 36.0 + - - +
166H GLU* 1.3 75.2 - - - +
168H SER* 1.3 59.0 - - - +
170H GLU* 2.8 45.3 + - - +
171H LYS* 2.9 21.7 + - + +
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Residues in contact with SER 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H PHE* 3.7 14.2 + - - +
164H ASN 2.7 22.8 + - - -
165H TRP* 3.4 5.2 - - - -
167H LYS* 1.3 75.9 - - - +
169H GLN* 1.3 60.0 + - - +
171H LYS* 3.6 10.7 - - - +
172H CYS* 3.4 27.9 + - - -
179H LEU* 4.0 5.9 - - - +
203H TRP* 3.5 18.2 - - - -
260H ALA 3.9 5.4 + - - -
262H SER* 3.6 25.3 + - - -
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Residues in contact with GLN 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H TRP* 2.8 38.1 + - + +
166H GLU* 3.1 20.6 - - - +
168H SER* 1.3 76.6 - - - +
170H GLU* 1.3 64.5 + - + +
172H CYS* 3.4 4.0 + - - +
173H LEU* 3.0 26.1 + - + +
179H LEU* 4.0 12.6 - - + -
218H GLU* 2.5 37.1 + - - +
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Residues in contact with GLU 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H GLU* 3.0 24.2 + - + +
167H LYS* 2.8 48.2 + - - +
169H GLN* 1.3 73.3 - - + +
171H LYS* 1.3 57.2 + - + +
173H LEU* 2.9 15.9 + - + +
174H SER* 2.7 35.9 + - - -
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Residues in contact with LYS 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H SER* 6.1 3.6 - - - -
163H PHE* 3.6 45.0 - - + -
167H LYS* 2.9 23.7 + - - +
168H SER* 3.6 12.6 - - - +
170H GLU* 1.3 76.8 - - + +
172H CYS* 1.3 64.6 + - - +
174H SER* 3.0 24.1 + - - +
175H LEU* 3.4 11.5 + - + +
262H SER* 5.4 3.1 - - - +
264H CYS* 4.7 3.8 - - - -
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Residues in contact with CYS 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H SER 3.4 6.3 + - - +
169H GLN 3.7 7.2 - - - +
170H GLU 3.2 0.4 - - - -
171H LYS* 1.3 77.9 - - - +
173H LEU* 1.3 66.7 + - - +
175H LEU* 2.9 16.8 + - - +
177H ALA* 3.2 16.3 + - - +
178H LYS* 3.7 19.5 - - - -
179H LEU* 3.5 29.4 - - + +
262H SER* 4.4 1.1 - - - -
264H CYS* 2.0 57.4 - - + -
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Residues in contact with LEU 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H GLN* 3.0 15.6 + - + +
170H GLU* 2.9 17.2 + - + +
172H CYS* 1.3 78.3 - - - +
174H SER* 1.3 54.2 + - - +
176H ASP* 2.6 30.7 + - - -
177H ALA 3.4 13.6 + - - +
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Residues in contact with SER 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H GLU 2.7 14.7 + - - -
171H LYS* 3.0 16.3 + - - +
173H LEU* 1.3 72.6 - - - +
175H LEU* 1.3 71.2 + - - +
176H ASP* 3.2 4.5 + - - +
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Residues in contact with LEU 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H TRP* 4.1 14.8 - - + +
157H LEU* 3.5 31.4 - - + -
171H LYS* 3.7 10.3 - - + +
172H CYS* 2.9 11.6 + - - +
173H LEU 2.9 0.2 + - - -
174H SER* 1.3 89.6 + - - +
176H ASP* 1.3 67.8 + - - +
177H ALA* 3.0 6.1 + - - +
264H CYS* 5.3 2.0 - - - -
266H LYS* 3.2 17.8 + - - -
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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