Contacts of the helix formed by residues 164 - 174 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D PHE* 1.3 81.6 - - - +
165D TRP* 1.3 63.8 + - - +
166D GLU* 2.9 18.4 + - - +
167D LYS* 2.7 56.7 + - - +
168D SER* 3.2 17.2 + - - -
203D TRP* 3.7 0.7 - - - -
256D CYS 3.4 10.8 - - - +
257D ILE* 3.9 19.1 - - - +
258D LEU 3.5 11.7 - - - -
259D ALA* 3.9 3.2 - - + +
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Residues in contact with TRP 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASN* 1.3 70.1 - - - +
166D GLU* 1.3 70.6 + - + +
168D SER* 4.2 1.2 - - - -
169D GLN* 3.2 52.6 + - - +
179D LEU* 3.7 20.3 - - + +
203D TRP* 3.5 45.8 - + + +
204D MET 3.1 22.8 + - - -
205D GLY* 4.4 2.7 - - - -
206D LEU 4.0 5.1 + - - -
207D SER* 4.0 18.8 - - - -
218D GLU* 3.8 15.3 - - + -
243D CYS* 3.1 31.4 - - + -
256D CYS* 3.0 21.5 + - + +
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASN* 2.9 11.0 + - - +
165D TRP* 1.3 86.8 - - + +
167D LYS* 1.3 76.9 + - - +
169D GLN* 3.1 14.2 - - - +
170D GLU* 3.0 42.9 + - + +
256D CYS* 5.4 1.2 - - - +
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Residues in contact with LYS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D PHE* 3.5 29.8 - - + -
164D ASN* 2.7 39.7 + - - +
166D GLU* 1.3 79.0 + - - +
168D SER* 1.3 56.5 + - - +
169D GLN 2.9 3.8 - - - -
170D GLU* 2.6 44.3 + - - +
171D LYS* 3.0 21.8 + - - +
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Residues in contact with SER 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D GLY 5.4 0.5 + - - -
163D PHE* 3.5 20.7 + - - +
164D ASN 3.2 16.0 + - - -
165D TRP 4.2 2.7 - - - -
167D LYS* 1.3 77.8 - - - +
169D GLN* 1.3 60.5 + - - +
171D LYS* 3.8 9.4 + - - +
172D CYS* 3.3 26.7 + - - -
179D LEU* 3.8 5.7 - - - +
203D TRP* 3.7 11.7 - - - -
260D ALA 3.7 3.6 + - - -
261D PHE 4.6 0.2 - - - -
262D SER* 3.5 31.7 + - - -
264D CYS* 4.5 0.3 - - - -
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Residues in contact with GLN 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D TRP* 3.2 40.9 + - + +
166D GLU* 3.1 20.2 + - - +
167D LYS 2.7 4.4 + - - -
168D SER* 1.3 74.5 - - - +
170D GLU* 1.3 65.5 + - - +
172D CYS* 3.1 15.1 + - - +
173D LEU* 3.3 26.8 + - + +
179D LEU* 3.7 16.8 - - + +
218D GLU* 3.1 27.9 + - - +
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D GLU* 3.2 40.0 - - + +
167D LYS* 2.6 27.6 + - - +
169D GLN* 1.3 80.4 - - + +
171D LYS* 1.3 57.9 + - + +
172D CYS 3.2 0.9 - - - -
173D LEU* 3.4 14.6 + - + +
174D SER* 2.9 26.0 + - - -
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Residues in contact with LYS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D PHE* 4.2 38.6 - - + -
167D LYS* 3.0 22.7 + - - +
168D SER* 3.8 7.8 + - - +
169D GLN 3.3 0.2 - - - -
170D GLU* 1.3 77.2 - - + +
172D CYS* 1.3 62.1 + - - +
173D LEU 3.4 0.2 - - - -
174D SER* 3.5 13.0 - - - +
175D LEU* 3.5 29.4 + - + +
264D CYS* 4.5 2.8 - - - -
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Residues in contact with CYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D SER 3.3 17.7 + - - -
169D GLN 3.1 9.6 + - - +
171D LYS* 1.3 77.2 - - - +
173D LEU* 1.3 56.6 + - + +
174D SER 3.2 0.4 - - - -
175D LEU* 3.2 4.8 + - - +
176D ASP 3.1 7.6 + - - -
177D ALA* 2.7 44.6 + - - +
178D LYS* 4.3 0.2 - - - -
179D LEU* 3.5 31.0 - - - +
264D CYS* 2.0 52.5 - - + -
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D GLN* 3.3 29.6 + - + +
170D GLU* 3.8 15.0 - - + +
172D CYS* 1.3 72.3 - - - +
174D SER* 1.3 57.8 + - - +
175D LEU 2.9 5.6 - - - -
176D ASP* 3.0 18.1 + - - +
177D ALA 3.2 19.3 - - - +
178D LYS* 5.0 5.4 - - + -
218D GLU* 5.7 3.6 - - - +
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Residues in contact with SER 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D GLU 2.9 19.1 + - - -
171D LYS* 3.5 18.6 - - - +
172D CYS 3.2 0.2 - - - -
173D LEU* 1.3 76.1 - - - +
175D LEU* 1.3 65.0 + - - +
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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