Contacts of the helix formed by residues 164 - 172 (chain C) in PDB entry 1U75
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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162C ASN 4.4 0.4 + - - -
163C MET* 1.3 73.9 - - - +
165C ASP* 1.3 55.7 + - - +
166C ARG* 3.0 43.2 - - - +
167C GLU* 2.9 51.3 + - - +
168C VAL* 3.0 14.1 + - - +
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Residues in contact with ASP 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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155C ARG* 2.7 50.9 + - - +
164C ASN* 1.3 72.8 - - - +
166C ARG* 1.3 57.9 + - - +
168C VAL* 3.8 2.8 + - - +
169C VAL* 3.2 31.5 + - - +
243C LYS* 4.1 10.3 + - - +
244C TYR* 3.6 18.2 - - + -
247C ILE* 3.8 16.0 - - + +
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Residues in contact with ARG 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* 3.0 16.3 - - - +
165C ASP* 1.3 77.7 - - - +
167C GLU* 1.3 60.3 + - + +
169C VAL* 3.7 1.6 + - - +
170C ALA* 3.1 28.3 + - - +
247C ILE* 3.9 24.4 - - + +
250C GLU* 2.7 46.0 + - - -
251C TYR* 3.7 20.8 + - - +
257C LYS* 3.6 26.7 - - - +
261C ASP* 3.3 17.2 + - - +
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Residues in contact with GLU 167 (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 MET* 3.5 23.2 - - - -
164C ASN* 2.9 42.6 + - - +
166C ARG* 1.3 75.8 - - + +
168C VAL* 1.3 60.1 + - - +
170C ALA* 3.5 6.2 + - - +
171C LEU* 2.9 34.5 + - - +
261C ASP 5.8 0.2 - - - -
264C LYS* 5.5 1.6 - - - +
265C ALA* 4.1 16.4 + - + +
268C LYS* 3.0 40.4 + - - +
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Residues in contact with VAL 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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154C VAL* 4.2 14.4 - - + -
155C ARG* 5.9 1.1 - - - +
158C PHE* 3.8 38.6 - - + -
163C MET* 4.1 7.2 - - + +
164C ASN 3.0 23.1 - - - +
165C ASP* 3.8 2.7 + - - +
167C GLU* 1.3 72.5 - - - +
169C VAL* 1.3 64.6 + - + +
171C LEU* 3.3 5.9 + - - +
172C MET* 3.0 39.4 + - + +
238C LEU* 4.6 1.3 - - + -
244C TYR* 3.6 35.2 - - + +
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Residues in contact with VAL 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 ASP 3.2 20.4 + - - +
166C ARG 4.1 0.4 - - - +
168C VAL* 1.3 76.6 - - - +
170C ALA* 1.3 53.1 + - - +
172C MET* 3.6 2.8 + - - +
173C GLY 3.6 6.1 + - - -
203C TYR* 2.5 36.9 + - + -
238C LEU* 4.0 19.1 - - + -
244C TYR* 3.5 32.5 - - + +
247C ILE* 3.8 27.8 - - + -
248C VAL* 3.7 26.7 - - + +
251C TYR* 4.1 2.2 - - + -
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Residues in contact with ALA 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 ARG 3.1 19.4 + - - +
167C GLU* 3.6 7.6 - - - +
169C VAL* 1.3 75.4 - - - +
171C LEU* 1.3 64.0 + - - +
173C GLY 3.2 3.5 + - - -
203C TYR* 3.5 5.8 - - - -
251C TYR* 3.7 19.0 - - + +
258C PHE* 3.2 14.5 - - + -
261C ASP* 4.1 26.5 - - + +
262C PHE* 3.1 22.1 - - - +
265C ALA* 4.8 0.7 - - + -
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Residues in contact with LEU 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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158C PHE* 4.4 20.6 - - + -
163C MET* 4.4 15.3 - - + -
167C GLU 2.9 20.1 + - - +
168C VAL* 3.3 4.9 + - - +
170C ALA* 1.3 76.0 - - - +
172C MET* 1.3 61.9 + - - +
173C GLY 3.2 1.0 + - - -
174C ALA* 3.3 21.3 + - - +
262C PHE* 3.6 11.5 - - + -
265C ALA* 3.8 34.3 - - + +
266C PHE* 3.8 22.4 - - + +
269C LEU* 4.2 25.1 - - + -
1201C ZNH 3.6 21.6 - - + +
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Residues in contact with MET 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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154C VAL* 4.1 15.0 - - + -
158C PHE* 3.9 16.4 - - + -
168C VAL* 3.0 22.7 + - + +
169C VAL 3.8 2.0 - - - +
170C ALA 3.3 0.2 - - - -
171C LEU* 1.3 71.1 - - - +
173C GLY* 1.3 60.6 + - - +
174C ALA 3.1 5.6 - - - -
175C HIS* 3.2 25.4 + - - +
202C PHE* 3.7 7.9 - - + -
234C THR 5.1 2.9 - - - +
235C ASP* 3.6 24.5 - - - +
238C LEU* 3.8 32.1 - - + -
1201C ZNH 3.7 56.1 - - + -
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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