Contacts of the helix formed by residues 165 - 171 (chain C) in PDB entry 1AUT
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 HIS 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C VAL 3.5 3.5 + - - -
164C PRO* 1.3 70.7 - - - +
166C ASN* 1.3 77.8 + - - +
168C CYS* 3.0 10.1 + - - +
169C SER* 3.0 33.8 + - - -
176C VAL* 2.9 40.2 + - + +
177C SER 3.2 22.9 + - - -
178C GLU* 3.7 28.2 + - + +
180C MET 4.3 6.1 + - - -
182C CYS* 5.7 1.1 - - - -
230C LYS* 5.3 0.6 + - - +
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Residues in contact with ASN 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 PRO* 3.4 4.5 - - + +
165C HIS* 1.3 87.8 - - - +
167C GLU* 1.3 64.1 + - + +
169C SER* 3.4 9.0 + - - -
170C GLU* 3.2 34.4 + - - +
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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
----------------------------------------------------------
163C VAL* 5.1 0.4 - - + -
164C PRO* 3.2 33.1 + - + +
165C HIS 3.2 0.6 - - - -
166C ASN* 1.3 75.0 - - + +
168C CYS* 1.3 67.1 + - - +
170C GLU* 3.2 32.7 + - - +
171C VAL* 3.3 17.3 + - - +
185C LEU* 6.1 0.2 - - - +
225C TYR* 4.2 19.5 + - + +
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Residues in contact with CYS 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 VAL* 4.0 1.6 - - + -
164C PRO 3.1 8.4 + - - +
165C HIS* 3.0 10.7 + - - +
167C GLU* 1.3 77.8 - - - +
169C SER* 1.3 61.6 + - - +
171C VAL* 3.0 4.9 + - - +
172C MET* 2.9 44.0 + - - +
176C VAL* 4.0 5.2 - - + -
182C CYS* 2.0 54.5 - - + -
225C TYR* 3.9 19.0 - - - -
227C VAL* 4.5 1.3 - - - -
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C HIS* 3.0 34.7 + - - -
166C ASN* 3.6 9.2 - - - -
168C CYS* 1.3 75.4 - - - +
170C GLU* 1.3 61.7 + - - +
172C MET 3.3 15.8 - - - +
174C ASN 5.2 1.6 - - - +
176C VAL* 3.9 20.7 + - - +
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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
----------------------------------------------------------
166C ASN* 3.2 23.5 + - - +
167C GLU* 3.4 28.5 - - - +
168C CYS 3.2 0.2 - - - -
169C SER* 1.3 77.6 - - - +
171C VAL* 1.3 65.9 + - + +
172C MET 4.6 1.0 - - - +
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Residues in contact with VAL 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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167C GLU 3.3 6.9 + - - +
168C CYS 3.0 11.5 + - - +
170C GLU* 1.3 84.0 - - + +
172C MET* 1.3 64.7 + - - +
173C SER 3.9 1.0 + - - -
185C LEU* 4.9 9.0 - - + -
217C GLU* 4.4 2.6 - - - +
223C HIS* 3.7 24.4 + - - +
224C ASN* 4.0 18.6 + - - +
225C TYR* 3.4 40.4 - - + -
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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