Contacts of the helix formed by residues 177 - 182 (chain C) in PDB entry 3O9Z
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 GLY 177 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C LYS 5.0 2.9 - - - -
170C VAL* 6.0 2.0 - - - -
172C GLU* 3.7 19.2 - - - +
175C SER* 2.9 13.9 + - - -
176C GLY* 1.3 77.8 - - - +
178C LEU* 1.3 61.5 + - - -
179C ALA 3.3 2.5 - - - -
180C THR 3.0 2.3 + - - -
181C ASN* 2.8 29.8 + - - +
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Residues in contact with LEU 178 (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 TYR* 4.0 12.3 - - + +
169C LYS 5.7 0.2 - - - -
177C GLY* 1.3 71.4 - - - -
179C ALA* 1.3 58.5 + - - +
181C ASN* 4.5 2.0 - - - +
182C ILE* 3.0 53.7 + - + +
183C GLY 3.1 4.7 + - - -
206C THR 4.5 1.8 - - - +
207C PRO 3.9 10.8 - - - +
208C THR 3.8 31.2 - - - +
209C VAL 3.9 4.0 - - - +
210C ASN* 4.0 27.0 - - - +
225C LEU* 3.6 15.1 - - + +
226C SER* 5.0 0.4 - - - -
227C ILE* 3.8 23.6 - - + -
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Residues in contact with ALA 179 (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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176C GLY 5.8 0.7 - - - +
177C GLY 3.3 0.2 - - - -
178C LEU* 1.3 78.5 - - - +
180C THR* 1.3 58.5 + - - +
183C GLY* 3.1 23.4 - - - -
184C ILE* 3.3 0.7 + - - -
187C PHE* 3.5 24.1 - - + -
210C ASN* 3.3 23.9 - - + +
223C TRP* 5.0 1.1 - - + -
225C LEU* 3.7 13.0 - - + -
289C ALA* 4.3 5.2 - - - +
292C LEU* 4.4 20.6 - - + -
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Residues in contact with THR 180 (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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102C PRO* 3.6 27.8 - - + +
104C VAL 5.5 0.2 - - - +
105C LEU* 3.9 1.6 - - + -
175C SER 3.5 13.2 - - - +
176C GLY 3.2 20.4 + - - -
177C GLY 3.0 2.6 + - - -
179C ALA* 1.3 79.3 - - - +
181C ASN* 1.3 67.1 + - - +
182C ILE 3.4 0.2 - - - -
184C ILE* 3.1 30.9 + - + +
289C ALA* 3.5 20.2 + - + +
293C ARG* 2.8 32.9 + - - +
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Residues in contact with ASN 181 (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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80C ASN* 2.9 24.9 + - - +
101C LYS* 2.6 32.3 + - - +
102C PRO* 5.0 0.2 - - - -
164C TYR* 3.0 28.2 + - - +
168C TRP* 3.7 6.7 - - - -
169C LYS* 3.8 18.7 - - - +
175C SER* 3.8 20.2 - - - +
177C GLY 2.8 20.8 + - - +
178C LEU 4.5 0.4 - - - +
180C THR* 1.3 75.8 - - - +
182C ILE* 1.3 64.6 + - - +
311C NAD 3.3 16.5 + - - -
312C AKG 3.7 8.0 + - - +
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Residues in contact with ILE 182 (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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156C TYR* 3.6 22.6 - - + -
158C THR* 3.6 11.9 - - + -
160C ARG* 4.0 11.7 - - - +
164C TYR* 3.6 29.4 - - + +
178C LEU* 3.0 22.3 + - + +
181C ASN* 1.3 80.3 - - - +
183C GLY* 1.3 67.5 + - - +
184C ILE 3.1 3.6 + - - -
185C HIS* 3.4 22.5 + - - +
225C LEU* 3.6 24.7 - - + -
227C ILE* 4.1 7.2 - - + -
312C AKG 3.6 29.4 - - + +
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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