Contacts of the helix formed by residues 176 - 181 (chain C) in PDB entry 1UU1
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 TYR 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASN* 3.0 17.3 + - - -
147C PRO* 3.9 39.5 - - + +
148C ASN 5.0 0.2 - - - -
149C ASN* 3.3 14.3 + - + -
174C GLU* 3.0 1.4 - - - +
175C ALA* 1.3 85.3 - - + +
177C TYR* 1.3 63.1 + - - +
178C GLU* 3.4 2.7 - - - -
179C PHE* 3.3 23.7 + + + +
180C HIS* 3.3 13.3 + - - +
202C LYS* 2.7 33.3 + - + -
281C GLY* 4.1 9.0 - - - -
282C ASN* 3.3 25.8 - - - -
283C PHE* 3.9 19.3 - + - -
1335C PMP 2.7 40.8 + + + -
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Residues in contact with TYR 177 (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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68C TYR* 3.9 13.4 + + - -
146C ASN 5.3 0.4 - - - -
147C PRO* 4.3 3.3 - - - +
174C GLU* 3.0 25.1 + - + +
175C ALA 3.5 0.6 - - - -
176C TYR* 1.3 75.6 - - - +
178C GLU* 1.3 86.4 + - + +
180C HIS* 2.8 10.3 + - - -
181C GLY* 2.7 59.3 + - - -
182C GLU 3.9 11.0 - - - -
183C SER* 3.6 28.2 - - - -
198C ARG* 3.4 36.7 + - - +
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Residues in contact with GLU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 2.8 35.1 + - - +
174C GLU 4.4 1.6 - - - +
175C ALA 4.2 8.5 - - - +
176C TYR 3.4 0.4 - - - -
177C TYR* 1.3 100.1 + - - +
179C PHE* 1.3 61.6 + - + +
180C HIS 3.5 0.3 + - - -
181C GLY* 4.4 4.4 + - - -
198C ARG* 4.3 4.9 + - - +
199C THR 4.7 9.9 + - - +
203C ALA* 3.2 36.6 - - + +
204C PHE* 4.3 9.8 - - + -
213C TYR* 4.4 2.8 + - - -
255C THR* 3.2 22.7 - - + +
259C VAL* 5.0 0.5 - - - +
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Residues in contact with PHE 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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29C ASN* 4.7 2.5 - - - -
175C ALA 4.9 0.9 - - - -
176C TYR* 3.3 20.3 + + - +
177C TYR 3.2 0.6 - - - -
178C GLU* 1.3 76.8 - - + +
180C HIS* 1.3 58.6 + - - +
202C LYS* 3.6 27.8 - - + -
203C ALA* 3.7 28.7 - - + -
255C THR* 3.5 32.8 - - + -
258C ILE* 4.1 24.5 - - + -
259C VAL* 3.9 12.5 - - + +
262C ARG* 3.2 23.1 + - - +
280C ARG* 3.4 6.6 - - - +
281C GLY 3.6 16.8 - - - +
282C ASN* 3.6 39.0 - - + -
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Residues in contact with HIS 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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146C ASN* 4.3 3.8 + - - -
147C PRO* 3.6 23.7 - - + +
154C VAL* 3.3 26.8 - - + +
176C TYR 3.3 10.7 + - - +
177C TYR 2.8 8.5 + - - +
178C GLU 4.7 0.4 - - - -
179C PHE* 1.3 80.9 - - - +
181C GLY* 1.3 58.1 + - - +
182C GLU* 3.3 54.7 + - + +
280C ARG* 3.7 34.2 + - + +
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Residues in contact with GLY 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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177C TYR* 2.7 37.6 + - - -
178C GLU 4.4 3.9 + - - -
180C HIS* 1.3 72.1 - - - +
182C GLU* 1.3 57.5 + - - +
183C SER 4.0 0.5 + - - -
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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