Contacts of the helix formed by residues 172 - 178 (chain C) in PDB entry 1YA8
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 LEU 172 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C CYS* 4.2 18.3 - - + +
88C THR 4.2 7.5 + - - +
89C GLN* 3.9 12.1 - - + +
140C HIS* 4.2 3.4 - - + +
144C LEU* 3.4 23.1 - - - +
145C MET 3.5 12.8 - - - +
146C VAL 3.7 21.1 - - - +
147C GLY 3.6 24.0 - - - +
170C TYR* 3.5 42.0 - - + +
171C ARG* 1.3 74.4 - - - +
173C GLY* 1.3 69.5 + - - +
174C ILE 3.4 0.2 + - - -
175C TRP* 3.2 19.1 + - - +
176C GLY* 3.1 10.2 + - - -
177C PHE* 4.5 0.4 - - - -
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Residues in contact with GLY 173 (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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144C LEU 2.9 17.4 + - - -
145C MET* 4.1 27.9 + - - +
172C LEU* 1.3 71.1 - - - +
174C ILE* 1.3 55.7 + - - -
175C TRP* 5.0 2.0 - - - -
177C PHE* 2.7 41.7 + - - +
178C PHE 4.0 0.2 + - - -
298C THR* 6.2 1.3 - - - -
319C LEU* 4.6 6.7 - - - -
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Residues in contact with ILE 174 (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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65C PHE* 3.3 23.1 - - + -
145C MET* 5.4 0.2 - - - +
172C LEU 3.4 0.6 + - - -
173C GLY* 1.3 71.8 - - - -
175C TRP* 1.3 75.0 + - + +
178C PHE* 3.1 44.8 + - + +
268C ILE* 4.0 26.0 - - + -
286C LEU* 5.3 2.2 - - + -
294C LEU* 3.8 29.2 - - + +
297C THR* 4.2 12.6 - - + -
298C THR* 3.7 25.5 + - - +
301C MET* 5.5 2.9 - - + -
303C PHE* 5.3 8.3 - - + -
319C LEU* 4.4 11.4 - - + +
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Residues in contact with TRP 175 (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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64C ARG* 4.0 19.2 - - + +
65C PHE* 4.1 12.3 + - - -
88C THR* 3.1 53.8 - - + -
89C GLN* 4.8 1.3 - - - -
114C GLU* 2.9 40.6 + - + -
171C ARG* 3.8 27.2 + - + -
172C LEU 3.2 15.3 + - - +
173C GLY* 5.5 0.9 - - - -
174C ILE* 1.3 84.9 - - + +
176C GLY* 1.3 59.1 + - - +
189C TRP* 3.3 16.1 - - - -
291C GLU* 3.5 22.2 - - + -
294C LEU* 3.5 25.7 - - + +
295C LEU* 3.9 20.2 - - + -
298C THR* 4.1 14.6 - - + -
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Residues in contact with GLY 176 (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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171C ARG* 3.4 28.9 - - - +
172C LEU 3.1 9.7 + - - -
173C GLY 3.8 0.9 - - - -
175C TRP* 1.3 77.0 - - - +
177C PHE* 1.3 69.4 + - - +
189C TRP* 3.1 18.0 + - - -
190C GLY 2.9 21.1 + - - -
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Residues in contact with PHE 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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144C LEU* 3.7 46.7 - - + -
170C TYR* 4.8 1.8 - + - -
171C ARG 3.6 19.1 - - - -
173C GLY* 2.7 30.3 + - - +
176C GLY* 1.3 90.1 - - - +
178C PHE* 1.3 65.4 + - - +
179C SER* 3.3 8.9 + - - -
187C GLY* 4.9 0.9 - - - -
188C ASN* 4.2 14.6 - - - +
189C TRP* 4.4 1.6 - - - -
190C GLY* 3.8 17.7 - - - -
191C HIS* 3.7 31.4 - + - -
319C LEU* 4.2 18.8 - - + +
320C GLY* 3.3 40.9 + - - +
322C VAL* 5.3 1.0 - - - +
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Residues in contact with PHE 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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65C PHE* 3.8 21.5 - + + -
173C GLY 4.0 0.6 + - - -
174C ILE* 3.1 26.0 + - + +
176C GLY 4.0 0.2 - - - -
177C PHE* 1.3 75.5 - - - +
179C SER* 1.3 60.4 + - - +
180C THR* 3.8 29.8 - - + -
185C SER* 3.1 25.2 + - - +
187C GLY* 3.9 0.5 - - - -
189C TRP* 3.1 15.7 + - - +
265C ALA* 3.9 34.1 - - + -
268C ILE* 4.0 25.1 - - + -
282C MET* 4.8 7.4 - - + -
283C VAL* 4.3 11.9 - - + -
286C LEU* 3.5 32.1 - - + -
319C LEU* 4.4 6.7 - - + +
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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