Contacts of the strand formed by residues 185 - 189 (chain C) in PDB entry 1YAA
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 ILE 185 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C PHE* 3.7 39.0 - - + -
131C LYS* 4.0 18.4 - - + -
132C LEU 2.9 18.3 + - - +
133C VAL* 3.5 27.0 - - + -
134C TYR* 2.7 33.6 + - - +
147C PHE* 5.6 0.2 - - + -
184C SER* 1.3 71.2 - - - +
186C PHE* 1.3 59.4 + - - +
187C VAL* 3.7 4.7 + - + -
218C ILE* 3.5 43.3 - - + +
220C LEU* 4.5 17.7 - - + -
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Residues in contact with PHE 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C TYR* 3.8 25.4 - + + -
158C TYR* 3.7 40.2 - + + -
173C PHE* 4.8 3.6 - + - -
176C ALA 4.1 1.3 - - - -
177C ILE* 3.8 40.4 - - + -
180C ALA* 3.8 17.0 - - + -
184C SER* 4.0 3.8 - - - -
185C ILE* 1.3 75.2 - - - +
187C VAL* 1.3 61.3 + - - +
188C LEU* 3.2 20.4 + - + +
212C ILE* 4.8 11.7 - - + -
217C HIS* 3.8 34.5 - + + -
218C ILE 3.0 12.4 + - - +
219C ALA* 3.8 1.8 - - - -
220C LEU 3.1 21.8 + - - -
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Residues in contact with VAL 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LEU* 5.5 0.2 - - + -
133C VAL* 3.6 31.2 - - + -
134C TYR 3.1 12.4 + - - +
135C LEU* 3.9 11.4 - - + -
136C SER 4.8 3.1 + - - -
143C HIS* 4.0 34.5 - - + +
147C PHE* 3.8 17.0 - - + -
158C TYR* 2.8 24.6 + - - -
185C ILE* 4.6 6.3 - - + -
186C PHE* 1.3 68.3 - - - +
188C LEU* 1.3 56.5 + - - +
189C HIS* 4.3 5.2 + - - -
220C LEU* 3.6 25.6 - - + +
222C ASP* 4.6 4.9 - - + -
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Residues in contact with LEU 188 (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 TYR* 3.6 18.6 - - + +
173C PHE* 4.0 21.5 - - + -
186C PHE* 3.4 21.8 - - + +
187C VAL* 1.3 73.7 - - - +
189C HIS* 1.3 57.5 + - - +
205C TRP* 4.2 19.5 - - + -
208C ILE* 4.9 0.4 - - + -
209C VAL* 5.9 0.7 - - + -
212C ILE* 3.8 26.9 - - + -
219C ALA* 4.1 9.9 - - + -
220C LEU 2.8 12.8 + - - +
221C PHE* 3.4 37.3 - - + -
222C ASP* 2.7 35.3 + - - +
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Residues in contact with HIS 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C SER* 4.0 6.3 + - - -
139C THR* 3.2 21.8 + - - -
140C TRP 4.2 0.7 - - - -
143C HIS* 3.7 13.6 - + - -
158C TYR* 5.2 1.3 + - - -
187C VAL 4.6 7.0 - - - -
188C LEU* 1.3 73.2 - - - +
190C SER* 1.3 67.1 + - - +
191C CYS* 3.2 5.9 + - - +
192C ALA 5.0 0.6 + - - -
193C HIS* 3.4 40.6 + + + -
194C ASN* 2.8 38.2 + - - +
199C ASP* 5.2 1.7 - - - +
205C TRP* 3.4 20.4 - - - -
222C ASP* 3.8 9.0 + - - +
907C PLP 3.7 25.9 - - + +
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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