Contacts of the strand formed by residues 218 - 223 (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 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C PHE* 4.4 3.6 - - + -
131C LYS* 3.8 17.0 - - + +
183C GLY 3.7 18.2 - - - +
184C SER 2.9 8.3 + - - -
185C ILE* 3.5 35.5 - - + +
186C PHE* 3.0 24.5 + - - -
217C HIS* 1.3 73.6 - - - +
219C ALA* 1.3 61.8 + - - +
220C LEU* 3.7 1.1 + - + -
248C SER* 4.2 16.6 - - - +
249C PRO* 3.5 25.1 - - + +
251C PHE* 3.8 23.6 - - + -
2D SER* 4.6 5.8 - - - +
5D LEU* 3.9 16.4 - - + -
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Residues in contact with ALA 219 (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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186C PHE* 3.8 5.8 - - - -
188C LEU* 4.1 13.9 - - + -
212C ILE* 4.3 10.8 - - + -
217C HIS 3.8 3.6 + - - -
218C ILE* 1.3 73.1 - - - +
220C LEU* 1.3 59.4 + - - +
221C PHE* 3.8 20.2 - - + -
244C LEU* 3.8 27.1 - - + +
249C PRO 4.2 3.4 + - - +
250C VAL* 3.8 7.0 - - + +
251C PHE* 3.2 23.2 + - - +
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Residues in contact with LEU 220 (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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112C LEU* 4.0 21.1 - - + -
115C SER* 4.0 28.9 - - - +
119C PHE* 4.5 10.8 - - + -
147C PHE* 4.4 18.6 - - + -
185C ILE* 4.5 11.9 - - + -
186C PHE 3.1 10.6 + - - +
187C VAL* 3.9 22.9 - - + -
188C LEU* 2.8 30.6 + - - +
218C ILE* 3.7 1.0 + - + -
219C ALA* 1.3 72.7 - - - +
221C PHE* 1.3 61.2 + - - +
222C ASP 4.1 7.2 - - - +
251C PHE* 3.3 21.1 - - + +
253C CYS* 4.0 9.4 - - - -
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Residues in contact with PHE 221 (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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188C LEU* 3.4 32.1 - - + -
190C SER* 3.4 20.0 - - - +
205C TRP* 4.3 6.1 - + - -
209C VAL* 5.0 6.7 - - + -
219C ALA* 3.8 19.7 - - + -
220C LEU* 1.3 71.4 - - - +
222C ASP* 1.3 60.7 + - - +
223C THR* 3.2 8.3 + - - +
239C ALA* 3.3 36.1 - - + -
240C VAL* 3.7 26.9 - - + -
242C GLY* 4.1 15.3 - - - -
244C LEU* 5.7 0.2 - - + -
250C VAL* 3.8 26.9 - - + -
251C PHE 2.8 12.1 + - - +
252C VAL* 3.5 4.5 - - + -
253C CYS 3.0 25.2 + - - -
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Residues in contact with ASP 222 (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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108C GLY* 5.5 0.9 - - - -
112C LEU* 4.0 10.1 - - - +
143C HIS* 2.8 26.2 + - + +
187C VAL* 4.6 2.2 - - + -
188C LEU 2.7 17.7 + - - +
189C HIS* 3.8 5.7 + - - +
190C SER* 3.2 18.9 + - - -
191C CYS 5.4 0.9 - - - +
220C LEU* 3.5 10.7 + - + +
221C PHE* 1.3 68.7 - - - +
223C THR* 1.3 60.2 + - - +
224C ALA* 3.7 6.4 + - - +
253C CYS* 3.9 12.2 - - - +
907C PLP 2.5 50.6 + - - +
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Residues in contact with THR 223 (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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87C ILE* 3.4 34.0 - - + +
190C SER* 2.7 29.5 + - - +
191C CYS* 5.6 1.1 - - - -
221C PHE 3.3 9.0 + - - -
222C ASP* 1.3 68.6 - - - +
224C ALA* 1.3 59.9 + - - +
225C TYR 4.5 0.4 - - - +
226C GLN* 3.8 31.5 + - + +
236C ASP 5.4 0.9 - - - +
237C ALA* 6.3 0.2 - - - -
240C VAL* 4.0 1.2 - - + +
252C VAL* 3.7 3.3 - - - +
253C CYS 2.8 15.2 + - - -
254C GLN* 3.5 5.9 - - + +
255C SER* 3.0 24.1 + - - +
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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